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Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.
Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs. PMID:24562682
Khadivi-Khub, Abdollah; Soorni, Aboozar
Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs
Three molecular marker protocols, chemiluminescent restriction fragment length polymorphisms (c-RFLPs), radioactivity-based restriction fragment length polymorphisms (r-RFLPs), and randomly amplified DNA polymorphisms (RAPDs) were compared in terms of cost and time efficiency. Estimates of cost of supplies and time requirements were obtained from simulations of maize (Zea mays L.) genotyping experiments utilizing protocols currently in use. The increase in total cost
M. Ragot; D. A. Hoisington
Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR.
The genotypes of the strawberry (Fragaria x ananassa), apple (Malus domestica) and Ribes species (R. nigrum, R. rubrum and R. glossularia), maintained in our Institute's collection and used in breeding programs, were screened for DNA markers. Twenty primers for RAPD (among 60 tested) and seven for ISSR (among 10 tested) were chosen as creating polymorphic DNA bands differentiating the investigated genotypes. Based on those identity markers, the genetic distance between genotypes was determined, and their relatedness was estimated. In many cases, both RAPD- and ISSR-based genetic similarity confirmed relatedness connected with biological origin and with the place where the cultivar was developed. However, some diversity connected with the technique used for molecular marker generation was observed. Generally, the similarity values based on ISSR data were higher than those based on RAPD. Parallel study using two data sets seems to enable a reduction in the number of potential mistakes connected with each method's, technical limitations and ensures more precise relatedness determination. PMID:12378239
Korbin, Ma?gorzata; Kuras, Anita; Zurawicz, Edward
Isolation of molecular markers for tomato ( L. esculentum ) using random amplified polymorphic DNA (RAPD)
A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (�RAPD mapping�). We have now adapted the
R. M. Klein-Lankhorst; A. Vermunt; R. Weide; T. Liharska; P. Zabel
Molecular Markers (RAPD) Associated with Growth, Yield, and Origin of the Silkworm, Bombyx mori L. in India
To identify the molecular markers associated with growth and yield parameters in silkworm, Bombyx mori, RAPD profiles generated with seven UBC primers for fourteen silkworm stocks, originated from China, Japan, India, and Russia, were statistically analyzed. Stepwise multiple regression analysis establishes significant association of 45 markers with larval span, growth indices and four cocoon yield parameters relevant for silk production
S. N. Chatterjee; A. R. Pradeep
[Study on RAPD marker linked to sex in Siraitia grosvenorii].
RAPD (Random Amolified Polymorphism DNA) was employed to detect molecular markers linked to sex in S. grosvenorii by BSA (Bulked Segregant Analysis). 18 RAPD markers linked to sex were selected in BSA by screening 90 primers. Only the marker amplified by S1431 was present in all 8 male individuals tested while absent from all 8 female individuals tested. It showed that S1431 was a male RAPD marker linked to sex. PMID:16913480
Wei, Di; Yang, Mei-Chun; Chen, Ting-Su; Yu, Wei-Hua; Jiang, Wen
Molecular characterization of Fusarium oxysporum f. melongenae by ISSR and RAPD markers on eggplant.
Fusarium oxysporum f. melongenae is a major soil-borne pathogen of eggplant (Solanum melongena). ISSR and RAPD markers were used to characterize Fusarium oxysporum f. melongenae isolates collected from eggplant fields in southern Turkey. Those isolates were not pathogenic to tomato. Pathogens were identified by their morphology, and their identity was confirmed by PCR amplification using the specific primer PF02-3. The isolates were classified into groups on the basis of ISSR and RAPD fingerprints, which showed a level of genetic specificity and diversity not previously identified in Fusarium oxysporum f. melongenae, suggesting that genetic differences are related to the pathogen in the Mediterranean region. The primers selected to characterize Fusarium oxysporum f. melongenae may be used to determine genetic differences and pathogen virulence. This study is the first to characterize eggplant F. oxysporum species using ISSR and RAPD. PMID:20390339
Baysal, O; Siragusa, M; Gumrukcu, E; Zengin, S; Carimi, F; Sajeva, M; Teixeira da Silva, Jaime A
Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee.
The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random sequence. Parents were scored for the presence or absence of individual bands. An average of 6.3 bands and 1.3 polymorphisms for presence/absence were observed per primer between the parents. Thirteen of these primers were used to determine the inheritance of RAPD marker alleles in the resulting progeny and in haploid drones from a daughter queen. Four types of polymorphisms were observed. Polymorphisms for band presence/absence as well as for band brightness were inherited as dominant markers, meeting Mendelian expectations in haploid and diploid progeny. Polymorphisms for fragment-length were also observed. These segregated in a near 1?1 ratio in drone progeny. The last type of polymorphism was manifested as a diploid-specific band. Mixing of amplification products after PCR showed that the diploid-specific band was the result of heteroduplex formation from the DNA of alternate alleles in heterozygotes. In two of the four cases of heteroduplex formation, the alternative alleles were manifested as small fragment-length polymorphisms, resulting in co-dominant markers. This is the first demonstration that a proportion of RAPD markers are not inherited in a dominant fashion. PMID:24197223
Hunt, G J; Page, R E
Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker
In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle�s were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources.
Khatun, M. Mahfuza; Hossain, Khondoker Moazzem; Mahbubur Rahman, S. M.
Molecular variation in melon ( Cucumis melo L.) as revealed by RFLP and RAPD markers
DNA polymorphism among Cucumis melo accessions was assessed using RFLPs and RAPDs. Thirteen varieties that represent diverse melon-types were surveyed using 18 RAPD primers. Cluster analysis indicated that the largest divergence among melon-types occurred between C. melo var. momordica from India and the North American and European muskmelon cultivars. The latter were also well-diverged from vars. conomon, chito and dudaim
Leah Silberstein; Irina Kovalski; Ruguo Huang; Kostas Anagnostou; Molly M Kyle Jahn; Rafael Perl-Treves
Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker.
Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination. PMID:21441863
Mostafa, Noroozi; Omar, Hishamuddin; Tan, Soon Guan; Napis, Suhaimi
Molecular phylogeny of Heritiera Aiton (Sterculiaceae), a tree mangrove: variations in RAPD markers and nuclear DNA content
Random amplified polymorphic DNA (RAPD) markers are used to estimate interspecific variation among mangrove and non-mangrove Heritiera fomes, H. littoralis and H. macrophylla. All the species have 2n =38 chromosomes, with minute structural changes distinguishing the karyotype of each species. Significant variation of 4C DNA content occurs at the interspecific level. Interspecific polymorphism ranged from 14.09% between H. fomes and
Molecular characterization and genetic relationships among most common identified morphotypes of critically endangered rare Moroccan species Argania spinosa (Sapotaceae) using RAPD and SSR markers
��\\u000a \\u000a � The objective of this work is the molecular characterization of most common identified morphotypes of critically endangered\\u000a rare Moroccan species Argania spinosa.\\u000a \\u000a \\u000a \\u000a \\u000a ��\\u000a \\u000a � Eighteen RAPD markers and twenty SSR markers have been assayed in 38 argan tree accessions from the three most commonly\\u000a identified morphotypes: oval, spherical and spindle fruit types.\\u000a \\u000a \\u000a \\u000a \\u000a ��\\u000a \\u000a � A total of 140
Khalid Majourhat; Youssef Jabbar; Abdellatif Hafidi; Pedro Mart�nez-G�mez
[The use of RAPD and ITE molecular markers to study genetical structure of the Crimean population of Triticum boeoticum Boiss].
Wild wheat Triticum boeoticum Boiss. is the rare species are included in the Red Book of Ukraine. This species are reducing the magnitude of population and the area of distribution under anthropogenic activity. We studied genetic structure of two populations of T. boeoticum, located on Sapun Mountain and in Baidar Valley in Crimea. According RAPD and ITE molecular analysis we have estimated that the population of T. boeoticum on Sapun Mountain is genetically more impoverished than a population from the Baidar Valley. For preservation of maximal natural genetic polymorphism of the rare species it is recommended to direct efforts to preservations of a population of T. boeoticum from the Baidar Valley. PMID:17649626
Mallabaeva, D Sh; Ignatov, A N; She?ko, I A; Isikov, V P; Geliuta, V P; Bo?ko, N G; Seriapin, A A; Dorokhov, D B
Comparison of genomes of eight species of sections Linum and Adenolinum from the genus Linum based on chromosome banding, molecular markers and RAPD analysis.
Karyotypes of species sects. Linum and Adenolinum have been studied using C/DAPI-banding, Ag-NOR staining, FISH with 5S and 26S rDNA and RAPD analysis. C/DAPI-banding patterns enabled identification of all homologous chromosome pairs in the studied karyotypes. The revealed high similarity between species L. grandiflorum (2n = 16) and L. decumbens by chromosome and molecular markers proved their close genome relationship and identified the chromosome number in L. decumbens as 2n = 16. The similarity found for C/DAPI-banding patterns between species with the same chromosome numbers corresponds with the results obtained by RAPD-analysis, showing clusterization of 16-, 18- and 30-chromosome species into three separate groups. 5S rDNA and 26S rDNA were co-localized in NOR-chromosome 1 in the genomes of all species investigated. In 30-chromosome species, there were three separate 5S rDNA sites in chromosomes 3, 8 and 13. In 16-chromosome species, a separate 5S rDNA site was also located in chromosome 3, whereas in 18-chromosome species it was found in the long arm of NOR-chromosome 1. Thus, the difference in localization of rDNA sites in species with 2n = 16, 2n = 30 and 2n = 18 confirms taxonomists opinion, who attributed these species to different sects. Linum and Adenolinum, respectively. The obtained results suggest that species with 2n = 16, 2n = 18 and 2n = 30 originated from a 16-chromosome ancestor. PMID:18500654
Muravenko, Olga V; Yurkevich, Olga Yu; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Nosova, Inna V; Zelenina, Daria A; Volkov, Alexander A; Popov, Konstantin V; Zelenin, Alexander V
A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers.
Using a population of 105 interspecific F(2) hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. 'Fairway' as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future. PMID:22462407
Yu, Xiaoxia; Li, Xiaolei; Ma, Yanhong; Yu, Zhuo; Li, Zaozhe
Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex
Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B.setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use.
Development of a second generation linkage map for almond using RAPD and SSR markers.
Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragn�s' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragn�s' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragn�s' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed. PMID:10984177
Joobeur, T; Periam, N; de Vicente, M C; King, G J; Ar�s, P
Identification of Prunus armeniaca cultivars by RAPD and SCAR markers
Nineteen cultivars of apricot (Prunus armeniaca) were distinguished using random amplified polymorphic DNA (RAPD) markers. One decamer out of 44 used was useful to differentiate cultivars of the Campania Region from those of Northern Italy, North America and Greece. A sequence characterized amplified region (SCAR) marker was obtained. The results provide a protocol to fingerprint DNA of apricots as an
Loredana Mariniello; Maria Grazia Sommella; Angela Sorrentino; Marcello Forlani; Raffaele Porta
Genetic diversity in Hemileia vastatrix based on RAPD markers.
Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs. PMID:16396347
Gouveia, M Manuela C; Ribeiro, Ana; V�rzea, V�tor M P; Rodrigues, Carlos J
Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes
Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars.
J. B. dos Santos; J. Nienhuis; P. Skroch; J. Tivang; M. K. Slocum
Diversity among populations of switchgrass based on RAPD markers
Information on the amount of genetic diversity in switchgrass (Panicum virgatum L.) is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. This study characterized and assessed genetic diversity by means of RAPD markers among 14 populations representing upland and lowland switchgrass ecotypes. Forty-five of 128 primers produced polymorphic markers among sets of genomic DNA pooled from individual genotypes of each population. Five primers were selected to amplify a total of 91 polymorphic loci among genotypes. The RAPD markers were scored for presence or absence of bands to generate distance matrices for cluster analysis. Overall similarity was 65% among population compared to 81% within populations. Blackwell and Caddo were the most similar populations (78%) based on RAPD markers, whereas Alamo and Forestburg were the most divergent (53%). Cluster analysis clearly segregated populations into two main groups (putatively based on ecotype) and united individual genotypes within a population into discrete groups within the larger clusters. Although the relationship between ploidy level and ecotype remained unclear, RAPD profiles can be used to identify switchgrass populations and may be useful in predicting relationship between experimental germplasm sources and released populations. 50 refs., 2 figs., 2 tabs.
Gunter, L.E.; Tuskan, G.A.; Wullschleger, S.D. [Oak Ridge National Lab., TN (United States)
Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach
The identification of molecular markers linked to economically important traits for use in crop improvement is very important in long-lived perennial species. Three-hundred-and-sixty RAPD primers were used with bulked segregant analysis to identify markers linked to loci of specific interest in peach [(Prunus persica) L. Batch] and peach x almond [(Prunus dulcis) Batch] crosses. The traits analyzed included flesh color,
M. L. Warburton; V. L. Becerra-Vel�squez; J. C. Goffreda; F. A. Bliss
Evaluation of RFLP and RAPD markers in a comparison of Brassica napus breeding lines
RFLP and RAPD markers were evaluated and compared for their ability to determine genetic relationships in a set of three B. napus breeding lines. Using a total of 50 RFLP and 92 RAPD markers, the relatedness between the lines was determined. In total, the RFLP and the RAPD analysis revealed more than 500 and 400 bands, respectively. The relative frequencies
C. Halld�n; N.-O. Nilsson; I. M. Rading; T. S�ll
RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).
For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis. PMID:22205351
Zhao, Ya-E; Wu, Li-Ping
The genetic structure of tetraploid Avena: a comparison of isozyme and RAPD markers.
Isozymes were the first widely used molecular markers in plant population analysis. They yielded valuable information on the amount and the structure of genetic variability. DNA technology has provided new types of markers based on DNA sequence, which make it possible to study polymorphisms in a much greater proportion of the genome. This is the reason why the use of isozymes is less popular nowadays. This effect would be justified if all markers provided the same type of information on polymorphism and genetic relationships among populations; otherwise, it would be necessary to use different markers to obtain the complete picture of the genetic structure of populations and species. In this study, we compared data of isozyme and RAPD markers in the populations of two tetraploid species of wild oats: Avena barbata populations collected in Argentina, and Avena murphyi populations collected in Spain and Morocco. The samples were evaluated for 9 isozymatic systems and 10 primers. The structure of genetic variability was studied using Nei's method, and the relationships between populations were estimated using Hedrick and Jaccard's similarities for isozymes and RAPDs, respectively. As expected, RAPDs were more polymorphic than isozymes, but the information obtained from both markers was weakly correlated. The various reasons for this observation are discussed, but our conclusion is that in order to study the structure of genetic variability, several types of markers should be used. PMID:12378251
Benchacho, Mohammed; Guma, Rosana; P�rez De La Vega, Marcelino; Garc�a, Pedro
Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species
Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic
C. E. Thormann; M. E. Ferreira; L. E. A. Camargo; J. G. Tivang; T. C. Osborn
Identification of RAPD markers linked to sex determination in guggal [ Commiphora wightii (Arnott.)] Bhandari
Decamer RAPD primers were tested on dioeceious and hermaphrodite plants of Commiphora wightii to identify sex-specific molecular markers. Sixty different random decamer primers were screened out of which only three\\u000a primers were found to be associated with sex expression. A ~1,280-bp fragment from the primer OPN06 was found to be present\\u000a in all the female individuals. Another primer OPN 16
Sanghamitra Samantaray; K. A. Geetha; K. P. Hidayath; Satyabrata Maiti
Genetic analysis of two common carp broodstocks by RAPD and microsatellite markers
The whole broodstock of two Hungarian common carp farms�80 and 196 individuals�was analyzed by using random amplified polymorphic DNA (RAPD) assay and microsatellite analysis. Ten polymorphic RAPD markers and four microsatellites were selected to genotype both of the stocks. As expected, microsatellite analysis revealed more detailed information on genetic diversities than RAPD assay. Results obtained with both types of DNA
Rich�rd B�rtfai; S�ndor Egedi; Gen Hua Yue; Bal�zs Kov�cs; B�la Urb�nyi; Gizella Tam�s; L�szl� Horv�th; L�szl� Orb�n
Predicting quantitative variation within rice germplasm using molecular markers
Diverse Asian rice (Oryza sativa) germplasm has been used to identify associations between various quantitative traits and RAPD molecular markers using multiple regression analysis. This has allowed us to predict for other samples of germplasm their performance for traits such as culm length and number, days to flowering, grain width, and panicle and leaf length using only RAPD marker data.
Parminder S Virk; Brian V Ford-Lloyd; Michael T Jackson; Harpal S Pooni; Tomas P Clemeno; H John Newbury
RAPD markers linked to eastern filbert blight resistance in Corylus avellana
A total of 1,110 decamer primers were screened for RAPD markers linked to a dominant allele in hazelnut ( Corylus avellana) that confers resistance to eastern filbert blight caused by Anisogramma anomala. Twenty RAPD markers linked in coupling, and five markers linked in repulsion, were found. A seedling population was used to construct a linkage map of the region flanking
S. A. Mehlenbacher; R. N. Brown; J. W. Davis; H. Chen; N. V. Bassil; D. C. Smith; T. L. Kubisiak
The use of molecular markers for germplasm management in a French olive collection
With more than 100 accessions, the CBNMP olive collection includes a major part of the French germplasm. We used molecular markers to characterise all accessions and to study genetic relationships between cultivars. Firstly, 497 olive trees were genotyped using 32 RAPD markers. We identified 114 RAPD profiles and detected several cases of mislabelling, synonymy and homonymy. Secondly, for each RAPD
B. Khadari; C. Breton; N. Moutier; J. P. Roger; G. Besnard; A. Bervill�; F. Dosba
Analysis of genetic diversity in Larix gmelinii (Pinaceae) with RAPD and ISSR markers.
Dahurian larch (Larix gmelinii), a deciduous conifer, is the northernmost tree, native to eastern Siberia and nearby regions of China. We used growth traits and molecular markers to assess genetic variation in different L. gmelinii growing regions; 105 individual samples were collected from seven regions of the Qingshan Forestry Centre, Heilongjiang Province, China. The greatest genetic regional variation was seen in the Youhao area, based on coefficients of variation for tree height, diameter and volume (14.73, 28.25, and 55.27%, respectively). Analysis using molecular markers showed rich genetic diversity. The RAPD and ISSR methods both indicated that most variation came from within populations. The seven regions were divided into two groups (Daxing'an and Xiaoxing'an Mountain ranges) by RAPD cluster analysis: Tianchi, Xiaojiuya, Yuanjiang, and Taiping regions were placed in the first group at a genetic distance of 0.08; while the other regions were in the second group. The correlation between RAPD markers and geographical distance was significant, with a correlation coefficient of 0.752. PMID:23408406
Zhang, L; Zhang, H G; Li, X F
Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups
Genetic linkage maps of the guppy ( Poecilia reticulata) were constructed from independent crosses between the Tuxedo strain and a feral line (Wildtype). Segregation patterns of random amplified polymorphic DNA (RAPD) markers and phenotypic markers were investigated in F 2 offspring of Tuxedo ?? � Wildtype ?? and Wildtype ?? � Tuxedo ?? crosses. Among the 300 and 276 RAPD
Gideon Khoo; Meng Huat Lim; Haridas Suresh; Damien K. Y. Gan; Kok Fang Lim; Fan Chen; Woon-Khiong Chan; Tit Meng Lim; Violet P. E. Phang
Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers.
An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results. PMID:18464866
Sun, G L; Salomon, B; Bothmer, R
Use of random amplified polymorphic DNA (RAPD) markers in the study of the parasitic weed Orobanche
Despite the tremendous economic impact of broomrapes (Orobanche spp.) on agriculture in many countries little is known of the pattern of genetic variation within this group of parasitic weeds. The present paper describes the use of RAPD markers for the study of five Orobanche species in agricultural fields in Israel. Pronounced genetic differentiation was found between the species, and RAPD
N. Katzir; V. Portnoy; G. Tzuri; D. M. Joel; M. Castej�n-Mu�oz
Identification of Anoectochilus formosanus and Anoectochilus koshunensis species with RAPD markers.
RAPD (random amplified polymorphic DNA) markers were developed to distinguish Anoectochilus formosanus from Anoectochilus koshunensis and their putative hybrids. Morphological differentiation of these two species beyond the flowering period is difficult. RAPD markers provide a rapid and easy tool for identification of the two Anoectochilus species. In the study, forty arbitrary decamer primers were screened, and nineteen species-specific RAPD markers generated from polymerase chain reactions (PCR) with eight random primers were obtained. Nine were specific to A. formosanus and ten to A. koshunensis. Two primers, OPC-08 and OPL-07, produced two markers, one specific to A. formosanus and the other specific to A. koshunensis, which simultaneously appeared in the hybrids pattern. The RAPD markers can be applied both to identification of A. formosanus and A. koshunensis species and to assessment of the extent fo hybridization in hybrids between them. This information facilitates the breeding program process. PMID:17253217
Cheng, K T; Fu, L C; Wang, C S; Hsu, F L; Tsay, H S
Genetic Differentiation Among Goats Using Randomly Amplified Polymorphic DNA (RAPD) Markers
Anbarasan, K., Sharma, A.K., Singh, R.K., Deb, S.M. and Sharma, D. 2001. Genetic differentiation among goats using randomly amplified polymorphic DNA (RAPD) markers. J. Appl. Anim. Res., 20: 83�88.To develop population specific markers using randomly amplified polymorphic DNA�ploymerase chain reaction (RAPD�PCR) in meat (Black Bengal and Non-descript Rohilkhand Local), milk (Barbari) and pashmina (Chegu) producing goats, a total of 35
K. Anbarasan; A. K. Sharma; R. K. Singh; S. M. Deb; D. Sharma
Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers.
Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker. PMID:10382290
Sun, G L; D�az, O; Salomon, B; von Bothmer, R
Genetic diversity of Palestine landraces of faba bean (Vicia faba) based on RAPD markers.
Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine. PMID:24065673
Basheer-Salimia, R; Shtaya, M; Awad, M; Abdallah, J; Hamdan, Y
Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata , Using RAPD and ISSR Markers
With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low\\u000a genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the
Zhi-Yong Zhang; Yong-Yan Chen; De-Zhu Li
Evaluation of genetic diversity in Turkish melons ( Cucumis melo L.) based on phenotypic characters and RAPD markers
The genetic relationships among 56 melon (Cucumis melo L.) genotypes collected from various parts of Turkey were determined by comparing their phenotypic and molecular traits with\\u000a those of 23 local and foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish\\u000a melon germplasm. Sixty-one phenotypic characters and 109 polymorphic RAPD markers obtained from 33 primers were used
Suat Sensoy; Saadet B�y�kalaca; Kazim Abak
Development and application of RAPD-SCAR marker for identification of Phyllanthus emblica LINN.
Correct genotype identification of medicinal plant material remains important for botanical drug industry. Limitations of chemical and morphological approaches for authentication have generated need for newer methods in quality control of botanicals. The present study was carried out to develop DNA based marker for identification of Phyllanthus emblica LINN. A putative marker (1.1 kb) specific for P. emblica was identified by Random Amplified Polymorphic DNA (RAPD) technique. Sequence Characterized Amplified Region (SCAR) marker was developed from the RAPD amplicon. The SCAR marker was found useful for identification of P. emblica in its commercial samples and Triphalachurna, a multi-component Ayurvedic formulation. PMID:17077537
Dnyaneshwar, Warude; Preeti, Chavan; Kalpana, Joshi; Bhushan, Patwardhan
Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers
As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated
Jing-Zhong Lin; Kermit Ritland
Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays
Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500�3000 bp in size. One-hundred-nineteen of these were polymorphic (92%), with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid) species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.
Awasthi, Arvind K; Nagaraja, GM; Naik, GV; Kanginakudru, Sriramana; Thangavelu, K; Nagaraju, Javaregowda
A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.
A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations. PMID:16498462
Mehlenbacher, Shawn A; Brown, Rebecca N; Nouhra, Eduardo R; G�kirmak, Tufan; Bassil, Nahla V; Kubisiak, Thomas L
Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization.
The development and use of RAPD markers for applications in crop improvement has recently generated considerable interest within the plant breeding community. One potential application of RAPDs is their use for "tagging" simply-inherited (monogenic) pest-resistance genes and enabling more efficient identification and selection of genotypes carrying specific combinations of resistance genes. In this report, we propose and describe the use of heterogeneous inbred populations as sources of near-isogenic lines (NILs) for targeting RAPD markers linked to major pest resistance genes. The development of these NILs for RAPD marker analyses involved a sequence of line and mass selection during successive generations of inbreeding. DNA bulks derived from the NILs were used to identify a RAPD marker (designated OK14620, generated by 5'-CCCGCTACAC-3' decamer) that was tightly linked (2.23�1.33 centiMorgans) to an important rust [Uromyces appendiculatus (Pers.) Unger var. appendiculatus] resistance gene (Ur-3) in common bean (Phaseolus vulgaris L.). The efficiency of this approach was demonstrated by a low rate of false-positives identified, the tightness of the linkage identified, and the ability to detect polymorphism between genomic regions that are representative of the same gene pool of common bean. This method of deriving NILs should find application by researchers interested in utilizing marker-assisted selection for one or more major pest resistance genes. The identification of OK14620 should help to facilitate continued use of the Ur-3 resistance source and will now enable marker-assisted pyramiding of three different bean rust resistance sources (two previously tagged) to provide effective and stable resistance to this important pathogen. PMID:24186016
Haley, S D; Afanador, L K; Miklas, P N; Stavely, J R; Kelly, J D
Genetic linkage mapping in peach using morphological, RFLP and RAPD markers
We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F2 individuals derived from the self-fertilization of four F1 individuals of a cross between �New Jersey Pillar� and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh
S. Rajapakse; L. E. Belthoff; G. He; A. E. Estager; R. Scorza; I. Verde; R. E. Ballard; W. V. Baird; A. Callahan; R. Monet; A. G. Abbott
Genetic diversity analysis in Boerhavia diffusa L. of different geographic locations in India using RAPD markers
Boerhavia diffusa is extensively used in herbal medicines as well as in the Ayurvedic system, because it contains a set of clinically important compounds. In the present study, the genetic variability in Boerhavia diffusa between accessions of different geographical origin within the Indian territory is assessed through random amplified polymorphic DNA (RAPD) markers. Twenty-eight accessions of Boerhavia were screened with
Nidhi Shukla; N. S. Sangwan; H. O. Misra; R. S. Sangwan
Genetic diversity assessment in nine cultivars of Catharanthus roseus from Central Gujarat (India) through RAPD, ISSR and SSR markers
The genetic relationship study was carried out among nine different cultivars of Catharanthus roseus using RAPD, ISSR and SSR markers. In RAPD analysis, out of twenty primers, six primers amplified 592 bands out of which 466 were polymorphic while rest was monomorphic. This gave high (78.71%) polymorphism among nine cultivars. In ISSR analysis, 78.94% polymorphism was observed, while in SSR
Sanjay Lal; Kinnari N. Mistry; Smit D. Shah; Riddhi Thaker
Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury.
The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F(2) progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16(905 bp) showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F(2) progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16(826 bp)). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934
Dutta, Suhrid R; Kar, Prasanta K; Srivastava, Ashok K; Sinha, Manoj K; Shankar, Jai; Ghosh, Ananta K
Genetic Diversity and Species-Diagnostic Markers of Mud Crabs (Genus Scylla) in Eastern Thailand Determined by RAPD Analysis.
Genetic diversity of three mud crab species, Scylla serrata (Forsk�l), S. oceanica (Dana), and S. tranquebarica (Fabricius), collected from two locations in eastern Thailand (Chanthaburi and Trat) was examined by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Ninety-one reproducible RAPD fragments, generated by UBC456, UBC457, and YNZ22, were polymorphic. The percentage of polymorphic bands within populations ranged from 47.92% to 77.59%. Species-specific RAPD markers were also observed and used to construct a molecular diagnostic key in these taxa. Large genetic differences between species were found (D(ij) = 0.425 to 0.751), whereas those between populations within each species were much lower (D(ij) = 0.171 to 0.199). The neighbor-joining tree based on genetic distances among pairs of individuals indicated three distinct groups, corresponding to S. serrata, S. oceanica, and S. tranquebarica. No genotypes were shared among these three species. This suggests the absence of genetic exchanges between sympatric mud crab species in eastern Thailand. Therefore, mud crabs in this area should be recognized as three different species rather than a single panmictic species exhibiting different morphs. PMID:10811958
Klinbunga; Boonyapakdee; Pratoomchat
Segregating random amplified polymorphic DNAs (RAPDs) in Betula alleghaniensis
Molecular markers are currently being developed for Betula alleghaniensis Britton using random amplified polymorphic DNA (RAPD). Arbitrarily designed 11-mer primers were tested on three intraspecific controlled crosses for which more than 15 full-sibs were available. Using two of these primers, we were able to genetically characterize a total of nine polymorphic RAPD markers. Segregation of these markers was consistent with
A. Roy; N. Frascaria; J. MacKay; J. Bousquet
Evaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP markers
Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate\\u000a genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity. Genetic variability was estimated with 18 primers and 43\\u000a RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins. The\\u000a majority
E. Lerceteau; T. Robert; V. P�tiard; D. Crouzillat
RAPD markers linked to a clubroot-resistance locus in Brassica rapa L
Linkage of random amplified polymorphic DNA (RAPD) markers with resistance genes to clubroot (Plasmodiophora brassicae Wor.)\\u000a in Brassica rapa L. was studied in a doubled haploid (DH population obtained by microspore culture. Thirty-six DH lines were\\u000a obtained from F1 plants from a cross between susceptible �Homei P09� and resistant �Siloga S2� plants. �Homei P09� was a DH line obtained\\u000a by
Yasuhisa Kuginuki; Hidetoshi Ajisaka; Mamiko Yui; Hiroaki Yoshikawa; Ken-ichi Hida; Masashi Hirai
Identification of RAPD markers linked to fusarium crown and root rot resistance (Frl) in tomato
In tomato ( Lycopersicon esculentum Mill.) a single dominant gene ( Frl) on chromosome 9 confers resistance to fusarium crown\\u000a and root rot (crown rot) incited by Fusarium oxysporum f. sp. radicis-lycopersici. To identify randomly amplified polymorphic\\u000a DNA (RAPD) markers linked to Frl, crown rot susceptible and resistant tomato lines were screened for polymorphisms using 1000\\u000a random 10-mer primers and
Gennaro Fazio; Mikel R. Stevens; John W. Scott
Coupling- and repulsion-phase RAPDs for marker-assisted selection of PI 181996 rust resistance in common bean.
The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20490 tightly linked (no recombinants) in coupling phase and OAE19890 linked in repulsion phase (at 6.2�2.8 cM) to PI 181996 rust resistance. These RAPDs, generated by single decamer primers in the polymerase chain reaction, were identified in near-isogenic bulks of non-segregating resistant and susceptible BC4F2 (NX-040*4/PI 181996) lines. Linkage of the RAPD markers was confirmed by screening 19 BC4F2 and 57 BC4F3 individuals segregating for PI 181996 resistance. Utility of the RAPDs OAC20490 and OAE19890 was investigated in a diverse group of common bean cultivars and lines. All cultivars into which the PI 181996 resistance was introgressed had the RAPD OAC20490. A RAPD similar in size to OAC20490, observed in some susceptible common bean lines, was confirmed by Southern blotting to be homologous to the RAPD OAC20490. Use of the RAPDs OAC20490 and OAE19890 in marker-assisted selection (MAS) is proposed. The coupling-phase RAPD is most useful for MAS of resistant BCnF1individuals during traditional backcross breeding. The repulsion-phase RAPD has greatest utility in MAS of homozygous-resistant individuals in F2 or later-segregating generations. PMID:24174024
Johnson, E; Miklas, P N; Stavely, J R; Martinez-Cruzado, J C
In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm.
RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000?bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm. PMID:22474414
Premkrishnan, Balakrishnan Vasanthakumari; Arunachalam, Vadivel
In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm
RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000?bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.
Premkrishnan, Balakrishnan Vasanthakumari; Arunachalam, Vadivel
Identification of RAPD markers linked to A and B genome sequences in Musa L.
Plantains and bananas (Musa spp. sect. eumusa) originated from intra- and interspecific hybridization between two wild diploid species, M. acuminata Colla. and M. balbisiana Colla., which contributed the A and B genomes, respectively. Polyploidy and hybridization have given rise to a number of diploid, triploid, and tetraploid clones with different permutations of the A and B genomes. Thus, dessert and highland bananas are classified mainly as AAA, plantains are AAB, and cooking bananas are ABB. Classification of Musa into genomic groups has been based on morphological characteristics. This study aimed to identify RAPD (random amplified polymorphic DNA) markers for the A and B genomes. Eighty 10-mer Operon primers were used to amplify DNA from M. acuminata subsp. burmannicoides clone 'Calcutta 4' (AA genomes) and M. balbisiana clone 'Honduras' (BB genomes). Three primers (A17, A18, and D10) that produced unique genome-specific fragments in the two species were identified. These primers were tested in a sample of 40 genotypes representing various genome combinations. The RAPD markers were able to elucidate the genome composition of all the genotypes. The results showed that RAPD analysis can provide a quick and reliable system for genome identification in Musa that could facilitate genome characterization and manipulations in breeding lines. PMID:11081965
Pillay, M; Nwakanma, D C; Tenkouano, A
RAPD fingerprints were performed on DNA extracted trom the internal leaves of the offshoots of five date palm cultivars (Samanie, Seaweae, Hyeane, Amhat and Zaghlool). Two random primers (OPC2 and OPD16) out of ten were selected on the basis of the number and frequency of polymorphic bands produced. Distinguishable RAPD fingerprints among the different varieties were obtainable if suitable primers
Mahmoud M. Saker; Hamdy A. Moursy
Molecular distinction amongst varieties of Mulberry using RAPD and DAMD profiles
Background Mulberry trees are the most important host for rearing mulberry silkworms in sericulture. Improved varieties of mulberry tree have been developed through traditional breeding procedures. Not much work, however, has been carried out on the molecular characterization of these varieties. Random Amplified Polymorphic DNA (RAPD) and Directed Amplification of Minisatellite DNA (DAMD) methods based on Polymerase Chain Reaction are important tools to analyze genetic diversity of mulberries. These have been used to determine variation amongst nine varieties of Morus spp. maintained at Banthra Research Station of National Botanical Research Institute, Lucknow. Results and Discussion The varieties were analyzed using 23 arbitrary sequence decamer primers for RAPD, and 3 minisatellite core sequence primers for DAMD reactions. The RAPD and DAMD band data, (a total of 200 bands), were used to determine the pair wise distances according to Jaccard's algorithm. From these distance values Neighbour Joining (NJ) analyses were carried out separately for the RAPD and the DAMD data. The triploid varieties were found to be most similar to each other using RAPD analysis, while the varieties S13 and S34 were more similar using DAMD analysis. Nearly 85% of the RAPD bands and 91% of the DAMD bands were polymorphic across the nine varieties. Conclusions The mulberry varieties could be distinguished by their RAPD and DAMD profiles. As many as five RAPD primers and one DAMD primer generated profiles that can together differentiate all the nine varieties in terms of unique bands.
Bhattacharya, Esha; Ranade, Shirish Anand
Specific genetic markers for wheat, spelt, and four wild relatives: comparison of isozymes, RAPDs, and wheat microsatellites.
Three types of markers-isozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatellites- were tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites. PMID:11550895
Guadagnuolo, R; Bianchi, D S; Felber, F
Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.
The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation. PMID:24338421
Rodr�guez-Bernal, A; Pi�a-Escutia, J L; V�zquez-Garc�a, L M; Arzate-Fern�ndez, A M
Analysis of a Detailed Genetic Linkage Map of Lactuca sativa (Lettuce) Constructed From RFLP and RAPD Markers
A detailed genetic map has been constructed from the F, population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified
Rick V. Kesseli; Pt Ilan Parant; Richard W. Michelmore
Genetic diversity in Tunisian Crataegus azarolus L. var. aronia L. populations assessed using RAPD markers
��\\u000a \\u000a � The genetic diversity of nine wild Tunisian Crataegus azarolus var. aronia L. populations from different bioclimates was assessed using RAPD markers.\\u000a \\u000a \\u000a \\u000a \\u000a ��\\u000a \\u000a � Eight selected primers generated a total of 105 bands, 81 of which were polymorphic. Shannon�s index (H?) ranged from 0.222 to 0.278 according to a population with an average of 0.245. The genetic variation within
Chayma Rajeb; Chokri Messaoud; Hnia Chograni; Afef Bejaoui; Abdennacer Boulila; Mohamed Nejib Rejeb; Mohamed Boussaid
Genetic diversity assessment of summer squash landraces using molecular markers.
Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102
Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E
RAPD-based genetic linkage maps of Tribolium castaneum.
A genetic map of the red flour beetle (Tribolium castaneum) integrating molecular with morphological markers was constructed using a backcross population of 147 siblings. The map defines 10 linkage groups (LGs), presumably corresponding to the 10 chromosomes, and consists of 122 randomly amplified polymorphic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total map length is 570 cM, giving an average marker resolution of 4.3 cM. The average physical distance per genetic distance was estimated at 350 kb/cM. A cluster of loci showing distorted segregation was detected on LG9. The process of converting RAPD markers to sequence-tagged site markers was initiated: 18 RAPD markers were cloned and sequenced, and single-strand conformational polymorphisms were identified for 4 of the 18. The map positions of all 4 coincided with those of the parent RAPD markers.
Beeman, R W; Brown, S J
Induced mutagenesis in Jatropha curcas L. using gamma rays and detection of DNA polymorphism through RAPD marker.
The aim of this study is to examine the effect of different doses (control, 5, 10, 15, 20 and 25 Kr) of gamma irradiation on seed germination, flowering, fruit and seed traits of Jatropha curcas and to identify DNA polymorphism among the mutants through a Randomly Amplified Polymorphic DNA (RAPD) marker analysis. The improved agronomic traits such as flowering, fruits and seeds were recorded in 5 Kr dose and seed germination percentage in 10 Kr dose treated plants, while corresponding parameters were reduced significantly (P>0.05) in 25 Kr dose gamma rays treated plants when compared to that of control. All the twenty-three random primers used except six primers, namely OPAW16, OPAK07, OPAK15, OPS01, OPAK20 and OPAL09 were showed polymorphic bands. The primers: OPAW16, OPAK07, OPAK15, OPS01, OPAK20 and OPAL09 produced only one band each across the six mutants, while the primers: OPU13, OPAB 15, OPF01 and OPAB11 were produced with maximum number of bands (8). The number of amplicons varied from 1 to 8 with an average of 3.9 bands, of which 2.3 were polymorphic. The percentage of polymorphism per primer ranged from 0 to 100 with an average of 55.16%. The Jaccard's coefficients of dissimilarity varied from 0.324 to 0.397, indicative of the level of genetic variation among the mutants studied. The maximum dissimilarity value (0.397) was observed in 5 Kr mutant while the minimum value (0.250) was observed in 20 Kr mutant when compared to that of control. In a dendrogram constructed based on genetic similarity coefficients, the mutants were grouped into three main clusters; (a) control, 10, 15 and 20 Kr dose mutants clustered together, (b) 25 Kr dose grouped alone, (c) 5 Kr dose also grouped alone. The mutants showing the differences in morphological traits showed DNA polymorphism in PCR profile amplified by RAPD marker. It is concluded that DNA polymorphism detected by RAPD analysis offered a useful molecular marker for the identification of mutants in gamma radiation treated plants. PMID:21262483
Dhakshanamoorthy, Dharman; Selvaraj, Radhakrishnan; Chidambaram, A L A
Genetic Linkage Maps of Eucalyptus Grandis and Eucalyptus Urophylla Using a Pseudo-Testcross: Mapping Strategy and Rapd Markers
We have used a ``two-way pseudo-testcross'' mapping strategy in combination with the random amplified polymorhic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F(1) progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, ? = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support >/=1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organism. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.
Grattapaglia, D.; Sederoff, R.
RGA- and RAPD-derived SCAR markers for a Brassica B-genome introgression conferring resistance to blackleg in oilseed rape.
An introgression derived from the B genome of Brassica juncea in spring-type oilseed rape (B. napus) conferring recessively inherited cotyledon resistance against several pathotypes of the blackleg fungus Leptosphaeria maculans was mapped using PCR-based molecular markers. Resistance-associated B-genome-specific randomly amplified (RAPD) and resistance gene analog (RGA) DNA polymorphisms were converted into three sequence-specific markers (SCARs; B5-1520, C5-1000, RGALm). The flanking sequence of the RGALm locus was determined by genomic walking, leading to a 1,610-bp EcoRV fragment which showed extensive homology to known and putative resistance genes of a cluster on Arabidopsis chromosome 5. Partial sequence analysis of the genomic RAPD segment OPC-05-1700 revealed strong homology to the gibberellin 2-oxidase gene of Arabidopsis. The SCAR markers were analyzed in two segregating populations and were found to be linked in coupling to each other, and in repulsion to the resistance locus. In both populations, markers deviated significantly from a monogenic 3:1 segregation ratio, with plants lacking the markers being more frequent than expected. Although the mode of introgression is yet unknown, the recombinant individuals observed among susceptible progeny suggest homeology between the B-genome-specific segment and its B. napus counterpart. This would offer prospects for reducing the size of the introgression and further fine mapping of the resistance locus. PMID:15887037
Saal, B; Struss, D
Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers
Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic\\u000a and endangered yellow catfish, Horabagrus\\u000a brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened\\u000a initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy
P. M. Abdul Muneer; A. Gopalakrishnan; K. K. Musammilu; Vindhya Mohindra; K. K. Lal; V. S. Basheer; W. S. Lakra
Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers
Background Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea. Results Seventeen accessions of Trigonella foenum-graecum and nine accessions of Trigonella caerulea representing various countries were analyzed using ISSR and RAPD markers. Genetic diversity parameters (average number of alleles per polymorphic locus, percent polymorphism, average heterozygosity and marker index) were calculated for ISSR, RAPD and ISSR+RAPD approaches in both the species. Dendrograms were constructed using UPGMA algorithm based on the similarity index values for both Trigonella foenum-graecum and Trigonella caerulea. The UPGMA analysis showed that plants from different geographical regions were distributed in different groups in both the species. In Trigonella foenum-graecum accessions from Pakistan and Afghanistan were grouped together in one cluster but accessions from India and Nepal were grouped together in another cluster. However, in both the species accessions from Turkey did not group together and fell in different clusters. Conclusions Based on genetic similarity indices, higher diversity was observed in Trigonella caerulea as compared to Trigonella foenum-graecum. The genetic similarity matrices generated by ISSR and RAPD markers in both species were highly correlated (r = 0.78 at p = 0.001 for Trigonella foenum-graecum and r = 0.98 at p = 0.001 for Trigonella caerulea) indicating congruence between these two systems. Implications of these observations in the analysis of genetic diversity and in supporting the possible Center of Origin and/or Diversity for Trigonella are discussed.
Dangi, Rakhee S; Lagu, Meena D; Choudhary, Lal B; Ranjekar, Prabhakar K; Gupta, Vidya S
[Clone and development of RAPD and SCAR markers linked to sex determination in the dioecious species Humulus scandens L].
In dioecious plants, the important differences of male and female individuals exist in the genome, so it is very significant to do a comparative study on the sex differences with the DNA markers. In this article, Random Amplification Polymorphic DNA (RAPD) technology was used to increase the Humulus scandens female and male genome teams. The results show that two of the 100 primers, S1519 and S2142, respectly produced a sex-linked band only found in tested males, with the length of 1207 bp and 762 bp. These fragments were cloned and sequenced and then aligned with the GenBank database by BLAST, finding that they are abundant in AT (individually 64%, 54.7%), and no sequence was significantly similar. The RAPD markers were then converted into male-linked SCAR (Sequence Characterized Amplified Regions) markers. PMID:19697703
Gao, Wu Jun; Sun, Fu Cong; Yin, Wei Zhi; Ji, Yan Ke; Deng, Chuan Liang; Lu, Long Dou
DNA profiling of banana and plantain cultivars using random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers.
Polymerase chain reaction (PCR) amplification of genomic DNA from 57 Musa cultivars with 60 random 10-mer primers generated 605 polymorphic amplification products which were useful in unambiguous cultivar identifications. Unweighted pair-group method analysis of this data grouped the cultivars into specific clusters depending on their genomic similarities. The diploid ancestral species of cultivated banana and plantains, namely Musa acuminata sp malaccensis, an A genome donor and M. balbisiana, a B genome donor, were farthest apart from each other in the phenogram. The edible fruit yielding cultivars with the genomic constitutions AA, AAA, AB, AAB, ABB, and ABBB grouped in different clusters according to overall genetic homologies. The restriction fragment length polymorphisms (RFLPs) prevalent among the cultivars were studied by hybridization of 19 random genomic clones to blots of HindIII, EcoRI and MspI digests. Cluster analysis of these data on 107 polymorphic alleles resulted in a phenogram comparable to the one obtained with random amplified polymorphic DNA (RAPD) analysis. Two multilocus probes useful in distinguishing all the 57 cultivars analyzed were also identified. The A and B types of cytoplasms in the cultivars were further distinguished by hybridization of heterologous chloroplast DNA probes. Results showed that use of different kinds of molecular markers in gene banks is essential for characterization and classification of germplasm collections. PMID:8582364
Bhat, K V; Jarret, R L; Rana, R S
Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris , a medicinal herb
Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP),\\u000a selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified\\u000a polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb\\u000a from samples collected from various geographical regions of
Maryam Sarwat; S. Das; P. S. Srivastava
Identification of RAPD markers linked to a locus involved in quantitative resistance to TYLCV in tomato by bulked segregant analysis
In tomato, Bulked Segregant Analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a quantitative\\u000a trait locus (QTL) involved in the resistance to the Tomato Yellow Leaf Curl Virus. F4 lines were distributed into two pools, each consisting of the most resistant and of the most susceptible individuals, respectively.\\u000a Both pools were screened using 600 random
V. Chagu�; J. C. Mercier; M. Gu�nard; A. de Courcel; F. Vedel
Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers
Genetic variation among 43 date palm (Phoenix dactylifera L.) accessions, including 37 accessions from Morocco and 6 cultivars\\u000a from Iraq and Tunisia, was studied using Random Amplified Polymorphic DNA (RAPD) markers. The pre-screening of 123 primers\\u000a on four genotypes allowed selection of 19 primers which revealed polymorphism and gave reproducible results. All 43 analysed\\u000a genotypes were distinguishable by their band
My. Hassan Sedra; Philippe Lashermes; Pierre Trouslot; Marie-Christine Combes
Genetic mapping of RAPD markers linked to the densonucleosis refractoriness gene, nsd-1, in the silkworm, Bombyx mori.
In the silkworm, Bombyx mori, nonsusceptibility to B. mori densonucleosis virus type-1 (BmDNV-1) is controlled by a recessive gene, nsd-1 (nonsusceptibility to DNV-1), located on the twenty-first chromosome. We investigated genetic linkage between five random amplified polymorphic DNA (RAPD) markers and the +nsd-1 gene. Initially, we constructed the CSD-1 strain (nsd-1/+) which is congenic to strain C137 (nsd-1/nsd-1) for the twenty-first chromosome, starting with a female of C137 and a male of strain J137 (+nsd-1/+nsd-1). For the crossing over experiment, a female of C137 was crossed with a male (nsd-1/+) of CSD-1. Segregation analysis showed that the most closely linked RAPD marker mapped 3.0 cM distant from +nsd-1. A more specific marker for +nsd-1 was made by converting this RAPD band into a sequence characterized amplified region (SCAR) using a series of newly designed primer pairs based on its DNA sequence. PMID:9880921
Abe, H; Harada, T; Kanehara, M; Shimada, T; Ohbayashi, F; Oshiki, T
Identification and genetic mapping of RAPD markers linked to the densonucleosis refractoriness gene, nsd-2, in the silkworm, Bombyx mori.
In the silkworm, Bombyx mori, nonsusceptibility to B. mori densonucleosis virus type-2 (BmDNV-2) is controlled by a recessive gene, nsd-2 (nonsusceptibility to DNV-2). We investigated the genetic linkage between two random-amplified polymorphic DNA (RAPD) markers and the +nsd-2 gene. Initially, we constructed the JSD-2 strain (nsd-2/+), which is congenic to strain J137 (nsd-2/nsd-2) with respect to the chromosome containing the +nsd-2 gene, starting with a female of strain J137 and a male of strain C137 (+nsd-2/+nsd-2). Genomic DNAs were compared between infected individuals of the JSD-2 strain and J137 by a polymerase chain reaction (PCR) with 700 arbitrary 10-mer primers. Two RAPD markers (OPH19R and OPP01R) linked to the +nsd-2 gene were found. For the crossing-over experiment, a female of J137 was crossed with a male (nsd-2/+) of JSD-2. Segregation analysis showed that the most closely linked RAPD marker (OPP01R) was mapped 4.7 cM distant from +nsd-2. PMID:10925787
Abe, H; Sugasaki, T; Kanehara, M; Shimada, T; Gomi, S J; Ohbayashi, F; Oshiki, T
A molecular marker-based linkage map of diploid bananas ( Musa acuminata )
A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36%
S. Faur�; J. L. Noyer; J. P. Horry; F. Bakry; C. Lanaud; D. Go?zalez de Le�n
[Discrimination of interspecific hybrids in natural populations of Amur sturgeon fishes using multilocus RAPD-PCR markers].
RAPD-PCR analysis of 46 individuals of sturgeons from Amur River has been carried out. Genetic status of Amur sturgeon Acipenser schrenckii Brandt, 1869 and kaluga Huso dauricus Georgi, 1775 native populations has been estimated. Genetic evidences of hybrid origin for two phenotypical hybrids were obtained; estimations of genetic distances between species and hybrids appeared to be at interspecific level. The exact test for differentiation of populations (Exact test) and multidimensional scaling (MDS) analysis were estimated to be the most effective for species and hybrid discrimination, respectively. According to data obtained populations of sturgeon fishes which inhabit Amur River maintained an essential level of genetic variability; the presence of hybrids is regarded as one of risk factors. Multilocus RAPD-PCR markers admit as the convenient and reliable tool for genetic monitoring of Amur River sturgeons to preserve their gene pool. PMID:19140442
Chelomina, G N; Rozhkovan, K V; Ivanov, S A
Genetic diversity of bitter gourd ( Momordica charantia L.) genotypes revealed by RAPD markers and agronomic traits
Bitter gourd or bitter melon (Momordica charantia L.) is considered as minor cucurbitaceous vegetable in spite of having considerable nutritional and medicinal properties. Although some reports on genetic diversity based on morphological characterization are available, no work has been conducted to estimate genetic diversity using molecular markers in this crop. In the present study, 38 genotypes of M. charantia including
S. S. Dey; A. K. Singh; D. Chandel; T. K. Behera
Genetic diversity of spineless Cereus jamacaru accessions using morphological and molecular markers.
This is the first study to examine the genetic diversity of mandacaru cactus (Cereus jamacaru P. DC.). Plants of spineless mandacaru are commonly found in gardens and parks of urban areas in northeastern Brazil. In addition to exploring their ornamental potential, morphological, and genetic characterization may contribute to the development of plant materials that can be used as a source of macromolecules of potential economic interest. The goal of this study was to estimate the genetic variability of spineless mandacaru accessions using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers, and to characterize their morphology. Ten samples of newly emitted shoots with differentiated areolas and ribs were collected from each accession from the Cactaceous Germplasm Collection of Embrapa Agroind�stria Tropical, in Fortaleza, CE. Shoot shape and aspects of spine primordia (presence, location, grouping, and size of spines) were evaluated. The morphological analysis showed that the spineless mandacaru presented spine primordia. Twenty-six RAPD and 15 ISSR primers were polymorphic. A total of 262 markers were obtained, 129 of which were polymorphic. The average polymorphism of ISSR markers was higher than that of RAPD markers. The dendrograms for both analyses showed differentiation between accessions. Nevertheless, the molecular markers detected higher levels of diversity and a different pattern of diversity than those found using morphological markers. The molecular results revealed significant genetic variability both within and between groups. PMID:24222234
Oliveira, F I C; Bordallo, P N; Castro, A C R; Correia, D
Survey of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) biotypes in Brazil using RAPD markers
In 1991, the poinsettia strain, silverleaf whitefly or B biotype of Bemisia tabaci was detected in Brazil. This variant is a far more serious agricultural pest than the previously prevalent non-B (BR) biotype. The correct identification of B. tabaci is problematic since it is highly polymorphic with extreme plasticity in key morphological characters that vary according to the host. RAPD-PCR
L. H. C. Lima; D. N�via; P. W. Inglis; M. R. V. de Oliveira
Identification of a RAPD marker for palmitic-acid concentration in the seed oil of spring turnip rape ( Brassica rapa ssp. oleifera )
F2 progeny (105 individuals) from the cross Jo4002 x Sv3402 were used to identify DNA markers associated with palmitic-acid content in spring turnip rape (Brassica rapa ssp. oleifera). QTL mapping and ANOVA analysis of 140 markers exposed one linkage group with a locus controlling palmitic-acid content (LOD score 27), and one RAPD (random amplified polymorphic DNA) marker, OPB-11a, closely linked
P. K. Tanhuanp��; J. P. Vilkki; H. J. Vilkki
Detection of Two Fungal Biocontrol Agents against Root-knot Nematodes by RAPD Markers
The strain ZK7 of Pochonia chlamydosporia var. chlamydosporia and IPC of Paecilomyces lilacinus are highly effective in the biological control against root-knot nematodes infecting tobacco. When applied, they require\\u000a a specific monitoring method to evaluate the colonization and dispersal in soil. In this work, the randomly amplified polymorphic\\u000a DNA (RAPD) technique was used to differentiate between the two individual strains
Ming Liang Zhu; Ming He Mo; Zhen Yuan Xia; Yun Hua Li; Shu Jun Yang; Tian Fei Li; Ke Qin Zhang
Construction of a combined sorghum linkage map from two recombinant inbred populations using AFLP, SSR, RFLP, and RAPD markers, and comparison with other sorghum maps
Sorghum [Sorghum bicolor (L.) Moench] is an important crop in the semi-arid tropics that also receives growing attention in genetic research. A comprehensive reference map of the sorghum genome would be an essential research tool. Here, a combined sorghum linkage map from two recombinant inbred populations was constructed using AFLP, SSR, RFLP and RAPD markers. The map was aligned with
B. I. G. Haussmann; D. E. Hess; N. Seetharama; H. G. Welz; H. H. Geiger
Inheritance of plant regeneration from maize ( Zea mays L.) shoot meristem cultures derived from germinated seeds and the identification of associated RAPD and SSR markers
The inheritance of shoot regeneration through shoot-tip meristem culture derived from maize seedling was evaluated, and the markers (RAPD and SSR) associated with this regeneration character were identified both in a group of North American maize inbreds and a crossing population. A discrete distribution of percent regeneration and no. of shoots per explant was observed in the inbred group and
W. Li; G. Sun; J. Liu; P. Masilamany; J. H. Taylor; W. Yan; K. J. Kasha; K. P. Pauls
Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers.
Gliricidia sepium and G. maculata are multi-purpose leguminous trees native to Central America and Mexico. Research programmes have been initiated to define the native distribution of Gliricidia and sample the spectrum of genetic variation. To date, there has been little systematic assessment of genetic variability in multi-purpose tree species. Accurate estimates of diversity between- and within-populations are considered a prerequisite for the optimization of sampling and breeding strategies. We have used a PCR-based polymorphic assay procedure (RAPDs) to monitor genetic variability in Gliricidia. Extensive genetic variability was detected between species and the variability was partitioned into between- and within-population components. On average, most (60 per cent) of the variation occurs between G. sepium populations but oligonucleotide primers differed in their capacity to detect variability between and within populations. Population-specific genetic markers were identified. RAPDs provide a cost-effective method for the precise and routine evaluation of variability and may be used to identify areas of maximum diversity. The approaches outlined have general applicability to a range of organisms and are discussed in relation to the exploitation of multi-purpose tree species of the tropics. PMID:1385362
Chalmers, K J; Waugh, R; Sprent, J I; Simons, A J; Powell, W
Evaluation of synthetic hexaploid wheats (derivative of durum wheats and Aegilops tauschii accessions) for studying genetic diversity using randomly amplified polymorphic DNA (RAPD) markers.
Synthetic hexaploid (SH) wheat derived from crossing tetraploid durum wheat and diploid Aegilops tauschii provide germplasm for wheat improvement as the conventional wheat varieties possess very low genetic diversity. This study aims to identify diverse SH lines which can be used in breeding programs for transferring the desired traits into bread wheat. The study was conducted on 24 SH lines using 10 pairs of randomly amplified polymorphic DNA (RAPD) markers. Application of RAPDs showed the presence of some diagnostic bands in SH wheats that were absent in durum parents suggest that these bands are donated by D genome of the wild relative Ae. tauschii. PMID:23192610
Shakeel, Muhammad; Ilyas, Muhammad; Kazi, Mujeeb
[RAPD markers linked to the stripe rust resistance gene Yr5 in the wheat variety Triticum spelta album].
A total of 520 10-mer random primers were used to identify the RAPD markers linked to the Yr5 gene between the near-isogenic line Yr5/6 x Avocet S and recurrent parent Avocet S. Three polymorphic DNA fragments, S1496(761), S1453(880) and S1418(1950), were found linked to the Yr5 gene. In which the genetic distance between S1496(761) and Yr5 gene was 2.7 cM. The fragment S1496(761) was recovered from the gel and cloned and sequenced. A pair of specific PCR primers was designed based on the sequence. The specific primers amplified the same fragment about 761bp as the random primer S1496 did. Because the primers could amplify another non-specific fragment, the PCR products must be analyzed by electrophoresis on polyacrylamide gels. PMID:12200864
Zhong, Ming; Niu, Yong-Chun; Xu, Shi-Chang; Wu, Li-Ren
Identification of RAPD-SCAR marker linked to white spot syndrome virus resistance in populations of giant black tiger shrimp, Penaeus monodon Fabricius.
White spot disease (WSD) caused by white spot syndrome virus (WSSV) creates severe epizootics in shrimp aquaculture industry worldwide. Despite several efforts, no such permanent remedy was yet developed. Selective breeding using DNA markers would be a cost-effective strategy for long-term solution of this problem. In the present investigation, out of 30 random primers, only one primer produced a statistically significant (P < 0.01) randomly amplified polymorphic DNA (RAPD) marker of 502 bp, which provided a good discrimination between disease resistant and disease susceptible populations of Penaeus monodon from three geographical locations along the East coast of India. Because RAPD markers are dominant, a sequence characterized amplified region (SCAR) marker was developed by cloning and sequencing of 502 bp RAPD fragment, which generates a single 457 bp DNA fragment after PCR amplification only in the disease resistant shrimps. Challenge experiment was also conducted to validate this 457 bp SCAR marker, and the results suggested that the WSSV loads were 2.25 � 10(3) fold higher in disease susceptible than that in disease resistant shrimps using real-time PCR. Therefore, this 457 bp DNA SCAR marker will be very valuable towards the development of disease-free shrimp aquaculture industry. PMID:23952572
Dutta, S; Biswas, S; Mukherjee, K; Chakrabarty, U; Mallik, A; Mandal, N
Genetic characterization of fig tree mutants with molecular markers.
The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes. PMID:22911583
Rodrigues, M G F; Martins, A B G; Desid�rio, J A; Bertoni, B W; Alves, M C
Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume
Background and aims Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati. Methodology The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated. Principal results Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33�0.49, 0.18�0.49 and 0.26�0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (hsp) was highest when compared with intra-population diversity (hpop) and the gene flow (Nm) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering. Conclusions Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes.
Kesari, Vigya; Madurai Sathyanarayana, Vinod; Parida, Ajay; Rangan, Latha
Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (Uromyces viciae-fabae) in Vicia faba L.
Bulk segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a gene determining hypersensitive resistance in Vicia faba line 2N52 against race 1 of the rust fungus Uromyces viciae-fabae. The monogenic nature of the resistance was determined by analyzing the F(2) population from a cross between resistant line 2N52 and susceptible line VF-176, and further confirmed in the F(2:3)-derived families. Linkage of the RAPD markers was confirmed by screening 55 F(2) plants segregating for resistance. Three RAPD markers (OPD13(736), OPL18(1032) and OPI20(900)) were mapped in coupling phase to the resistance gene for race 1 ( Uvf-1). No recombinants between OPI20(900) and Uvf-1 were detected. Two additional markers (OPP02(1172) and OPR07(930)) were linked to the gene in repulsion phase at a distance of 9.9 and 11.5 cM, respectively. The application of marker-assisted selection to develop new faba bean varieties with rust resistance genes is discussed. PMID:12698251
Avila, C M; Sillero, J C; Rubiales, D; Moreno, M T; Torres, A M
A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.
Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM.
Laurent, V; Wajnberg, E; Mangin, B; Schiex, T; Gaspin, C; Vanlerberghe-Masutti, F
Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers
We have extended the combined use of the �pseudo-testcross� mapping strategy and RAPD markers to map quantitative trait loci (QTLs) controlling traits related to vegetative propagation in Eucalyptus. QTL analyses were performed using two different interval mapping approaches, MAPMAKER-QTL (maximum likelihood) and QTL-STAT (non-linear least squares). A total of ten QTLs were detected for micropropagation response (measured as fresh weight
D. Grattapaglia; F. L. Bertolucci; R. R. Sederoff
Species-diagnostic markers in Larix spp. based on RAPDs and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications
Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among\\u000a four larch species [Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had\\u000a good diagnostic value, and 3 out of 12 nuclear
Marie-Claude Gros-Louis; Jean Bousquet; Luc E. P�ques; Nathalie Isabel
The concordance of terpenoid, ISSR and RAPD markers, and ITS sequence data sets among genotypes: an example from Juniperus
Twelve individual genotypes selected from Juniperus populations, varieties and species were analyzed using ITS sequences, RAPDs, ISSRs, and leaf volatile terpenoids. These four data sets, all analyzed in the same manner, illustrated that these data sets can be used at different organizational levels: specific, inter-specific and intraspecific. Similarity matrices for the ITS, RAPD, and ISSR data sets were highly correlated
Robert P. Adams; Andrea E. Schwarzbach; R. Naresh Pandey
Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers.
DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes. PMID:24783778
Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A
In vitro clonal propagation and genetic fidelity of the regenerants of Spilanthes calva DC. using RAPD and ISSR marker.
An efficient in vitro protocol has been established for clonal propagation of elite plant of Spilanthes calva DC., an important source of spilanthol, an antimalarial larvicidal compound. Nodal explants excised from field grown plant of S. calva DC. when reared on Murashige and Skoog's medium augmented with different cytokinins, viz. N(6)-Benzyladenine (BA), N(6)-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn), differentiated multiple shoots from the axils. BA at 10�?M proved optimum for elicitation of multiple shoots in 91.6�% cultures with an average of 7.12 shoots per explant within 6�weeks. The excised shoots rooted on half strength Murashige and Skoog's medium supplemented with 0.1�?M IBA. Micropropagated plants were hardened and transferred to field for acclimatization, where 95�% plants survived and were phenotypically similar to the donor plant. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to evaluate the genetic fidelity amongst the regenerants. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 71 scorable bands, ranging in size from 100�bp to 1,100�bp were generated by a combination of the two markers in the aforesaid plants. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant. The similarity values amongst the aforesaid plants varied from 0.967 to 1.000. The dendrogram generated through UPGMA (Unweighted Pair Group Method with arithmetic mean) analysis revealed 98�% similarity amongst them, thus confirming the genetic fidelity of the in vitro clones. PMID:24431493
Razaq, Mohd; Heikrujam, Monika; Chetri, Siva K; Agrawal, Veena
Random amplified polymorphism DNA (RAPD) was used as a DNA fingerprinting technique in rice germplasm evaluation. The high efficiency and random coverage of RADP markers were established to analyse the biodiversity of 72 rice germplasm accessions . We examined the amplification products in both their size and their polymorphism. Correlation matrix was carried out using the Genstat program. Cluster analysis
Analysis of randomly amplified polymorphic DNA (RAPD) for identifying genetic markers associated with canine hip dysplasia
Canine hip dysplasia is a heritable developmental disease resulting, in part, from increased laxity in hip joints and is a precursor to degenerative joint disease. Iden- tification of genetic markers linked to joint laxity would foster development of more accurate diagnostic methods, facilitate identification of the disease gene(s), and supplement efforts to establish physical\\/genetic maps of the canine genome. Work
X. Wang; A. B. Miller; A. J. Lepine; J. D. Scott; K. E. Murphy
Genetic diversity and relationships in mulberry (genus Morus ) as revealed by RAPD and ISSR marker assays
Background��The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity\\u000a and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust\\u000a alternative, PCR based marker assays
Arvind K Awasthi; GM Nagaraja; GV Naik; Sriramana Kanginakudru; K Thangavelu; Javaregowda Nagaraju
Genetic Diversity and Species-Diagnostic Markers of Mud Crabs (Genus Scylla ) in Eastern Thailand Determined by RAPD Analysis
:�� Genetic diversity of three mud crab species, Scylla serrata (Forsk�l), S. oceanica (Dana), and S. tranquebarica (Fabricius), collected from two locations in eastern Thailand (Chanthaburi and Trat) was examined by randomly amplified polymorphic\\u000a DNA�polymerase chain reaction (RAPD-PCR). Ninety-one reproducible RAPD fragments, generated by UBC456, UBC457, and YNZ22,\\u000a were polymorphic. The percentage of polymorphic bands within populations ranged from 47.92%
S. Klinbunga; A. Boonyapakdee; B. Pratoomchat
Evidence for tetrasomic inheritance in a tetraploid Solanum commersonii (+) S. tuberosum somatic hybrid through the use of molecular markers
In order to assess the potential for interspecific recombination between the cultivated Solanum tuberosum (tbr) and the sexually isolated wild species Solanum commersonii (cmm), genetic analysis of a F2 progeny obtained by selfing one tetraploid cmm (+) tbr somatic hybrid was performed through molecular markers. For this purpose,\\u000a the extent of disomic and\\/or tetrasomic inheritance of species-specific RAPD and AFLP
A. Barone; J. Li; A. Sebastiano; T. Cardi; L. Frusciante
RAPD, SCAR and conserved 18S rDNA markers for a red-listed and endemic medicinal plant species, Knema andamanica (Myristicaceae).
Knema andamanica is a red-listed endemic medicinal species of Myristicaceae restricted to Andaman and Nicobar (A&N) Islands, India. This species is used in tribal medicines and has immense bioprospective potential. With a view to generate suitable genomic markers for classification and identification, we have generated RAPD, SCAR and conserved 18S rDNA markers from K. andamanica. A unique 585�bp fragment, that distinguished it from seven other related species of Myristicaceae was first amplified using the random primer OPE 06 and converted to SCAR marker (GenBank accession # JN228256). The conserved sequences of 18S rDNA loci from K. andamanica were also amplified and sequenced (GenBank accession #JN228265). The sequence revealed deviations including 18 variable regions and 15 indels that were unique to K. andamanica. These markers can help in definite identification of K. andamanica even at the juvenile stages. PMID:24431492
Sheeja, T E; Anju, P R; Shalini, R S; Siju, S; Dhanya, K; Krishnamoorthy, B
An analysis of the pattern of genetic variation in Vitellaria paradoxa using RAPD markers
Vitellaria paradoxa C.F.Gaertn. is one of the most economically and socially important tree species in the Sudano-Sahelian region. Little is known of the pattern of variation within its natural range. Eight populations covering most of the natural range from Senegal to Uganda were sampled and leaves of 118 individual trees were collected. An analysis of molecular diversity was carried out
Jean-Marc Bouvet; Christelle Fontaine; Haby Sanou; C�line Cardi
Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...
Dye-free protein molecular weight markers.
Protein molecular weight markers are widely used in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. Here, we describe novel protein molecular weight markers in which a prestaining procedure is no longer needed. Green fluorescent protein (GFP) is stable and resistant to denaturing agents/conditions. Various histidine-tagged GFP fusion proteins were overexpressed in Escherichia coli and purified by metal affinity chromatography. The minimal amount of each protein marker needed for analysis in SDS-PAGE and Western blot under visible light was 62.5 and 125 ng, respectively. Under ultraviolet (UV) ray, the minimal amount of each protein marker needed for analysis in SDS-PAGE and Western blot was half of those amounts used under visible light, respectively. Collectively, the accuracy, sensitivity, ease, economy, and flexibility of our strategy may reinforce the application of GFP in molecular biology. PMID:16041708
Chang, Microsugar; Hsu, Hsue-Yin; Lee, Han-Jung
The application of molecular markers in the study of diversity in acarology: a review.
The application of molecular markers to the study of ticks and mites has recently yielded new insights into their population structures and taxonomic relationships. Ticks have been studied at individual, population and species level. Mites are a more diverse group and those that have been studied to the same degree as the ticks include the Tetranychidae (spider mites), Phytoseiidae (predatory mites) and the Eriophyidae. Population variation has also been studied in the important bee parasitic mite Varroa jacobsoni Oudemans. The methods used to study these organisms have much in common. At the individual level these range from general approaches, such as AFLP, RAPD or DALP, to highly specific microsatellite analysis. Although these markers also work at the population and species level, additional analysis of specific nuclear or mitochondrial genes has been conducted either by RFLP or sequencing. Molecular applications have had particular success in facilitating the identification of taxonomically difficult species, understanding population structures and elucidating phylogenetic relationships. PMID:11345314
Navajas, M; Fenton, B
Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae) revealed by RAPD markers
Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the FST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.
Assessing Genetic Structure with Multiple Classes of Molecular Markers: A Case Study Involving the Introduced Fire Ant Solenopsis invicta
We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, co- dominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial
Kenneth G. Ross; D. DeWayne Shoemaker; Michael J. B. Krieger; Christopher J. DeHeer; Laurent Keller
Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers
Fifty-eight accessions of sesame (Sesamum indicum L.), an important oil seed crop of the tropics and subtropics were analysed using random amplified polymorphic DNA (RAPD)\\u000a technique. The material analysed comprised 36 collections from 18 different states of India and four adjoining countries of\\u000a the Indian subcontinent, and 22 exotic accessions from 21 sesame growing countries around the world. The results
K. Venkataramana Bhat; Prashant P. Babrekar; Suman Lakhanpaul
Antibiograms and randomly amplified polymorphic DNA-polymerase chain reactions (RAPD-PCR) as epidemiological markers of gonorrhea.
The development of antimicrobial resistance of Neisseria gonorrhoeae arising from wide dissemination of resistant clones is a major global health problem. In this study, a total of 235 isolates of N. gonorrhoeae isolated from patients of Bangrak Hospital were tested for their antibiotic susceptibilities to penicillin, norfloxacin, ofloxacin, ciprofloxacin, spectinomycin, and ceftriaxone. Mutation (Ser-91) in the quinolone resistance determining regions of gyrA and random amplification of the polymorphic DNA polymerase chain reaction (RAPD-PCR) were examined from 145 isolates. Among these, 55 isolates were obtained during January-March 2000, 46 isolates during January-March 2002, and 44 isolates during October-December 2002. The occurrence of combination resistance between penicillin and quinolone was 20% in January-March 2000, which was increased to 57.8% during the period of October-December 2002 (P<0.0001). Mutation of Ser-91 in gyrA could be directly linked with the resistance or declining of susceptibility to ciprofloxacin. Using RAPD-PCR, we could classify the 145 isolates into 4 and 5 groups by primers D11344 (5'-AGTGAATTCGCGGTGAGATGCCA-3') and D8635 (5'-GAGCGGCCAAAGGGAGCA GAC-3'), respectively. Combination of the data obtained from these two primers produced 11 fingerprint groups. Our findings conclude that monitoring of the Ser-91 mutation of gyrA and RAPD-PCR methods are most useful for epidemiological screening. PMID:20087948
Lawung, Ratana; Charoenwatanachokchai, Angkana; Cherdtrakulkiat, Rungrot; Thammapiwan, Sivarak; Mungniponpan, Tharinda; B�low, Leif; Prachayasittikul, Virapong
Evaluation of genetic variability in micropropagated propagules of ornamental pineapple [Ananas comosus var. bracteatus (Lindley) Coppens and Leal] using RAPD markers.
The objective of the present study was to evaluate the genetic variability in micropropagated plantlets of ornamental pineapple, after the fourth period of subculture. The basal culture medium consisted of MS salts, vitamins, 3% sucrose, liquid formulation, supplemented with 6-benzylaminopurine (BAP) at concentrations of 0.125, 0.25, 0.5, 1.0, and 2.0 mg/L. The addition of BAP influenced the occurrence of genetic variation revealed using random amplified polymorphic DNA (RAPD) markers. Of a total of 520 primers tested, 44 were selected and amplified; 402 monomorphic bands (97.2%) and 18 polymorphic bands (2.8%) resulted among regenerated plantlets. The polymorphic fragments were produced by 12 primers (OPA-01, OPA-20, OPB-01, OPB-19, OPC-19, OPF-13, OPL-17, OPM-13, OPP-16, OPT-07, OPV-19, and OPX-03). Among the primers that identified polymorphism, OPA-01, OPA-20, OPB-19, OPC-19, OPL-17, OPP-16, and OPX-3 each showed, one polymorphic band and OPF-13 amplified a maximum of three bands. In this study, the RAPD technique was effective in showing the occurrence of somaclonal variations that occur during the micropropagation process of ornamental pineapple cultivation in BAP-supplemented medium, and it is possible to detect the presence of genetic variation in early stages of plant development. PMID:19048488
Santos, M D M; Buso, G C S; Torres, A C
Genetic variation and phylogenetic relationships among worldwide collections of the Russian wheat aphid, Diuraphis noxia (Mordvilko), inferred from allozyme and RAPD-PCR markers.
Genetic analyses were conducted on Diuraphis noxia (Mordvilko) populations collected from wheat, barley and other grasses from various countries throughout the world. These collections had been found to contain clones that differed in virulence from various cultivars, cuticular hydrocarbon profiles and life cycle characters. Discrete genetic markers analysed in this study included allozymes and arbitrary regions of the genome amplified by the polymerase chain reaction (RAPD-PCR). In all, 23 enzymes were evaluated; 17 of these enzymes representing 20 isozyme loci, were judged suitable for allozyme analysis. Polymorphisms were detected at three (15 per cent) loci: beta-esterase (beta-EST), phosphoglucose isomerase (PGI), and 6-phosphogluconate dehydrogenase (6-PGDH). The average expected heterozygosity amongst these loci was 4.9 per cent in the worldwide collection. Allozyme variation was absent within most populations, particularly within those countries where the species was recently introduced. Much greater genetic variation was detected when populations were analysed with RAPD-PCR. Populations were analysed with 69 polymorphic bands amplified by seven primers. All populations could be distinguished with this method. Cluster analyses indicated strong similarities between U.S.A. populations and collections from South Africa, Mexico, France and Turkey. The most variation was detected among populations from the Middle East and southern Russia. PMID:8335479
Puterka, G J; Black, W C; Steiner, W M; Burton, R L
Molecular markers for diagnosis and prognosis
A plethora of aberrations are associated with progress and outcome for head and neck cancer patients and some have been shown to provide prognostic information independent of the TNM staging system. These findings justify future studies that will harness recent advances in technologies to refine the range of molecular markers available. Important lessons have been learnt during the last two
Max Partridge; Kamis Gaballah; Xiaohong Huang
Prognostic molecular markers in early breast cancer
A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfuly used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development.
Esteva, Francisco J; Hortobagyi, Gabriel N
Morphological characterization and molecular fingerprinting of Nostoc strains by multiplex RAPD.
Morphological parameters studied for the twenty selected Nostoc strains were mostly found to be consistent with the earlier reports. But the shape of akinetes observed in this study was a little deviation from the existing descriptions and heterocyst frequency was also found to be different in different strains in spite of growing in the same nitrogen free media. Multiplex RAPD produced reproducible and completely polymorphic amplification profiles for all the strains including some strain specific unique bands which are intended to be useful for identification of those strains. At least one to a maximum of two unique bands was produced by different dual primer combinations. For ten strains out of twenty, strain specific bands were found to be generated. Cluster analysis revealed a vast heterogeneity among these Nostoc strains and no specific clustering based on geographical origin was found except a few strains. It was also observed that morphological data may not necessarily correspond to the genetic data in most of the cases. CCC92 (Nostoc muscorum) and CCC48 (Nostoc punctiforme) showed a high degree of similarity which was well supported by high bootstrap value. The level of similarity of the strains ranged from 0.15 to 0.94. Cluster analysis based on multiplex RAPD showed a good fit revealing the discriminatory power of this technique. PMID:23610928
Hillol, Chakdar; Pabbi, Sunil
[Identification and analysis of the specific molecular marker associated with fertile maintenance of cytoplasmic male sterility cauliflower].
Analysis of RAPD (Randomly Amplification Polymorphic DNA) was performed between cytoplasmic male sterility line and its maintainer line of cauliflower. Totally 2160 detectable bands were obtained by RAPD using 406 10-bp random primers. Averagely, 5 to 10 bands were produced per primer. Among all the primers only the amplification of primer S2121 was polymorphic in two lines. A 934-bp specific band was only detected in maintainer line. After cloning and sequencing, specific primers were designed to transform the RAPD marker to PCR marker, which was named S2121(900). To identify the specificity of S2121(900), southern dot blotting was performed. To further identify its specificity, individual plant and candidate materials testing were also performed. All these results indicated that the S2121(900) was specific. It can be used to screen the maintainer lines of cauliflower in early stage. Analysis of the sequence suggested that this fragment was high homologous with the part sequences of mitochondrial genome in Brassica napus and Arabidopsis thaliana. So we supposed the S2121(900) may also derive from mitochondrial genome. Our results here offer new clues for explaining the molecular mechanism of cytoplasic male sterility of cauliflower in other way. PMID:16944598
Wang, Chun Guo; Li, Hui; Song, Wen Qin
Genetic variability in Russian wildrye (Psathyrostachys juncea) assessed by RAPD
To assess the genetic variation within and among accessions of Russian wildrye (Psathyrostachys juncea), 88 individuals of 11 accessions originated from geographically diverse locations were analyzed using randomly amplified polymorphic DNA (RAPD). Under the optimized condition, 56% of the 200 tested primers produced polymorphic RAPDs among accessions. High level RAPD marker variations existed both within and among accessions. About 56%
J. Z. Wei; W. F. Campbell; R. R.-C. Wang
The use of nuclear DNA molecular markers for studying speciation and systematics as exemplified by the � Lacerta agilis complex� (Sauria: Lacertidae)
Four types of nuclear DNA markers identified by the taxonprint, RAPD, and IMP (Inter-MIR-PCR) methods, and the nucleotide\\u000a sequences of satellite DNA monomers have been used to analyze the molecular genetic similarity between some populations, subspecies,\\u000a and species of lizards combined into the group Lacerta s. str., as well as representatives of some other genera. The notions on the systematics
V. V. Grechko; L. V. Fedorova; D. M. Ryabinin; N. L. Ryabinina; D. G. Ciobanu; S. A. Kosushkin; I. S. Darevsky
Genetic diversity in barley from west China based on RAPD and ISSR analysis
Two types of molecular markers, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were assayed to determine the genetic diversity of 46 barley accessions, including 27 landraces of H. vulgare ssp vulgare (HV), 6 accessions of H. vulgare ssp. spontaneum (HS) and 13 accessions of H. vulgare ssp. agriocrithon (HA), from west China. A high level of polymorphism
Yong-Cui Hou; Ze-Hong Yan; Yu-Ming Wei; You-Liang Zheng
[Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae) in central Colombia with RAPD markers].
Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished as a consequence of anthropic activities. In this study, the Random Amplified Polymorphic DNA (RAPD) was used to estimate the actual genetic structure in this species. For the purpose, six sample sites located in the department of Antioquia (Central Chain Mountains of Colombia) were used. Thirty five primers (87.5%), out of forty used, yielded 1 466 reliable and consistent fragments; 417 were considered as unique fragments able to discriminate among the Magdalena (Humarada-1 and Humarada-2) and Cauca (Piedras, La Clara y Guaracfi) river basins samples, suggesting that each is a discrete unit. This diversity suggests that anthropic effects of over fishing, dam building, deforestation and water pollution, have contributed to the isolation of these fish groups on the high mountains. Brycon moorei and Colossoma macropomum, as an interspecific control groups, were placed out of the B. henni general group, confirming their taxonomic classification through morphologic data. The RAPD technique was useful to know the genetic diversity and to discriminate among B. henni populations from different geographic origins, as a basis for an appropriate plan of repopulation, conservation and wildlife management. PMID:19086404
Pineda Santis, Hermes; Arboleda Chac�n, Lucy; Echeverry Echavarria, Amparo; Urcuqui Inchima, Silvio; Pareja Molina, Diego; Olivera Angel, Martha; Builes G�mez, Juan
Molecular Prognostic Markers in Colon Cancer
\\u000a Colorectal cancer arises as a consequence of the accumulation of genetic and epigenetic alterations. Significant progress\\u000a has been made to identify the different biomarkers associated with the biological and clinical behaviour of colorectal tumours.\\u000a Several new molecular predictive and prognostic markers have been identified and are now being translated into routine clinical\\u000a practice. One of the challenges is that most
Thomas Winder; Heinz-Josef Lenz
Fecal Molecular Markers for Colorectal Cancer Screening
Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.
Kanthan, Rani; Senger, Jenna-Lynn; Kanthan, Selliah Chandra
Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers.
Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary. PMID:23506829
Ding, Ge; Zhang, Daizhen; Yu, Yanqiu; Zhao, Lingling; Zhang, Beibei
DNA typing of hops (Humulus lupulus) through application of RAPD and microsatellite marker sequences converted to sequence tagged sites (STS)
Both random amplified polymorphic DNA and microsatellite repeat sequences were investigated as DNA markers for distinguishing hop cultivars. Microsatellite sequences converted to STS markers proved to be most successful. The relative abundance of microsatellite repeat sequences in the hop genome varied depending on the sequence class. Of the repeat types investigated the dinucleotide repeats (GA)n and (GT)n are the most
Jamie L. Brady; Nigel S. Scott; Mark R. Thomas
The Genetic Structure of Anophelines (Culicidae: Diptera): RAPD Versus Allozymes
The genetic structure of the species related to genus Anopheles was studied using both allozymes and RAPDs (random amplified polymorphic DNA). More accurate genetic diversity and differentiation\\u000a could be detected with RAPD markers than with allozyme profiles. The degree of population subdivision was also much greater\\u000a for RAPDs than for allozymes. The dendrograms produced by each of these markers differed
Neetu; Sudarshan Chaudhry
Molecular Markers and Marker-Assisted Selection in Rice
The status of rice as a model crop and the sequencing of the indica and japonica genomes have provided breeders with the necessary tools for marker assisted breeding. Simple Sequence Repeat (SSR) markers\\u000a are easily available for any region of the genome, and candidate gene markers are being developed rapidly. The likely targets\\u000a of MAS include yield and agronomic traits,
David J. Mackill
Inheritance of citrus nematode resistance and its linkage with molecular markers
Eleven RAPD markers linked to a gene region conferring resistance to citrus nematodes in an intergen-eric backcross family\\u000a were identified. Two sequence- characterized amplified region markers linked to a citrus tristeza virus resistance gene and\\u000a one selected resistance gene candidate marker were evaluated for their association with citrus nematode resistance. A nematode-susceptible\\u000a citrus hybrid, LB6-2 [Clementine mandarin (Citrus reticulata)?Hamlin orange
P. Ling; L. W. Duncan; Z. Deng; D. Dunn; X. Hu; S. Huang; F. G. Gmitter Jr
Genetic diversity of Pleurotus pulmonarius revealed by RAPD, ISSR, and SRAP fingerprinting.
Pleurotus pulmonarius is one of the most widely cultivated and popular edible fungi in the genus Pleurotus. Three molecular markers were used to analyze the genetic diversity of 15 Chinese P. pulmonarius cultivars. In total, 21 random amplified polymorphic DNA (RAPD), 20 inter-simple sequence repeat (ISSR), and 20 sequence-related amplified polymorphism (SRAP) primers or primer pairs were selected for generating data based on their clear banding profiles produced. With the use of these RAPD, ISSR, and SRAP primers or primer pairs, a total of 361 RAPD, 283 ISSR, and 131 SRAP fragments were detected, of which 287 (79.5�%) RAPD, 211 (74.6�%) ISSR, and 98 (74.8�%) SRAP fragments were polymorphic. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of these three methods were structured similarly, grouping the 15 tested strains into four clades. Subsequently, visual DNA fingerprinting and cluster analysis were performed to evaluate the resolving power of the combined RAPD, ISSR, and SRAP markers in the differentiation among these strains. The results of this study demonstrated that each method above could efficiently differentiate P. pulmonarius cultivars and could thus be considered an efficient tool for surveying genetic diversity of P. pulmonarius. PMID:24241329
Yin, Yonggang; Liu, Yu; Li, Huamin; Zhao, Shuang; Wang, Shouxian; Liu, Ying; Wu, Di; Xu, Feng
Molecular determination of genotoxic effects of cobalt and nickel on maize (Zea mays L.) by RAPD and protein analyses.
Assessment of DNA damages stemming from toxic chemicals is an important issue in terms of genotoxicology. In this study, maize (Zea mays L.) seedlings were used for screening the genotoxic effects of cobalt (Co) and nickel (Ni) treatments at various concentrations (5 mM, 10 mM, 20 mM and 40 mM). For this purpose, randomly amplified polymorphic DNA (RAPD) technique was applied to genomic DNA extracted from metal-exposed and unexposed plant materials. Besides, changes in total protein contents were screened by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. For RAPD analysis, 16 RAPD primers were found to produce unique polymorphic band profiles on different concentrations of Co-/Ni-treated maize seedlings. Increased polymorphism resulting from the appearance of new bands or disappearance of normal bands was observed with increasing concentration of Co and Ni treatments. Genomic template stability, a qualitative measurement of changes in RAPD patterns of genomic DNA, decreased with increasing metal concentration. In SDS-PAGE analysis, it was observed that the total soluble protein content decreased by Co treatment, while it increased by Ni treatment. The results obtained from this study revealed that RAPD profiles and total soluble protein levels can be applied to detect genotoxicity, and these analyses can offer useful biomarker assays for the evaluation of genotoxic effects on Co- and Ni-polluted plants. PMID:22499271
Erturk, Filiz Aygun; Ay, Hilal; Nardemir, Gokce; Agar, Guleray
Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types
Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic.
Beverley J. Parsons; H. John Newbury; Michael T. Jackson; Brian V. Ford-Lloyd
Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers.
Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs. PMID:22576831
Cerqueira-Silva, C B M; Santos, E S L; Concei��o, L D H C S; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corr�a, R X
Molecular identification of pathogenic and nonpathogenic strains of Vibrio harveyi using PCR and RAPD
Fifteen environmental samples of Vibrio spp. isolated from healthy and diseased shrimps were tested for pathogenicity to juvenile shrimps. Two isolates, strains Z2 and Z3, were observed to be pathogenic, causing 100% mortality of the target host compared to the control strain Vibrio harveyi ATCC 14126. Environmental and type strains were subjected to molecular characterization by restriction fragment length polymorphism
G. Hern�ndez; J. Olmos
Molecular Characterization of Black Bengal and Jamuna Pari Goat Breeds By RAPD Markers
This experiment was conducted in the Genetics, Breeding and Reproductive Biotechnology Laboratory under Goat and Sheep Production Research Division, Bangladesh Livestock Research Institute (BLRI), Saver, Dhaka, Bangladesh. DNA was extracted from 14 goat breeds and the extracted DNA was observed by gel electrophoresis. Eight goat specific primers were synthesized by ASM-800 DNA synthesizer and screened in the study and all
M. A. Rahman; S. M. M. Rahman; M. A. Jalil; Sarder Nasir Uddin
Precise detection and tracing of Trichoderma hamatum 382 in compost-amended potting mixes by using molecular markers.
Randomly amplified polymorphic DNA (RAPD) analysis and the PCR assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of Trichoderma hamatum 382, a biocontrol agent utilized in compost-amended mixes. Distinct and reproducible fingerprints were obtained upon amplification of purified genomic DNA of T. hamatum 382 with the random primers OPE-16, OPH-19, and OPH-20. Three amplified DNA fragments of 0.35 (OPE-16(0.35)), 0.6 (OPH-19(0.6)), and 0.65 (OPH-20(0.65)) kb were diagnostic for T. hamatum 382, clearly distinguishing it from 53 isolates of four other Trichoderma spp. tested. Some isolates of T. hamatum shared these low-molecular-weight fragments with T. hamatum 382. However, RAPD analysis of isolates of T. hamatum with all three random primers used in consecutive PCR tests distinguished T. hamatum 382 from other isolates of T. hamatum. These three RAPD amplicons were cloned and sequenced, and pairs of oligonucleotide primers for each cloned fragment were designed. Use of the primers in the PCR assay resulted in the amplification of DNA fragments of the same size as the cloned RAPD fragments from genomic DNA of T. hamatum 382. A combination of dilution plating on a semiselective medium for Trichoderma spp. and PCR, with the RAPD primers OPH-19, OPE-16, and OPH-20 or the three sequence-characterized primers, was used successfully to verify the presence of T. hamatum 382 propagules in nine different soil, compost, and potting mix samples. All 23 Trichoderma isolates recovered on semiselective medium from commercial potting mixes fortified with T. hamatum 382 were identified as T. hamatum 382, whereas 274 Trichoderma isolates recovered from the other nine samples were negative in the PCR assay. Thus, this highly specific combination of techniques allowed detection and enumeration of propagules of T. hamatum 382 in fortified compost-amended potting mixes. Sequence-characterized amplified region markers also facilitated the development of a very simple procedure to amplify DNA of T. hamatum 382 directly from fortified compost-amended potting mixes. PMID:10583998
Abbasi, P A; Miller, S A; Meulia, T; Hoitink, H A; Kim, J M
Listeria monocytogenes in pork slaughtering and cutting plants. Use of RAPD, PFGE and PCR-REA for tracing and molecular epidemiology.
In order to determine the origin of pork cuts contamination by Listeria monocytogenes, 287 isolates, collected from five French pork slaughtering and cutting plants, from live pigs to pork cuts, were characterised using three molecular typing methods: random amplification of polymorphic DNA (RAPD) carried out with five different primers, genomic macrorestriction using ApaI with pulsed-field gel electrophoresis (PFGE) and a PCR-restriction enzyme analysis (PCR-REA) based on the polymorphism existing within the inlA and inlB genes. Results obtained from RAPD and PFGE were closely related and distinguished respectively 17 RAPD types (r1-r17) and 17 PFGE types (a1-a17) among the 287 isolates, whereas the PCR-REA analysis only yielded two profiles (p1 and p2). Considering the combined results obtained with the three molecular typing methods, 19 Listeria monocytogenes genotypes (1-19) were distinguished. Serotyping led at least four serotypes being distinguished: 1/2a, 3a, 1/2c and 3c. The application of genotyping identified the predominance of a Listeria monocytogenes strain of type (1) and other very closely related ones (5, 9, 10, 12, 13, 14, 16 and 19) which were present on pork as well as in the environment within the five investigated plants. This study also pointed out the presence of these closely related Listeria monocytogenes strains over a 1-year period in the environments of two plants, even after cleaning and disinfection procedures. This highlights the possibility for some Listeria monocytogenes strains to persist in pork processing environments and raises the problem of the efficiency of cleaning and disinfection procedures used in pork slaughterhouses, chilling and cutting rooms. PMID:10634704
Giovannacci, I; Ragimbeau, C; Queguiner, S; Salvat, G; Vendeuvre, J L; Carlier, V; Ermel, G
Detachment analysis of the translocated W chromosome shows that the female-specific randomly amplified polymorphic DNA (RAPD) marker, female-218, is derived from the second chromosome fragment region of the translocated W chromosome of the sex-limited p(B) silkworm (Bombyx mori ) strain.
The sex chromosomes of the silkworm, Bombyx mori, are designated ZW for the female and ZZ for the male. We previously characterized a female-specific randomly amplified polymorphic DNA (RAPD) marker, designated Female-218, from the translocation-bearing W chromosomes. These W chromosomes contain a region of the second chromosome, which carries visible larval markers of the p loci. We used strain TWPB in which female larvae have black skin due to the p(B) gene (T(W;2)p(B), +p/+p) while male larvae have whitish skin (+p/+p). To determine whether the Female-218 RAPD marker is derived from the "W region" or a "second chromosome fragment", we induced a detachment of the translocated W chromosome, T(W;2)p(B), by treating the eggs with hot water at an early developmental stage. After hot water treatment, we obtained 27 white female larvae out of 4850 female larvae. The Female-218 RAPD marker was not amplified in 26 out of 27 white female larvae, and was amplified from one white female larva. Moreover, we obtained 11 black male larvae out of 5377 male larvae. Eight out of 11 black male larvae became adult moths, and the Female-218 RAPD marker was amplified from all eight male moths. Examination of the genetic relationship between the Female-218 RAPD marker and the second chromosome fragment of the translocated W chromosome strongly indicates that the Female-218 RAPD marker is amplified from the region of second chromosome fragment of the T(W;2)p(B) chromosome. PMID:12921167
Yokoyama, Takeshi; Abe, Hiroaki; Irobe, Yasuo; Saito, Katsuji; Tanaka, Nobuhiko; Kawai, Shinya; Ohbayashi, Fumi; Shimada, Toru; Oshiki, Toshikazu
Molecular Serum Markers of Liver Fibrosis
Fibrosis is a hallmark histologic event of chronic liver diseases and is characterized by the excessive accumulation and reorganization of the extracellular matrix (ECM). The gold standard for assessment of fibrosis is liver biopsy. As this procedure has various limitations, including risk of patient injury and sampling error, a non-invasive serum marker for liver fibrosis is desirable. The increasing understanding of the pathogenesis of hepatic fibrosis has suggested several markers which could be useful indicators of hepatic fibrogenesis and fibrosis. These markers include serum markers of liver function, ECM synthesis, fibrolytic processes, ECM degradation and fibrogenesis related cytokines. Recently, neo-epitopes, which are post-translational modifications of proteins, have been successfully used in bone and cartilage diseases which are characterized by extensive ECM remodeling. Increasing numbers of studies are being undertaken to identify neo-epitopes generated during liver fibrosis, and which ultimately might be useful for diagnosing and monitoring fibrogenesis. To date, the metalloproteinases generated fragment of collagen I, III, IV and VI have been proven to be elevated in two rat models of fibrosis. This review summarizes the recent efforts that have been made to identify potentially reliable non-invasive serum markers. We used the recently proposed BIPED (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) system to characterize potential serum markers and neo-epitope markers that have been identified to date.
Liu, Tianhui; Wang, Xiaoming; Karsdal, Morten A.; Leeming, Diana J.; Genovese, Federica
Morphological and RAPD markers show a highly skewed distribution in a pair of reciprocal crosses between hemisexual dogrose species, Rosa sect. Caninae
The dogroses, Rosa sect. Caninae, are polyploid and characterized by their unique meiosis with an unequal number of chromosomes in the male and female gametes.\\u000a The pollen cells have 7 chromosomes and the egg cells 21, 28 or 35 depending on the ploidy level of the species. The resulting\\u000a matroclinal inheritance was studied with both morphological and molecular markers in
G. Werlemark; M. Uggla; H. Nybom
Molecular markers of serine protease evolution
The evolutionary history of serine proteases can be accounted for by highly conserved amino acids that form crucial structural and chemical elements of the catalytic apparatus. These residues display non- random dichotomies in either amino acid choice or serine codon usage and serve as discrete markers for tracking changes in the active site environment and supporting structures. These markers categorize serine proteases of the chymotrypsin-like, subtilisin-like and ?/?-hydrolase fold clans according to phylogenetic lineages, and indicate the relative ages and order of appearance of those lineages. A common theme among these three unrelated clans of serine proteases is the development or maintenance of a catalytic tetrad, the fourth member of which is a Ser or Cys whose side chain helps stabilize other residues of the standard catalytic triad. A genetic mechanism for mutation of conserved markers, domain duplication followed by gene splitting, is suggested by analysis of evolutionary markers from newly sequenced genes with multiple protease domains.
Krem, Maxwell M.; Di Cera, Enrico
Tissue-based molecular markers for renal cell carcinoma.
Since the introduction of targeted therapies in renal cell carcinoma (RCC), more individualized treatment options have become available. Molecular markers might support treatment planning due to more accurate individual risk stratification. Current molecular markers in RCC were reviewed to elucidate clinical impact and future perspectives. An English-language literature review of the Medline database (1990 to September 2010) of published data on tissue-based molecular markers and RCC was undertaken. Histological types, clinical and oncological behaviour are variable in renal masses. Molecular markers offer potential for additional information in tumour detection and diagnosis, prognostic and predictive values, as well as determination of therapeutic targets. Investigations on molecular biomarkers in RCC include hypoxia inducible factor (HIF-?), vascular endothelial growth factor (VEGF), carbonic anhydrase IX (CAIX), mammalian target of rapamycin (mTOR), survivin, B7-H1, p53, matrix metalloproteinases (MMP), Insulin-like growth factor II mRNA-binding protein 3 (IMP3), Ki-67, C-reactive protein (CRP), Vimentin, Fascin, platelet count, hemoglobin level and combinations of these factors. Although some markers offer promising results, utilization in daily practice is compromised due to limited specificity, predictive accuracy and tumour histology variablity. There is an imminent need for novel molecular markers that allow accurate histologic and biologic classification of RCC to improve upon current outcomes. It is very likely that a panel of molecular markers will be used to achieve a sufficient degree of certainty in order to guide clinical decisions. A large concerted effort is required to advance the field of RCC molecular marker through systematic discovery, verification, and validation. PMID:21996985
Rink, M; Chun, F K H; Robinson, B; Sun, M; Karakiewicz, P I; Bensalah, K; Fisch, M; Scherr, D S; Lee, R K; Margulis, V; Shariat, S F
Genetic distance detected with RAPD markers among selected Australian commercial varieties and boron-tolerant exotic germplasm of pea ( Pisum sativum L.)
The optimisation of polymerase chain reaction (PCR) for random amplified polymorphic DNA (RAPD) analysis in pea was investigated and the results were applied to an analysis of five representative Australian varieties and five selected boron-tolerant accessions derived from different geographical regions. Genotypes were compared using 34 random primers (Operon Technologies, Alameda, CA) which generated 180 polymorphic bands. Genetic similarity among
A. Bagheri; J. G. Paull; P. Langridge; A. J. Rathjen
Patterns of rapd markers and heavy metal concentrations in Perna viridis (L.), collected from metal-contaminated and uncontaminated coastal waters: are they correlated with each other?
Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors. This study used a Single Primer Amplification Reaction (SPAR) technique namely Random Amplified Polymorphic DNA (RAPD) to determine the genetic diversity of the populations of the green-lipped mussel Perna viridis collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively' uncontaminated sites (reference sites). Heavy metal levels (Cd, Cu, Pb and Zn) were also measured in the soft tissues and byssus of the mussels from all the sites. Cluster analyses employing UPGMA done based on the RAPD makers grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian and Kg. Pasir Puteh populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the genetic diversity based on bands resulting from the use of all four RAPD primers on P. viridis did not indicate its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis between a particular metal and a band resulting from a specific RAPD primer revealed some significant (P < 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues. Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer on P. viridis could be used as biomonitoring tool of heavy metal pollution. PMID:17633561
Yap, C K; Chua, B H; Teh, C H; Tan, S G; Ismail, A
Molecular Markers in Hereditary Breast Cancer.
National Technical Information Service (NTIS)
We are entering a new era of medicine where genetic markers are going to be used to make clinical management decisions. My long term career goal is to further our understanding of the genetic alterations which characterize human breast cancer in a way tha...
O. I. Olopade
Molecular Markers in Hereditary Breast Cancer.
National Technical Information Service (NTIS)
We are entering a new era of medicine where genetic markers are going to be used to make clinical management. decisions My long term career goal is to further our understanding of the genetic alterations which characterize human breast cancer in a way tha...
O. I. Olopade
Prognostic histopathological and molecular markers in feline mammary neoplasia.
Feline mammary tumours comprise approximately 11% of feline non-integumentary neoplasms, are more commonly malignant than benign, and carry a poor prognosis attributable to a high probability of local recurrence and metastasis. This review discusses histopathological and molecular markers that could aid in prognostic discrimination, and draws comparisons with studies examining prognostic markers in breast cancer. Tumour grade and mitotic index correlate with survival data and could be useful for prognostication. Although assessment of Ki67 expression might have prognostic potential, further studies are required to corroborate the correlation between expression and clinical outcome. Additional molecular markers that have been investigated for prognostic potential can be grouped according to the 'hallmarks of cancer'. Many studies utilise 'surrogate markers' of clinical outcome, such as correlation with histological grade, to assess the prognostic value of molecular markers, and further investigation is therefore necessary before reaching firm conclusions regarding the prognostic value of some markers. Feline mammary tumours have been proposed as spontaneous models of breast cancer but might only be suitable models for certain molecular sub-types. Compared to humans, cats tend to have a high percentage of mammary tumours which are oestrogen receptor-negative and they might therefore be suitable models for late stage oestrogen receptor-negative breast cancer. The basal-like properties of feline mammary carcinomas offer another avenue for future research in this field of comparative oncology. PMID:22841451
Hughes, K; Dobson, J M
Molecular markers linked to white rust resistance in mustard Brassica juncea
White rust, caused by Albugo candida (Pers.) Kuntze, is an economically important disease of Brassica juncea (L.) Czern. and Coss mustard, particularly in India. The most efficient and cost-effective way of protecting mustard plants\\u000a from white rust disease is through genetic resistance. The objective of this study was to identify RAPD markers for white\\u000a rust resistance in an F1-derived doubled-haploid
K. V. Prabhu; D. J. Somers; G. Rakow; R. K. Gugel
Molecular discrimination of six species of Bagrid catfishes from Indus river system using randomly amplified polymorphic DNA markers.
Bagrid catfishes constitute a very important group of fishes having immense commercial importance in south-east countries. The phylogenetic relationships and genome specificity among six species of Bagrid catfishes (Mystus bleekeri, M. cavasius, M. vittatus, M. tengara, M. aor and M. seenghala) were investigated using RAPD markers as discriminating characters for the first time. 511 RAPD fragments were generated using ten decamer primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 92 and 2,863 bp, which were assigned to 155 RAPD loci. Clearly resolved and repeatable bands were scored for their presence or absence in a binary matrix. Different RAPD profiles were observed for all the six Mystus species. In the present study three group diagnostic, eleven group exclusive and 18 species-specific markers were generated. Thus six Mystus species can be successfully differentiated on the basis of these 18 species-specific RAPD markers. UPGMA dendrogram constructed on the basis of genetic distance formed two distinct clusters, M. seenghala and M. aor form one separate cluster from other four species i.e., M. tengara, M. cavasius, M. bleekeri and M. vittatus. The inferences drawn from the above study clearly showed their genetic distinctness from the other four Mystus species and supported their inclusion into a separate genus, Sperata. PMID:20127179
Saini, Archana; Dua, Anish; Mohindra, Vindhya; Lakra, W S
Genetic diversity of F1 and F2 interspecific hybrids between dwarf birch (Betula nana L.) and Himalayan birch (B. utilis var. jacquemontii (Spach) Winkl. 'Doorenbos') using RAPD-PCR markers and ploidy analysis.
Crosses between Betula nana and B. utilis 'Doorenbos' were undertaken in order to obtain interspecific hybrids which could be characterized by wide spreading stems, strong branching habit, decorative clear white bark and an interesting shape of purple leaves. The research purpose was to examine genetic diversity of the 16 F1 and F2 putative progenies by using the RAPD-PCR method and the ploidy analysis. A total of 242 RAPD markers were scored with 24 primers and 220 (90.9%) polymorphic bands were found. In the NJ dendrogram, cluster I consisted of the female parent - B. nana and 12 hybrids and cluster II grouped the male parent - B. utilis 'Doorenbos' with 4 hybrids (F2/2, F1/8, F1/7 and F2/1). The 2-D scaling by PCoA was in agreement with the similarity index, i.e. two hybrids (F1/8, F2/2) grouped with the male parent while others with female parent. Classification of the hybrid plants by chromosome counting demonstrated that 13 hybrids were confirmed with accurate chromosome counts as being diploid (2n=2x=28) and 3 plants (F1/7, F1/8, F2/2) as triploid with 42 chromosomes. PMID:24904928
Czernicka, Ma?gorzata; P?awiak, Jaros?aw; Muras, Piotr
Genetic diversity in apricot cultivars based on AFLP markers
A set of cultivars used as genitors in apricot breeding programs aimed at introducing sharka resistance were examined by AFLP\\u000a molecular marker analysis. The markers obtained indicated that apricot cultivars resistant to sharka were related to the European\\u000a cultivars, but they potentially share a common ancestor donor of sharka outside of the European group. Segregation of AFLP\\u000a and RAPD markers
M. A. Hurtado; A. Westman; E. Beck; G. A. Abbott; G. Ll�cer; M. L. Badenes
Drosophila hematopoiesis: Markers and methods for molecular genetic analysis.
Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ. PMID:24613936
Evans, Cory J; Liu, Ting; Banerjee, Utpal
Ecological proteomics: finding molecular markers that matter.
It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation (Hoffmann & Willi 2008; Stapley et al. 2010). Recent advances in high-throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis (Pavlidis et al. 2008)], classical and quantitative genetics [e.g. quantitative trait locus analysis (MacKay et al. 2009)], and cellular and molecular biology [e.g. transcriptomics (Larsen et al. 2011)]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012). demonstrate how one such approach � high-throughput label-free proteomics (reviewed by Gstaiger & Aebersold 2009; Domon & Aebersold 2010) � can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish (Coregonus lavaretus L.) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter. PMID:22953332
Dalziel, Anne C; Schulte, Patricia M
Molecular Contributions to Conservation
Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective pop- ulation size, population-specific markers, etc. PCR (polymerase chain
Susan M. Haig
Pure morphological distinction of high-grade squamous intraepithelial lesions (HSILs) from their mimics can be challenging. Diagnosis can be difficult with nonconventional HSILs associated with a metaplastic phenotype, squamous intraepithelial lesions (SILs) that defy precise classification such as �eosinophilic dysplasias�, and those that overlap with columnar neoplasms, including stratified variants of adenocarcinoma in situ (�SMILE�). Gene expression and protein profiling have identified biomarkers with the potential to decrease diagnostic variability and increase specificity of histological and cytological analysis. Among the ones clinically useful for HSIL detection are p16INK4A and MIB-1 which complement each other, differentiating SIL from normal/atrophic (MIB-1 low) or reactive/immature metaplastic (p16INK4A scattered) epithelium. Additional markers, including ProExTM C, have been proposed but their added value is yet to be established. In the final analysis, biomarkers are most helpful for distinguishing benign immature or atrophic proliferations from HSIL. The distinction of LSIL from HSIL must be made on the hematoxylin and eosin-stained section and should be made with care, given the potential consequences of a diagnosis of CIN2 or CIN3.
Pinto, Alvaro P.; Crum, Christopher P.; Hirsch, Michelle S.
Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.
Background In the last 30?years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.
Genetic diversity of different Tunisian fig (Ficuscarica L.) collections revealed by RAPD fingerprints.
The genetic diversity in Tunisian fig (Ficus carica L.) was studied using RAPD markers. Thirty-five fig cultivars originating from diverse geographical areas and belonging to three collections were analysed. Random decamer primers were screened to assess their ability to detect polymorphisms in this crop. Forty-four RAPD markers were revealed and used to survey the genetic diversity and to detect cases of mislabelling. As a result, considerable genetic diversity was detected among the studied F. carica accessions. The relationships among the 35 varieties were studied by cluster analysis. The dendrogram showed two main groups composed of cultivars with similar geographic origin. Moreover, the male accessions (caprifigs) were clustered indistinctively within the female ones, suggesting a narrow genetic diversity among these accessions. Our data proved that RAPD markers are useful for germplasm discrimination as well as for investigation of patterns of variation in fig. Since this designed procedure has permitted to establish a molecular database of the reference collections, the opportunity of this study is discussed in relation to the improvement and rational management of fig germplasm. PMID:17362329
Salhi-Hannachi, Amel; Chatti, Khaled; Saddoud, Olfa; Mars, Messaoud; Rhouma, Abdelmajid; Marrakchi, Mohamed; Trifi, Mokhtar
Modeling the Genetic Architecture of Complex Traits With Molecular Markers
Understanding the genetic control of quantitatively inherited traits is fundamental to agricultural, evolutionary and biomedical genetic research. A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers. The parameters that quantify the genetic architecture of a trait include the number of individual quantitative trait loci (QTL), their genomic positions,
Rongling Wu; Wei Hou; Yuehua Cui; Hongying Li; Tian Liu; Song Wu; Chang-Xing Ma; Yanru Zeng
A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)
Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).
[Identification of RAPD markers linked to the resistance gene Yr5 against wheat stripe rust with denaturing PAGE-silver staining].
RAPD analysis was performed between a near-isogenic line (NIL) Yr5/6 x Avocet S carrying the resistance gene Yr5 against wheat stripe rust and its susceptible parent Avocet S, using the Yr5 gene donor parent Triticum spelta album as control. Amplified DNA fragments were separated on 4% denaturing PAGE (polyacrylamide gel electrophoresis) and displayed by silver staining. Fifty to 100 bands were detected, 5 folds more than those revealed on agarose gels. A total of 240 random primers were screened, and 23 reproducible polymorphic DNA fragments were found, out of which 6 polymorphic bands appeared to be linked to Yr5 gene. Genetic linkage was tested on 121 segregating F2 plants derived from a cross between Avocet S and Yr5/6 x Avocet S. It was showed that the polymorphic DNA fragment S1320(207) was completely linked to Yr5 gene, and S1348(363) closely linked to Yr5 gene. The results suggested that using denaturing PAGE-silver staining could increase the level of DNA polymorphisms detected in wheat and also improve the repeatability of RAPD analysis. PMID:15195566
Chen, Xiao-Hong; Niu, Yong-Chun; Hu, Bao-Zhong
Biological (molecular and cellular) markers of toxicity
The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.
Shugart, L.R.
Reviewing and Updating the Major Molecular Markers for Stem Cells
Stem cells (SC) are able to self-renew and to differentiate into many types of committed cells, making SCs interesting for cellular therapy. However, the pool of SCs in vivo and in vitro consists of a mix of cells at several stages of differentiation, making it difficult to obtain a homogeneous population of SCs for research. Therefore, it is important to isolate and characterize unambiguous molecular markers that can be applied to SCs. Here, we review classical and new candidate molecular markers that have been established to show a molecular profile for human embryonic stem cells (hESCs), mesenchymal stem cells (MSCs), and hematopoietic stem cells (HSCs). The commonly cited markers for embryonic ESCs are Nanog, Oct-4, Sox-2, Rex-1, Dnmt3b, Lin-28, Tdgf1, FoxD3, Tert, Utf-1, Gal, Cx43, Gdf3, Gtcm1, Terf1, Terf2, Lefty A, and Lefty B. MSCs are primarily identified by the expression of CD13, CD29, CD44, CD49e, CD54, CD71, CD73, CD90, CD105, CD106, CD166, and HLA-ABC and lack CD14, CD31, CD34, CD45, CD62E, CD62L, CD62P, and HLA-DR expression. HSCs are mainly isolated based on the expression of CD34, but the combination of this marker with CD133 and CD90, together with a lack of CD38 and other lineage markers, provides the most homogeneous pool of SCs. Here, we present new and alternative markers for SCs, along with microRNA profiles, for these cells.
Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, Joao Antonio Pegas
[Molecular markers linked to mono-dominant genic male sterile gene in rapeseed (Brassica napus L.)].
Bulked segregant analysis (BSA) was used to identify randomly amplified polymorphic DNA (RAPD) markers linked to the MS gene in mono-dominant GMS of rapeseed (Brassica napus L.), which was bred by Hybrid Rapeseed Research Center of Shaanxi Province. A total of 300 random 10-mer oligonucleotide primers were screened on the DNA from fertile and sterile bulks. Primer S(243) (5'CTATGCCGAC3') gave identical 1.5 kb DNA polymorphic segment OPU-03(1500) in the bulk S, but not in the bulk F (Fig.2). The DNAs from individual plants of each bulk and from their sister lines, which were generated from the same original crossing, were then screened with the primer S(243), and the same results were obtained (Figs.3,4). Other types of GMS and CMS were analyzed using primer S(243), and the specific 1.5 kb DNA segment was not found (Fig.5). Therefore, the RAPD marker OPU-03(1500) is linked to the mono-dominant GMS trait in rapeseed. This RAPD marker OPU-03(1500) was cloned into a T-easy vector and sequenced. The sequence here obtained was highly homologous to one of the Arabidopsis DNA sequences. According to this DNA conserved region in different species, we designed a pair of specific primers P1 (5'ATGTCGCTGAGGCCG-AGCAC3') and P2 (5'GGCACACTGTCACG-ATCCTTGG3') and amplified only one specific 2.3 kb DNA fragment in each bulk. There are two mutant loci between the two DNA fragments after sequencing. We designed another pair of specific primers P3 (5'CTCCAGCAGCAGCAGC-AGCCT3') and P4 (5'GCAGGAATGAGAA-CCGTAGG3') according to the DNA sequence at the mutant loci. A specific DNA segment was amplified only in the fertile line but not in the sterile line using the primers P3 and P4 (Fig.6). Therefore the RAPD marker were converted into SCAR marker. Moreover, the SCAR marker detection method was improved (Fig.7). PMID:17075173
Wang, Dao-Jie; Guo, Ai-Guang; Li, Dian-Rong; Tian, Jian-Hua
DNA marker applications to molecular genetics and genomics in tomato.
Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178
Shirasawa, Kenta; Hirakawa, Hideki
Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker
NASA Astrophysics Data System (ADS)
Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.
Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood
RAPD analyses of hybridization events in Cardamine (Brassicaceae)
Recent hybrid speciation events between the diploidCardamine rivularis and the diploidC. amara leading to the triploidC. xinsueta were investigated with random amplified polymorphic DNA (RAPD). The hybrid nature ofC. xinsueta was confirmed by the additivity of RAPD markers which discriminate the parent species. An unexpectedly high level of genetic\\u000a variation withinC. xinsueta argues for several hybridization events and\\/or backcrossing withC.
Barbara Neuffer; Petra Jahncke
[Application of ISSR molecular marker in invasive plant species study].
Alien species invasion is one of the most important drivers of worldwide environmental change, which may result in environmental degradation, biodiversity loss, and food and water shortage. It may also increase the possibility and severity of natural disasters, and damage international trade and benefits. In last two decades, DNA-based molecular markers were widely used to detect the genetic diversity of invaded alien species. Inter-simple sequence repeat (ISSR) is a microsatellite-based technique, with the superiorities of simple, quick, reliable, and generating higher levels of DNA polymorphism, and being used as a new molecular marker for genetic study. This paper introduced the principles, characteristics and procedures of ISSR, and summarized its applications in studying the genetic structure, genetic diversity, origin, distribution mode, phylogenesis, and breeding features of invasive plants. PMID:17615894
Gui, Fu-Rong; Guo, Jian-Ying; Wan, Fang-Hao
Identification of early molecular markers for breast cancer
BACKGROUND: The ductal carcinoma in situ (DCIS) of the mammary gland represents an early, pre-invasive stage in the development of invasive breast carcinoma. Since DCIS is a curable disease, it would be highly desirable to identify molecular markers that allow early detection. Mice transgenic for the WAP-SV40 early genome region were used as a model for DCIS development. Gene expression
C�line Kretschmer; Anja Sterner-Kock; Friederike Siedentopf; Winfried Schoenegg; Peter M Schlag; Wolfgang Kemmner
Discriminating ability of molecular markers and morphological characterization in the establishment of genetic relationships in cultivated genotypes of almond and related wild species
A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare\\u000a the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP)\\u000a and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related\\u000a wild species. SSRs presented a high level of
Karim Sorkheh; Behrouz Shiran; Soghra Kiani; Nazanin Amirbakhtiar; Sadegh Mousavi; Vahid Rouhi; Shahram Mohammady-D; Thomas M. Gradziel; Lyudmyla V. Malysheva-Otto; Pedro Mart�nez-G�mez
RAPD polymorphism of wild emmer wheat populations, Triticum dicoccoides, in Israel
Genetic diversity in random amplified polymorphic DNAs (RAPDs) was studied in 110 genotypes of the tetraploid wild progenitor\\u000a of wheat, Triticum dicoccoides, from 11 populations sampled in Israel and Turkey. Our results show high level of diversity of RAPD markers in wild wheat\\u000a populations in Israel. The ten primers used in this study amplified 59 scorable RAPD loci of which
T. Fahima; G. L. Sun; A. Beharav; T. Krugman; A. Beiles; E. Nevo
Potential of marker-assisted selection in hemp genetic improvement
Summary��The development and applications of molecular markers to hemp breeding are recent, dating back only to the mid-1990s. The main achievements in this field are reviewed. The analysis of Cannabis germplasm by RAPD, AFLP and microsatellites is discussed, with its consequence for the still debated species concept in Cannabis. DNA-based markers have also been exploited in the field of forensic
G. Mandolino; A. Carboni
Genetic fidelity of long-term micropropagated shoot cultures of vanilla (Vanilla planifolia Andrews) as assessed by molecular markers.
Occurrence of genetic variants during micropropagation is occasionally encountered when the cultures are maintained in vitro for long period. Therefore, the micropropagated multiple shoots of Vanilla planifolia Andrews developed from axillary bud explants established 10 years ago were used to determine somaclonal variation using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats markers (ISSR). One thousand micro-plants were established in soil of which 95 plantlets (consisting of four phenotypes) along with the mother plant were subjected to genetic analyses using RAPD and ISSR markers. Out of the 45 RAPD and 20 ISSR primers screened, 30 RAPD and 7 ISSR primers showed 317 clear, distinct and reproducible band classes resulting in a total of 30 115 bands. However, no difference was observed in banding patterns of any of the samples for a particular primer, indicating the absence of variation among the micropropagated plants. Our results allow us to conclude that the micropropagation protocol that we have used for in vitro proliferation of vanilla plantlets for the last 10 years might be applicable for the production of clonal plants over a considerable period of time. PMID:17427995
Sreedhar, Reddampalli V; Venkatachalam, Lakshmanan; Bhagyalakshmi, Neelwarne
The combination of Gilbert/Maxam chemical sequencing and the dideoxynucleotide chain termination approach facilitates the construction of species specific PCR-primers based on diagnostic RAPD bands.
The randomly amplified polymorphic DNA technique (RAPD) is a modification of PCR that uses short, arbitrarily generated single primers to amplify genomic DNA. Amplified DNA-fragments are often polymorphic and can be used as individual, population- or species-specific markers. Because the RAPD technique requires a very high degree of reproducibility at the instrumentation level and with regard to buffer conditions, we propose to synthesize highly specific conventional PCR primers, the sequence of which is based on the primary diagnostic RAPD bands. In this communication we present a fast and convenient experimental strategy for converting the non-stringent RAPD conditions with their low annealing temperatures to stringent PCR conditions. Diagnostic RAPD bands were sequenced by a combination of chemical (Gilbert/Maxam) and chain termination (Sanger) techniques. Based on this sequence information, highly specific oligonucleotide primers were synthesized. The value of this approach was demonstrated for the molecular diagnosis of the important rape seed (Brassica napus) pathogen Leptosphaeria maculans. PMID:8564365
Voigt, K; W�stemeyer, J
RAPD and phytochemical analysis of Thymus moroderi plantlets after cryopreservation.
Cryopreservation is at present the most reliable strategy to preserve plant germplasm. When aromatic plants are the object of conservation it is necessary to assess not only the genetic but also the phytochemical stability to ensure that plant material maintains its qualities after storage. In this work we present molecular and phytochemical stability data related to a previously described vitrification-based cryopreservation protocol for Thymus moroderi Pau ex Mart�nez. RAPD markers have been used to assess the genetic stability of T. moroderi explants and revealed 0.34 percent of variation in the cryopreserved material studied. Phytochemical data collected from GC-MS analysis of dichloromethane extracts from cryopreserved plantlets rendered a profile in which 1,8-cineole (14.5 percent), camphor (5.9 percent) and borneol (5.2 percent) were the major components. Both data confirmed the suitability of the cryopreservation protocol applied. PMID:23625080
Marco-Medina, Ana; Casas, Jos� Luis
Genetic diversity of two Portuguese populations of the pullet carpet shell Venerupis senegalensis, based on RAPD markers: contribution to a sustainable restocking program
NASA Astrophysics Data System (ADS)
The pullet carpet shell Venerupis senegalensis (= V. pullastra) is a commercially important species in Portugal, Spain, France, and Italy. In Portugal, this species was once abundant in the Ria Formosa (southern Portugal). However, in the early 1980s, its abundance declined dramatically due to overfishing. In order to reverse this negative trend, the genetic sustainable management of the wild stocks of V. senegalensis should be performed by promoting successful restocking actions and the development of an aquaculture commercial production program of this species. In order to find the best broodstock for aquaculture purposes and therefore minimize the deleterious effects of hatchery practices, we analyzed the genetic diversity of the natural population to be restocked (Ria Formosa) but also of another potential genetically close population (Ria de Aveiro) by RAPD. Similar and substantive percentage of polymorphic loci, effective number of alleles, Nei�s gene diversity, and Shannon�s diversity index was found within both populations. This high genetic variability within populations suggests that they might have a gene pool with sufficient genetic plasticity to support changes in the environmental conditions. Analyses of population genetic structure also revealed a small genetic differentiation between the two populations. The high genetic variability of the natural population to be restocked makes it the preferential broodstock for aquaculture purposes. However, the Ria de Aveiro population could also be a viable alternative, due to its genetic plasticity and the genetic similarity of both populations. The results of this study can be useful to the sustainable management of wild stocks as well as in promoting successful restocking actions based on aquaculture production.
Joaquim, Sandra; Pereira, Jorge; Leit�o, Alexandra; Matias, Domit�lia; Chaves, Raquel; Guedes-Pinto, Henrique; Ch�charo, Lu�s; Gaspar, Miguel
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.
Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242
Ariey, Fr�d�ric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; M�nard, Sandie; Rogers, William O; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M; Benoit-Vical, Fran�oise; Mercereau-Puijalon, Odile; M�nard, Didier
Molecular evidence for the hybrid origin of Paulownia Taiwaniana based on RAPD markers and RFLP of chloroplast DNA.
Genomic DNA of Paulownia fortunei, P. kawakamii and P. taiwaniana were amplified with 10-base primers of arbitrary sequences using the polymerase chain reaction (PCR). A total of 351 DNA fragments were amplified from 23 primers and of these 265 fragments (75.5%) were polymorphic. Almost all of the PCR-amplified products of P. taiwaniana were shared by either P. fortunei or P. kawakamii, or both, and the number of polymorphic fragments shared by P. taiwaniana and P. fortunei was about equivalent to those shared by P. taiwaniana and P. kawakamii. Restriction fragments of chloroplast DNA (cpDNA) purified from Paulownia species and from reciprocal crosses between P. fortunei and P. kawakamii were analyzed. Restriction enzyme SalI-digested cpDNA showed an identical pattern in both P. kawakamii and P. taiwaniana. These results further support the hypothesis that P. taiwaniana is the natural hybrid between P. fortunei and P. kawakamii and that the maternal parent of P. taiwaniana is P. kawakamii. PMID:24177840
Wang, W Y; Pai, R C; Lai, C C; Lin, T P
Genetic variation and phylogenetic relationships among worldwide collections of the Russian wheat aphid, Diuraphis noxia (Mordvilko), inferred from allozyme and RAPD-PCR markers
Genetic analyses were conducted on Diuraphis noxia (Mordvilko) populations collected from wheat, barley and other grasses from various countries throughout the world. These collections had been found to contain clones that differed in virulence from various cultivars, cuticular hydrocarbon profiles and life cycle characters. Discrete genetic markers analysed in this study included allozymes and arbitrary regions of the genome amplified
G J Puterka; W C Black; W M Steiner; R L Burton
Female Control of Paternity in the Internally Fertilizing Compound Ascidian Diplosoma listerianum. II. Investigation of Male Mating Success Using RAPD Markers
Randomly amplified polymorphic DNA paternity markers were used to assess male success during simultaneous, three-way mating opportunities between cultured clones of the hermaphroditic protochordate Diplosoma listerianum. The previously reported blockage of sperm movement in the oviduct, barring access to the site of fertilization in the ovary, was shown to prevent cross-fertilization between two particular clones. The same mechanism prevents selfing.
John D. D. Bishop; Cathy S. Jones; Leslie R. Noble
Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis
Three hundred random sequence 10-mer primers were used to screen a pair of near-isogenic lines of barley and their donor parent for markers linked to genes conferring resistance to Rhynchosporium secalis. One primer was identified which reproducibly generated a product, SC10-65-H400, from the donor parent and the Rhynchosporium-resistant near-isogenic line but not from the recurrent parent. Segregation analysis on a
U M Barua; K J Chalmers; C A Hackett; W T B Thomas; W Powell; R Waugh
Molecular marker diversity of SCN-resistant sources in soybean.
Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant. PMID:17036069
Chen, Yiwu; Wang, Dechun; Arelli, Prakash; Ebrahimi, Mohsen; Nelson, Randall L
Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers
Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system�s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-?B, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression.
Koedrith, Preeyaporn; Seo, Young Rok
Molecular markers of cell adhesion in ameloblastomas. An update
Ameloblastoma is the most common odontogenic tumor of epithelial origin, and though it is of a benign nature, it frequently infiltrates the bone, has a high rate of recurrence and could potentially become malignant. Cellular adhesion potentially plays an important role in the manifestation of these characteristics and in the tumor biology of ameloblastomas. Losses of cell-cell and extracellular matrix adhesion and cohesion are among the first events that occur in the invasion and growth of tumors of epithelial origin. The present review includes a description of the molecules that are involved in cell adhesion as reported for various types of ameloblastomas and discusses the possible roles of these molecules in the biological behaviors of this odontogenic tumor. Knowledge of the complex mechanisms in which these molecules play a role is critical for the research and discovery of future therapeutic targets. Key words:Ameloblastoma, cellular adhesion, molecular markers, cell-cell adhesion, extracellular matrix-cell adhesion.
Gonzalez-Gonzalez, Rogelio; Molina-Frechero, Nelly; Damian-Matsumura, Pablo
New models and molecular markers in evaluation of developmental toxicity
Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds.
Huuskonen, Hannele [National Product Control Agency for Welfare and Health, Chemicals Department, STTV c/o National Public Health Institute, P.O. Box 95, FIN-70701 Kuopio (Finland)]. E-mail: firstname.lastname@example.com
Molecular prognostic markers in pancreatic cancer: a systematic review.
Pancreatic cancer is one of the most lethal tumours of the gastrointestinal tract. The ability to predict which patients would benefit most from surgical intervention and/or chemotherapy would be a great clinical asset. Considerable research has focused on identifying molecular events in pancreatic carcinogenesis, and their correlation with clinicopathological variables of pancreatic tumours and survival. This systematic review examined evidence from published manuscripts looking at molecular markers in pancreatic cancer and their correlation with tumour stage and grade, response to chemotherapy and long-term survival. A literature search was undertaken using PubMed and MEDLINE search engines, using the keywords p53, p21, p16, p27, SMAD4, K-ras, cyclin D1, Bax, Bcl-2, EGFR, EGF, c-erbB2, HB-EGF, TGFbeta, FGF, MMP, uPA, cathepsin, heparanase, E-cadherin, laminins, integrins, TMSF, CD44, cytokines, angiogenesis, VEGF, IL-8, beta-catenin, DNA microarray, and gene profiling. A bewildering number of biomarkers are currently under evaluation. For the most part, the evidence regarding their application as prognostic indicators is conflicting. The advent of gene microarray and mass spectrometric protein profiling offers the potential to examine many different biomarkers simultaneously. This 'protein/gene signature' could revolutionise work in this field and allow researchers to develop accurate and reproducible predictions of survival based on protein or gene profiles. PMID:16146690
Garcea, G; Neal, C P; Pattenden, C J; Steward, W P; Berry, D P
Molecular Evolution and Diversity inBacillus anthracisas Detected by Amplified Fragment Length Polymorphism Markers
Bacillus anthraciscauses anthrax and represents one of the most molecularly monomorphic bacteria known. We have used AFLP (amplified fragment length polymorphism) DNA markers to analyze 78 B. anthracis isolates and six relatedBacillusspecies for molecular variation. AFLP markers are extremely sensitive to even small sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Using this approach, we examined ca.
Monitoring the cell number of Lactococcus lactis subsp. cremoris FC in human feces by real-time PCR with strain-specific primers designed using the RAPD technique
Strain-specific PCR primers for Lactococcus lactis subsp. cremoris FC were developed using the randomly amplified polymorphic DNA (RAPD) technique. RAPD was used to generate strain-specific markers. A 1164-bp RAPD marker found to be strain-specific was sequenced, and a primer pair specific for L. lactis subsp. cremoris FC was designed. The specificity of this primer pair was tested with 23 L.
Toshinari Maruo; Mitsuo Sakamoto; Toshiya Toda; Yoshimi Benno
Genetic diversity analysis of common beans based on molecular markers
A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.
Gill-Langarica, Homar R.; Muruaga-Martinez, Jose S.; Vargas-Vazquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Perez, Netzahualcoyotl
Molecular Markers of Lung Cancer in MAYAK Workers
The molecular mechanisms that result in the elevated risk for lung cancer associated with exposure to radiation have not been well characterized. Workers from the MAYAK nuclear enterprise are an ideal cohort in which to study the molecular epidemiology of cancer associated with radiation exposure and to identify the genes targeted for inactivation that in turn affect individual risk for radiation-induced lung cancer. Epidemiology studies of the MAYAK cohort indicate a significantly higher frequency for adenocarcinoma and squamous cell carcinoma (SCC) in workers than in a control population and a strong correlation between these tumor types and plutonium exposure. Two hypotheses will be evaluated through the proposed studies. First, radiation exposure targets specific genes for inactivation by promoter methylation. This hypothesis is supported by our recent studies with the MAYAK population that demonstrated the targeting of the p16 gene for inactivation by promoter methylation in adenocarcinomas from workers (1). Second, genes inactivated in tumors can serve as biomarkers for lung cancer risk in a cancer-free population of workers exposed to plutonium. Support for this hypothesis is based on exciting preliminary results of our nested, case-control study of persons from the Colorado cohort. In that study, a panel of methylation markers for predicting lung cancer risk is being evaluated in sputum samples from incident lung cancer cases and controls. The first hypothesis will be tested by determining the prevalence for promoter hypermethylation of a panel of genes shown to play a critical role in the development of either adenocarcinoma and/or SCC associated with tobacco. Our initial studies on adenocarcinoma in MAYAK workers will be extended to evaluate methylation of the PAX5 {alpha}, PAX5 {beta}, H-cadherin, GATA5, and bone morphogenesis 3B (BMP3B) genes in the original sample set described under Preliminary studies. In addition, studies will be initiated in SCC from workers and controls to identify genes targeted for inactivation by plutonium in this other common histologic form of lung cancer. We will examine methylation of the p16, O{sup 6}-methylguanine-DNA methyl-transferase (MGMT), and death associated protein kinase genes ([DAP-K], evaluated previously in adenocarcinomas) as well as the new genes being assessed in the adenocarcinomas. The second hypothesis will be tested in a cross-sectional study of cancer-free workers exposed to plutonium and an unexposed population. A cohort of 700 cancer-free workers and 700 unexposed persons is being assembled, exposures are being defined, and induced sputum collected at initial entry into the study and approximately 1-year later. Exposed and unexposed persons will be matched by 5-year age intervals and smoking status (current and former). The frequency for methylation of four genes that show the greatest difference in prevalence in tumors from workers and controls will be determined in exfoliated cells within sputum. These studies will extend those in primary tumors to determine whether difference in prevalence for individual or multiple genes are detected in sputum samples from high-risk subjects exposed to plutonium. Follow-up of this cohort offers the opportunity to validate these endpoints and future biomarkers as true markers for lung cancer risk.
Steven A. Belinsky, PhD
The molecular marker of kdr against fenpropathrin in Tetranychus cinnabarinus.
The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is one of the most important pests in agricultural industry. Pyrethroid insecticide has been used to control insects and mites worldwide. However, the intensive use of pyrethroid insecticide resulted in the development of resistance, which has mainly been induced by a variety of point mutations responsible for voltage-gated sodium channel (VGSC) insensitivity and has become the biggest obstacle to sustain the use of pyrethroid insecticide. In this study, we cloned cDNA full length of the para-homologous sodium channel gene from T. cinnabarinus named TC-vgsc. The complete open reading frame of TC-vgsc contains 6,579 nucleotides, encoding 2,193 amino acids. A point mutation, F1538I, was identified from both the DNA and RNA sequences of VGSC in fenpropathrin-resistant strain, which developed approximately 100-folds resistance against fenpropathrin. The result indicated the F1538I kdr mutation underwent DNA mutation events rather than RNA editing. Single nucleotide polymorphisms detection of F1538I mutation from indoor susceptible strain, fenpropathrin-resistant strain, and seven field populations found that this mutation appeared in all the strains (populations), but the frequency of mutation was closely related to the resistance level, with a r2 value of 0.665 (P < 0.05), that is, the higher the resistance level, the larger the mutation frequency. These results demonstrated that the F1538I mutation in the kdr gene can be used as a molecular marker for fenpropathrin-resistance monitoring in field T. cinnabarinus populations. PMID:24498748
Xu, Zhifeng; Shi, Li; Feng, Yaning; He, Lin
58th Annual Symposium on Fundamental Cancer Research Discovery, Validation, and Integration of Molecular Markers and Molecular Imaging: Towards Implementation into Clinical Practice
Print This Page 58th Annual Symposium on Fundamental Cancer Research Discovery, Validation, and Integration of Molecular Markers and Molecular Imaging: Towards Implementation into Clinical Practice News & Events
Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum
Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin.
Graser, Y.; Kuhnisch, J.; Presber, W.
Heritability of Phenolics in Quercus laevis Inferred Using Molecular Markers
Studies of quantitative inheritance of phenotypes do not generally encompass the range of environmental conditions to which a population may be exposed in a natural setting and are rarely conducted on long-lived species due to the time re- quired for traditional crossing experiments. We used a marker-based method to estimate relatedness with microsatellite markers in a natural population of a
R. Klaper; K. Ritland; T. A. Mousseau; M. D. Hunter
[Molecular markers linked to dwarf gene Rht3 in wheat].
The dwarf gene Rht3 derived from Tom Thumb variety, a Tibetan wheat of China, is a dominant gene with the insensitivity to gibberellic acid. Rht3 shows to depress alpha-amylase activity and hence enchance the resistance to preharvest sprouting mainly through its effect on the expression of alpha-Amy1. Near isogenic lines with Rht3 and their segregating population were analyzed by PCR and RFLP techonology. In RAPD analysis, out of 310 random primers (10 bp) screened, only three primers of UBC389, OPV-06 and S1060 revealed polymorphisms in NIL from 310 random primers. Fragments S1060(1900) and S1060(2000) amplified by primer S1060 were shown to be linked to Rht3 with a genetic distance 7.1 cM and 9.2 cM. Fifty-three probes specific for short arms of homoeologous group 4 were screened in RFLP analysis. Xpsr584, XksuF8 and Xcdo38 showed polymorphisms between the NIL. The linkage analysis indicateded that Xpsr584 was linked to Rht3 with a genetic distance 8.0 cM. PMID:11725637
Wan, P; Zhou, Q W; Ma, Z Q; Chen, P D; Liu, D J
Comparison of RAPD, AFLP, and EF-1? Sequences for the Phylogenetic Analysis of Fusarium oxysporum and Its formae speciales in Korea
Although Fursarium oxysporum causes diseases in economically important plant hosts, identification of F. oxysporum formae speciales has been difficult due to confusing phenotypic classification systems. To resolve these complexity, we evaluated genetic relationship of nine formae speciales of F. oxysporum with random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and translation elongation factor-1 alpha (EF-1?) gene. In addition, the correlation between mycotoxin content of fusaric acid and isolates based on molecular marker data was evaluated using the modified Mantel's test. According to these result, these fusaric acid-producing strains could not identify clearly, and independent of geographic locations and host specificities. However, in the identification of F. oxysporum formae speciales, especially, AFLP analysis showed a higher discriminatory power than that of a the RAPD and EF-1? analyses, all three techniques were able to detect genetic variability among F. oxysporum formae speciales in this study.
Park, Jae-Min; Kim, Gi-Young; Lee, Song-Jin; Kim, Mun-Ok; Huh, Man-Kyu; Lee, Tae-Ho
Multiple regression for molecular-marker, quantitative trait data from large F 2 populations
Molecular marker-quantitative trait associations are important for breeders to recognize and understand to allow application in selection. This work was done to provide simple, intuitive explanations of trait-marker regression for large samples from an F2 and to examine the properties of the regression estimators. Beginning with a(- 1,0,1) coding of marker classes and expected frequencies in the F2, expected values,
A. J. Wright; R. P. Mowers
Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize
QTLs with flanking markers showing significant allele frequency differences in the BSA studies will indicate The usual method to locate and compare loci regulat- those traits likely to be important in determining yield ing quantitative traits (QTLs) requires a segregating under drought. population of plants with each one genotyped with molecular markers. However, plants from such segreg- Key words: Bulk
Steve A Quarrie; Vesna Lazic; Dragan Kovacevic �; Andy Steed; Sofija Pekic
A review on SNP and other types of molecular markers and their use in animal genetics
During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high
Alain Vignal; Denis Milan; Magali SanCristobal; Andr� Eggen
Microsatellite Alterations as Molecular Markers in Breast Cancer Progression.
National Technical Information Service (NTIS)
Breast cancer detection and diagnosis has been limited by the lack of early and accurate markers of disease. Efforts to date have largely relied on insensitive measures such as mammography or breast examination for detection, with conventional histopathol...
S. Sukamar
Microsatellite Alterations as Molecular Markers in Breast Cancer Progression.
National Technical Information Service (NTIS)
Breast cancer detection and diagnosis has been limited by the lack of early and accurate markers of disease. Efforts to date have largely relied on insensitive measures such as mammography or breast examination for detection, with conventional histopathol...
S. Sukamar
Mapping quantitative trait loci using molecular marker linkage maps
High-density restriction fragment length polymorphism (RFLP) and allozyme linkage maps have been developed in several plant species. These maps make it technically feasible to map quantitative trait loci (QTL) using methods based on flanking marker genetic models. In this paper, we describe flanking marker models for doubled haploid (DH), recombinant inbred (RI), backcross (BC), F1 testcross (F1TC), DH testcross (DHTC),
S. J. Knapp; W. C. Bridges; D. Birkes
Molecular markers linked to PPO inhibitor tolerance in soybeans
US Patent & Trademark Office Database
This invention relates generally to the detection of genetic differences among soybeans. More particularly, the invention relates to soybean quantitative trait loci (QTL) for tolerance to protoporphyrinogen oxidase inhibitors, to soybean plants possessing these QTLs, which map to a novel chromosomal region, and to genetic markers that are indicative of phenotypes associated with protoporphyrinogen oxidase inhibitor tolerance. Methods and compositions for use of these markers in genotyping of soybean and selection are also disclosed.
Molecular characterization of a SCAR marker purportedly linked to seedlessness in grapevine ( Vitis )
Molecular markers associated with seedlessness in grapevine (Vitis vinifera) could be used for early trait selection in breeding programs and provide useful tools for elucidating the molecular mechanisms\\u000a underlying seed abortion. In this study, the sequence fidelity of a previously reported seedlessness-linked Sequence-Characterized\\u000a Amplified Region (SCAR) marker (GenBank accession #AY327513, Yang et al. in Chinese J Agri Biotech 3:13�17, 2006)
Zhijian T. Li; S. A. Dhekney; D. J. Gray
Cancer stem cell markers in breast neoplasias: their relevance and distribution in distinct molecular subtypes.
The identification and characterization of cancer stem cells might lead to more effective control of neoplastic disease, by directing therapies to the most aggressive cells. For that reason, the identification of cancer stem cells (CSCs) in breast tumours is one of the priorities in breast cancer research, which has resulted in many studies attempting to identify their presence based on the expression of specific molecular markers. In this review, we describe the main molecular markers that have been identified as being able to recognise CSCs in breast carcinomas, the major molecular pathways that regulate CSCs and their association with the different molecular subtypes. PMID:22562130
Schmitt, Fernando; Ricardo, Sara; Vieira, Andr� Filipe; Dion�sio, Maria Rita; Paredes, Joana
Estimation of Genetic Variability of Vigna radiata Cultivars by RAPD Analysis
DNA was isolated from 14 cultivars of Vigna radiata (L.) Wilczek and subjected to RAPD analysis using 14 random decamer primers. These cultivars revealed polymorphism with respect\\u000a to RAPD markers and were subjected to hierarchical cluster analysis. A dendrogram was prepared based on these data. Analysis\\u000a of banding patterns confirmed that two strongly aromatic cultivars IC1, IC4, were closely linked.
S. Betal; P. Roy Chowdhury; S. Kundu; S. Sen Raychaudhuri
Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes.
The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping. PMID:8458572
Kazan, K; Manners, J M; Cameron, D F
A novel method for estimating heritability using molecular markers
Heritability is usually estimated with individuals of known relatedness generated using a controlled breeding programme or through response to selection. In this paper, we use two single-locus VNTR DNA fingerprint markers in conjunction with a maximum likelihood method to infer relatedness among pairs of individuals in a captive population of Pacific chinook salmon (Oncorhynchus tshawytscha). Patterns of relatedness inferred from
ERIC Educational Resources Information Center
Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely�
Healthy Schools Network, Inc., 2011
The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.
Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...
Genetic characterization of Erwinia amylovora strains by random amplified polymorphic DNA fragments (RAPD).
Erwinia amylovora is the causative agent of fire blight, a destructive disease of rosaceous plants subjected to strict quarantine regulations worldwide. Previous studies showed that the population of E. amylovora in Romania is homogenous in its biochemical and serological characteristics, despite the different strains' geographical and host origin. The aim of the present study was to establish and test a typing method to quantify genetic diversity among the Romanian strains of this plant pathogen. Fourteen strains isolated from different hosts and geographical locations in Romania were examined by random amplified polymorphism DNA (RAPD) fragment analysis with two ten-base primers. This molecular method has not revealed any polymorphism, producing the same amplification patterns for all tested strains. Clustering of strains in the resulting dendrogram was not correlated with host, or region of isolation. The RAPD technique did not allow the detection of genetic markers in E. amylovora strains isolated in Romania and proved not to be discriminating among strains of this pathogen. The results presented in this study suggest that the population of E. amylovora in Romania is homogenous. PMID:20361537
M?ru?escu, Lumini?a; Manole, Filofteia; Sesan, Tatiana
Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques
The Alternaria brown spot (ABS) is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens). The application of two molecular markers Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA). Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control.
Dini-Andreote, Francisco; Pietrobon, Vivian Cristina; Andreote, Fernando Dini; Romao, Aline Silva; Sposito, Marcel Bellato; Araujo, Welington Luiz
Molecular markers to study competition and diversity of Rhizobium
The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in agricultural practice and was therefore addressed in this work using the developed tools. Furthermore, various molecular techniques have
A. Sessitsch
Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.
Kirk, Heather; Freeland, Joanna R.
Use of standard markers and incorporation of molecular markers into breast cancer therapy: Consensus recommendations from an International Expert Panel.
Breast cancer is a heterogeneous disease of different subtypes on the molecular, histopathological, and clinical level. Genomic profiling techniques have led to several prognostic and predictive gene signatures of breast cancer that may further refine outcome prediction, especially in clinically equivocal situations. In particular, the predictive value of today's most important therapeutic targets, ER and HER2, are strongly influenced by the proliferative status of the tumor. Genomic assays are generally performed in a centralized manner, whereas routine pathological evaluation is mostly done on a decentralized basis, making the comparison of these methods difficult. Thus, there remains considerable uncertainty about the use of the new molecular markers in routine clinical decision making and their role in patient selection or stratification for future clinical trials. To address this concern, a group of representatives from breast cancer research groups in the areas of breast pathology, genomic profiling, and clinical trials critically reviewed all available data. Consensus recommendations are made on the practical use of molecular markers in breast cancer management and their incorporation into future clinical trials. PMID:21472705
Kaufmann, Manfred; Pusztai, Lajos
Molecular and cellular markers of toxicity in the Japanese Medaka @
The Japanese Medaka (Oryzias latipes) has been recommended for use as a model organism to detect carcinogenic, teratogenic, cytotoxic, and genotoxic compounds in aquatic systems. Because a long latent period often occurs between initial contact with deleterious chemicals and subsequent expression of the pathology, we are investigating early biologically-relevant responses that can be used as genotoxicity markers of exposure and effect. This project focuses on the development of genotoxic bioassays and experimental protocols for exposing Japanese Medaka to genotoxic compounds. 21 refs., 8 figs, 2 tabs.
Shugart, L.R.; McCarthy, J.F.; D'Surney, S.J.; Greeley, M.S. Jr.; Hull, C.G.
[The systems of molecular genetic markers under cancer of stomach].
The study was organized to investigate the anomalous methylation of genes NA?1, RASSF1A, MLH1, N33, DAPK, the expression of genes hTERT. metalloproteinase MMP7, MMP9, survivin. COX-2, p53. The activity of telomerase in 106 samples of stomach tumors taken through intra-operation way and 53 samples of stomach tumors taken through endoscopic way and 50 samples of biopsy taken from patients with chronic calculous cholecystitis (comparison group) was analyzed too. These changes can be used as additional markers both in diagnostic of cancer of stomach and dynamic monitoring of operated patients. PMID:24640104
Nemtsova, M V; Bykov, I I; Tchekinova, N V; Zaletaev, D V; Glikhov, A I; Khorobrykh, T V
Improving Selection in Forage, Turf, and Biomass Crops Using Molecular Markers
\\u000a Selection of improved forage, turf, and bioenergy crops is optimized if measuring the phenotype of interest is rapid, inexpensive,\\u000a and repeatable. Phenotyping remains the most difficult issue to resolve for many important traits, including biomass yield,\\u000a abiotic stress tolerance, and long-term persistence. The identification of molecular markers may augment phenotypic selection\\u000a if markers are identified that are closely linked to
E. Charles Brummer; Michael D. Casler
Genetic Relationship of Curcuma Species from Northeast India Using PCR-Based Markers
Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific\\u000a genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD),\\u000a 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic\\u000a fragments. ISSR confirmed maximum polymorphism of
Archana Das; Vigya Kesari; Vinod M. Satyanarayana; Ajay Parida; Latha Rangan
Heritability of phenolics in Quercus laevis inferred using molecular markers.
Studies of quantitative inheritance of phenotypes do not generally encompass the range of environmental conditions to which a population may be exposed in a natural setting and are rarely conducted on long-lived species due to the time required for traditional crossing experiments. We used a marker-based method to estimate relatedness with microsatellite markers in a natural population of a long-lived oak, then used this inferred relatedness to examine quantitative genetic variation in the concentration of foliar phenolics. Estimating heritability using this method requires both significant relatedness and variance in relatedness over distance. However, this population did not show significant variance of relatedness, so only the presence of heritability, and its ranking among traits and environments, could be estimated. Seven foliar phenolics showed a significant relationship between phenotypic similarity and relatedness. The significance of this relationship varied among individual phenolic compounds, as well as by season. Genetic factors appeared to have a more measurable influence on the production of secondary compounds early in the season. After leaf expansion, covariance of relatedness and phenotypic variance appear to become less significant. Therefore heritability may vary seasonally for these traits. PMID:11773250
Klaper, R; Ritland, K; Mousseau, T A; Hunter, M D
Molecular prognostic markers in pancreatic cancer: A systematic review
Pancreatic cancer is one of the most lethal tumours of the gastrointestinal tract. The ability to predict which patients would benefit most from surgical intervention and\\/or chemotherapy would be a great clinical asset. Considerable research has focused on identifying molecular events in pancreatic carcinogenesis, and their correlation with clinicopathological variables of pancreatic tumours and survival. This systematic review examined evidence
G. Garcea; C. P. Neal; C. J. Pattenden; W. P. Steward; D. P. Berry
Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species
New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum??EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.
Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.
Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.
New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum??EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588
Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C
Characterization of Erwinia amylovora strains using random amplified polymorphic DNA fragments (RAPDs).
The genetic diversity among 16 strains of Erwinia amylovora, chosen to represent different host plant origins and geographical regions, was investigated by RAPD analysis. One strain of Erwinia herbicola and one of Agrobacterium vitis were used as outgroups. Ninety-eight different RAPD fragments were produced by polymerase chain reaction amplification with six different 10-mer primers. RAPD banding profiles were found that enabled the Erw. amylovora strains to be distinguished from one another. Cluster analysis based on the number of RAPD fragments shared between strains showed that strains of Erw. amylovora isolated from subfamily Pomoideae formed a single group, whereas two strains from Rubus (subfamily Rosoideae) formed a second group. Two strains isolated from Asian pear on Hokkaido, Japan, formed a third group. Sets of RAPD fragments were identified that enabled each of the two host-range groups and one geographical region (Hokkaido) of Erw. amylovora strains to be unambiguously distinguished from one another and from the outgroups. This study shows that strains of Erw. amylovora exhibit genetic diversity detectable by RAPD analysis, and that molecular and statistical analysis of RAPD fragments can be used both to distinguish between strains and to determine relatedness between them. PMID:12455904
Momol, M T; Momol, E A; Lamboy, W F; Norelli, J L; Beer, S V; Aldwinckle, H S
SEOM clinical guidelines for using molecular markers in clinical practice
Nowadays, treatment selection for most types of cancers is based on anatomical, histological and clinical criteria, which\\u000a are defined by the selection criteria used in registration phase III trials. However, different cancers present distinct molecular\\u000a features, so the current approach results in a lack of specificity of cancer therapy, which is associated with decreased efficacy\\u000a and unnecessary toxicities and costs.
Virginia Arrazubi; Roberto Pazo; Dolores Isla; Jos� Luis P�rez Gracia
Prognostic molecular markers in non-small cell lung cancer
Although TNM stage is the most significant prognostic parameter in lung cancer, additional parameters are required for explaining variability of survival. Hence molecular alterations in lung cancer have been extensively studied. Most prominent among them are alterations in the p53�p21 pathway, controlling the G1\\/S transition. They are the most commonly observed aberrations in non-small cell lung cancer (NSCLC). The results
Jacek Nikli?ski; Wies?awa Nikli?ska; Jerzy Laudanski; El?bieta Chyczewska; Lech Chyczewski
N605ab, a specific molecular marker for Phytophthora infestans , distinguishes three genotypes in Japan
Random amplified polymorphic DNA (RAPD) analysis using the OPG-06 primer generated specific patterns for Japanese genotypes\\u000a US-1, JP-1, and a new A1 (JP-2, JP-3, and JP-4) of Phytophthora infestans. N605, a specific RAPD fragment, was cloned and sequenced. PCR primers BD1\\/BD2 were constructed based on the N605 sequence\\u000a and were used to clarify the genotypes. PCR products using the BD1\\/BD2
Seishi Akino; Yuko Shirasawa; Norio Kondo; Shigeo Naito
Pedigree assessment using RAPD-DGGE in cereal crop species.
The introduction of molecular biology methodologies to plant improvement programs offers an invaluable opportunity for extensive germplasm characterization. However, the detection of adequate DNA polymorphism in self-pollinating species remains on obstacle. We have optimized a denaturing-gradient-gel electrophoresis (DGGE) system which, when used in combination with random amplified polymorphic DNA (RAPD) analysis, greatly facilitates the detection of reproducible DNA polymorphism among closely related plant lines. We have used this approach to estimate pedigree relationships among a spectrum of plant materials in wheat, barley and oat. Based on analysis with one or two primers, we were able to distinguish soft from hard winter wheat, and 2-rowed from 6-rowed barley. Further analysis with additional primers allowed resolution of polymorpisms even among closely related lines in highly selected populations. We placed 17 cultivars of oat into two distinct clusters that differed significantly from previous oat pedigree assessments. We believe that DGGE-RAPD is a superior method for detecting DNA polymorphism when compared to RFLP, agarose-RAPD, or polyacrylamide-RAPD methods. PMID:24195921
Dweikat, I; Mackenzie, S; Levy, M; Ohm, H
Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR
NASA Astrophysics Data System (ADS)
Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.
Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.
Volatility of organic molecular markers used for source apportionment analysis: measurements and implications for atmospheric lifetime.
Molecular markers are organic species used to define fingerprints for source apportionment of ambient fine particulate matter. Traditionally, these markers have been assumed to be stable in the atmosphere. This work investigates the gas-particle partitioning of eight organic species used as molecular markers in receptor models for biomass burning (levoglucosan), motor vehicles (5?-cholestane, n-hexacosane, n-triacontane, 1,2-benz[a]anthracene, coronene), and meat cooking (cholesterol, oleic acid). Experiments were conducted using a thermodenuder to measure the evaporation of single component particles. The data were analyzed using the integrated volume method to determine saturation concentrations and enthalpies of vaporization for each compound. The results indicate that appreciable quantities (>10%) of most of these markers exist in the gas phase under typical atmospheric conditions. Therefore, these species should be considered semivolatile. Predictions from a chemical kinetics model indicate that gas-particle partitioning has important effects on the atmospheric lifetime of these species. The atmospheric decay of semivolatile compounds proceeds much more rapidly than nonvolatile compounds because gas-phase oxidation induces evaporation of particle-phase material. Therefore, both gas-particle partitioning and chemical reactions need to be accounted for when semivolatile molecular markers are used for source apportionment studies. PMID:23013599
May, Andrew A; Saleh, Rawad; Hennigan, Christopher J; Donahue, Neil M; Robinson, Allen L
Identification of molecular markers of bipolar cells in the murine retina
Retinal bipolar neurons serve as relay interneurons that connect rod and cone photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies essential for correct routing of photoreceptor cell signals to specific postsynaptic amacrine and ganglion cells. The development and physiology of these interneurons have not been completely defined molecularly. Despite previous identification of genes expressed in several bipolar cell subtypes, molecules that mark each bipolar cell type still await discovery. In this report, novel genetic markers of murine bipolar cells were found. Candidates were initially generated by using microarray analysis of single bipolar cells and mining of retinal serial analysis of gene expression (SAGE) data. These candidates were subsequently tested for expression in bipolar cells by RNA in situ hybridization. Ten new molecular markers were identified, five of which are highly enriched in their expression in bipolar cells within the adult retina. Double-labeling experiments using probes for previously characterized subsets of bipolar cells were performed to identify the subtypes of bipolar cells that express the novel markers. Additionally, the expression of bipolar cell genes was analyzed in Bhlhb4 knockout retinas, in which rod bipolar cells degenerate postnatally, to delineate further the identity of bipolar cells in which novel markers are found. From the analysis of Bhlhb4 mutant retinas, cone bipolar cell gene expression appears to be relatively unaffected by the degeneration of rod bipolar cells. Identification of molecular markers for the various subtypes of bipolar cells will lead to greater insights into the development and function of these diverse interneurons.
Kim, Douglas S; Ross, Sarah E; Trimarchi, Jeffrey M; Aach, John; Greenberg, Michael E; Cepko, Constance L
QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum �נ Gossypium barbadense
A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful\\u000a for a marker-assisted breeding program. Four kinds of markers�simple sequence repeats (SSRs), sequence-related amplified polymorphism\\u000a (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)�were used\\u000a to assay an F2 population from a cross between �Handan208� (Gossypium hirsutum) and �Pima90� (Gossypium barbadense).
Dao-Hua He; Zhong-Xu Lin; Xian-Long Zhang; Yi-Chun Nie; Xiao-Ping Guo; Yan-Xin Zhang; Wu Li
Molecular marker analysis of Salmonella typhimurium from surface waters, humans, and animals
Salmonella contamination of North Sea water was detected for the first time in 1988 in Germany during routine examinations of bathing areas. Since then, subsequent isolations along the coast have been reported regularly. To define the source of contamination, strains isolated from seawater and rivers were studied by molecular marker methods. Their properties were compared with those of strains originating
I. Graeber; M. A. Montenegro; C. Bunge; U. Boettcher; H. Tobias; E. A. Heinemeyer; R. Helmuth
A general mixture model for mapping quantitative trait loci by using molecular markers
In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers. A method is discribed to fit the model to data. The model makes it possible to
R. C. Jansen
An Educational Software for Simulating the Sample Size of Molecular Marker Experiments
ERIC Educational Resources Information Center
We developed educational software to show graduate students how to plan molecular marker experiments. These computer simulations give the students feedback on the precision of their experiments. The objective of the software was to show students using a hands-on approach how: (1) environmental variation influences the range of the estimates of the�
Helms, T. C.; Doetkott, C.
Development of Molecular Markers of Response to Assess the Sensitivity of Children to Environmental Chemicals J.Allen, C. Blackman, M. Blaze, D. Delker, D. DeMarini, C. Doerr, R. Grindstaff, S. Hester, C. Jones, A. Kligerman, G. Knapp, M. Kohan, C. Nelson, R. Owen, J. P...
Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP
Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using
Shu-Jing Sun; Wei Gao; Shu-Qian Lin; Jian Zhu; Bao-Gui Xie; Zhi-Bin Lin
Evaluating the effects of non-neutral molecular markers on phylogeny inference.
Nucleotide substitution models used in molecular phylogenetics do not account for nucleotide sequences evolving under selection, yet selection is rarely tested for. If non-neutral markers violate these models (i.e. non-independence of sites), it is expected that their reconstructed topologies be incongruent with those inferred from neutral ones and conclusions made from those phylogenies should be reexamined. Using rhodopsin as a phylogenetic marker has recently been called into question for exactly this reason. Rhodopsin is assumed to have evolved under strong positive selection for organisms that inhabit similar aquatic environments, making it unsuitable for the phylogenetics of aquatic organisms, but it is unclear what the effects of non-neutrality on phylogeny estimation are. To evaluate potential incongruence of neutral versus non-neutral markers, and the notion that rhodopsin should not be used in the molecular phylogenetics of fishes, a molecular dataset of 78 acanthomorph taxa and sequences from four nuclear, protein coding loci (including rhodopsin), were examined. Only one marker was found to be neutral while the remaining tests, for all other loci, rejected the null hypothesis of neutrality. To evaluate the possible effect(s) of positively versus negatively selected sites, the three non-neutral markers were analyzed to determine the presence of positively and negatively selected codons. To determine congruence in topology among ML trees inferred by individual neutral and non-neutral markers, as well as the combined (concatenated) dataset, tree, comparisons of distances among trees and hypothesis (topology) testing were carried out. Results of the tree distance metrics and topology testing support the notion that neutrality alone does not determine congruence in topology, and those data that are inferred to have evolved under selection should not necessarily be excluded. In addition, the number of sites inferred to have evolved under positive selection does not predict congruence with other markers or the topology inferred with the concatenated dataset. PMID:24558367
Roje, Dawn M
Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers.
The distinctness, uniformity and stability (DUS) requirements involve expensive, space- and time-consuming measurements of morphological traits. Moreover, for a majority of traits, interactions between genotype and environment complicate the evaluation. Molecular markers have a potential to facilitate this procedure, increase the reliability of decisions, and substantially save the time and space needed for experiments. We chose 25 varieties of pea (Pisum sativum L.) from the list of recommended varieties for cultivation in the Czech Republic, and made both a standard classification by 12 morphological descriptors and a classification by biochemical-molecular markers. Two isozyme systems, 10 microsatellite loci, 2 retrotransposons for multilocus inter-retrotransposon amplified polymorphism (IRAP), and 12 retrotransposon-based insertion polymorphism (RBIP) DNA markers were analysed. The main objective of the study was to examine the potential of each method for discrimination between pea varieties. The results demonstrate a high potential and resolving power of DNA-based methods. Superior in terms of high information content and discrimination power were SSR markers, owing to high allelic variation, which was the only biochemical-molecular method allowing clear identification of all varieties. Retrotransposon markers in RBIP format proved to be the most robust and easy to score method, while multilocus IRAP produced informative fingerprint already in a single analysis. Isozyme analysis offered a fast and less expensive alternative. The results showed that molecular identification could be used to assess distinctness and complement morphological assessment, especially in cases where the time frame plays an important role. Currently developed pea marker systems might serve also for germplasm management and genetic diversity studies. PMID:18436990
Smykal, Peter; Horacek, Jiri; Dostalova, Radmila; Hybl, Miroslav
DNA fingerprinting of Flavobacterium columnare using RAPD-PCR.
In the present study, DNA fingerprinting of eight strains of Flavobacterium columnare was done by random amplification of polymorphic DNA (RAPD) fingerprinting method. The strains were collected from Fish Health Management Division, Central Institute of Freshwater Aquaculture, Bhubaneswar, India. A total number of 160 primers were screened for RAPD-PCR, of which 10 primers yielded amplification with all the strains. The molecular weight of amplified bands varied from 0.29-2.63 Kb. The number of bands varied from 1 to 8. Unique band was seen with primer OPY-15 with molecular weight 0.75 Kb that can be used for epidemiological study. Genetic variability was investigated using NTSYS software. Highest genetic similarity was found between MS1 and MS3 followed by MS5 and MS7. Minimum genetic similarity was found between MS2 and MS8. Phylogenetic tree was constructed using UPGMA and neighbor joining methods. PMID:22815565
Sahoo, Lopamudra; Das, B K; Parhi, J; Mukherjee, S C
Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India
The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard�s similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program.
Ashraf, Kamran; Ahmad, Altaf; Chaudhary, Anis; Mujeeb, Mohd.; Ahmad, Sayeed; Amir, Mohd.; Mallick, N.
Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India.
The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard's similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program. PMID:24600309
Ashraf, Kamran; Ahmad, Altaf; Chaudhary, Anis; Mujeeb, Mohd; Ahmad, Sayeed; Amir, Mohd; Mallick, N
Molecular characterization of Aspergillus flavus and aflatoxin contamination of wheat grains from Saudi Arabia.
Twelve species belonging to six fungal genera were found to be associated with wheat (Triticum aestivum L.) grain samples collected from three main regions in Saudi Arabia. The most common genera (average frequency) were Aspergillus (14.3%), Fusarium (29.1%), Penicillium (9.3%), and Alternaria (8.2%). Nineteen isolates of Aspergillus flavus were screened for their ability to produce aflatoxins using HPLC. Thirteen isolates produced aflatoxins ranging from 0.5 to 2.6 �g/kg. Inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) molecular markers were used, with the aim of genetically characterizing strains of A. flavus to discriminate between aflatoxigenic and non-aflatoxigenic isolates. RAPD and ISSR analysis revealed a high level of genetic diversity in the A. flavus population, useful for genetic characterization. Clustering based on RAPD and ISSR dendograms was unrelated to geographic origin. RAPD and ISSR markers were not suitable to discriminate aflatoxigenic and non-aflatoxigenic isolates, but ISSR primers were better compared to RAPD. PMID:24065675
Al-Wadai, A S; Al-Othman, M R; Mahmoud, M A; Abd El-Aziz, A R M
Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).
Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci. PMID:11380876
Buonaccorsi, V P; McDowell, J R; Graves, J E
Genetic diversity in cultivated carioca common beans based on molecular marker analysis
A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats � SSRs and amplified fragment length polymorphisms � AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger�s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.
Kupper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sergio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol
Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.
Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples. PMID:24313449
Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza
A review of molecular pathological markers in vulvar carcinoma: lack of application in clinical practice.
Vulvar carcinoma is a rare female genital neoplasia. Radical surgery, which has been the standard treatment approach, is often accompanied by considerable morbidity. To reduce the incidence of complications there has been a movement toward individualised therapy and less radical surgery. Associated with this, new tumour markers that could serve as prognostic indicators would be of considerable value to guide treatment decision. In this review, a brief update of molecular pathological markers of vulvar carcinomas is provided, and their impact as prognostic markers is addressed. p16, p21, p14, p27, cyclin A, cyclin D1, p53, vascular endothelial growth factor (VEGF), transforming growth factor alpha, HER-2 and epidermal growth factor receptor (EGFR) have been found to be important in the pathogenesis and/or progression of vulvar carcinomas. Furthermore, human papillomavirus, p16, p21, p14, p53, VEGF, CD44v3, CD44v6, CD44v4, CD44v9, CD44v10, HER-2, EGFR, matrix metalloproteinase-12, caspase 3, Bcl-2 and nm23-H1 have been correlated to clinical outcome of patients with vulvar carcinomas. However, due to the relative small number of studies reported for each molecular pathological marker, and the relative small number of vulvar carcinomas included and the lack of multivariate analysis in the majority of these studies, no conclusion regarding the prognostic value of these markers can be drawn. Therefore, the investigated markers have not yet earned a place in standard clinical diagnostics or treatment, and further studies are needed to clarify the clinical value of these markers. PMID:19251952
Knopp, S; Trop�, C; Nesland, J M; Holm, R
Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species.
Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with QST generally exceeding GST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of QST and GST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex. PMID:11681731
Morgan, K K; Hicks, J; Spitze, K; Latta, L; Pfrender, M E; Weaver, C S; Ottone, M; Lynch, M
How do molecular marker patterns of BC change at increasing age of chars?
NASA Astrophysics Data System (ADS)
Black carbon (BC) is considered to be a relatively stable form of organic carbon. However, previous results have shown that the physical and chemical properties of BC can vary considerably with formation temperature. Thus, to understand the long-term carbon sink potential of BC there is increasing interest to gain more information about i) the conditions under which BC was formed, and ii) the resulting degradability of BC under natural conditions. In a first step, we synthesised chars from two different sources of biomass (chestnut wood, rice straw) under well-defined conditions as model substances to analyse the changes in their molecular structure at increasing formation temperature. Results are presented obtained from a set of laboratory produced char samples pyrolysed at increasing temperatures with a high resolution between 200 and 1000 �C. The chars were characterized by a molecular marker method for pyrogenic carbon quantification, which additionally provides information about the degree of condensation of chars. At temperatures between 275 and 500�C, which typically are observed during wildfires and thus are relevant for natural char formation, the molecular marker pattern of the chars remains almost constant. In a next step, we analysed changes in the molecular marker patterns of chars from a chronosequence, with BC deposited between 0 and 100 years ago. Based on the data obtained from the laboratory char series, we compare changes in the molecular marker patterns of the chars from the chronosequence over time. These results show if less condensed forms of BC are degraded preferentially and more condensed, aromatic backbone of BC becomes enriched in the soils with time of degradation. Our results provide information about the fate of BC in the environment, which has important implications in the context of carbon sequestration strategies.
Schneider, M. P. W.; Hilf, M.; Schmidt, M. W. I.
RAPD analysis of genetic variation between a group of rose cultivars and selected wild rose species
The genetic variability based on random-amplified polymorphic DNA markers was analysed among 10 cultivated rose varieties and 9 wild species from three different series of the genus Rosa. Using 13 different RAPD primers, 104 polymorphic DNA fragments with a high potential to differentiate rose genotypes could be produced. A dendrogram displaying the relative genetic similarities among the genotypes shows the
Thomas Debener; Christian Bartels; Lore Mattiesch
Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae)
Eucalyptus globulus is an important species for pulpwood production in many countries. The pattern and partitioning of variation is important baseline knowledge for tree breeding. Currently the species is divided into four subspecies: globulus, bicostata, pseudoglobulus and maidenii. Random Amplified Polymorphic DNA (RAPD) markers were used to analyse variation in 173 representatives of 37 natural populations of E. globulus: 31
K A Nesbitt; B M Potts; R E Vaillancourt; A K West; J B Reid
RAPD analysis of somaclonal variants derived from embryo callus cultures of peach
Peach [Prunus persica (L.) Batsch] regenerants from cv �Sunhigh� embryo no. 156, regenerants obtained from cv �Redhaven� embryo no. 30, and two peach cultivars �Sunhigh� and �Redhaven�, were screened for polymorphic RAPD (Random Amplified Polymorphic DNA) markers with up to 60 10-mer primers. Although 35 primers produced results with scoreable bands, only 10 of the primers revealed polymorphism for regenerants
G. Hashmi; R. Huettel; R. Meyer; L. Krusberg; F. Hammerschlag
Molecular characterization of primary gene pool of chickpea based on ISSR markers.
Genetic diversity and relationships within and among members of the primary gene pool of chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum,, and four of C. echinospermum, were investigated using 31 ISSR markers. The study revealed moderate diversity, detecting 141 fragments, of which 79 (56%) were polymorphic. Averages were 0.125 for polymorphic information content, 0.350 for marker index, and 0.715 for resolving power. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation between wild and cultivated accessions. The clustering pattern did not strictly follow the grouping of accessions by geographic origin but was in good agreement with the pedigree data and the seed type. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in chickpea and can contribute to efficient identification, conservation, and utilization of germplasm for plant improvement through conventional as well as molecular breeding approaches. PMID:23329257
Choudhary, Pooja; Khanna, Suruchi M; Jain, Pradeep K; Bharadwaj, Chellapilla; Kumar, Jitendra; Lakhera, Pramesh C; Srinivasan, Ramamurthy
Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans.
Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides. PMID:24065642
Chang, S C; Mac�do, D P C; Souza-Motta, C M; Oliveira, N T
The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils.
The occurrence of Azotobacter spp., which has beneficial effects on plant development, is related to various soil properties, such as pH and fertility. This study evaluated the prevalence of Azotobacter spp. in industrial (H) and agricultural soils (P) in Nowa Huta, Cracow and determined the phenotypic and genetic diversity of these bacteria. The examined bacteria were present in 40% of H and in 50% of P soils. Taxonomic identification of the bacterial isolates indicated the presence of three species-A. salinestris, A. chroococcum and A. vinelandii. The genetic diversity, determined using two fingerprinting methods-Random Analysis of Polymorphic DNA (RAPD) and Rep-PCR (BOX) revealed high level of population diversity. In AMOVA analysis most of diversity was attributed to within-population variation (76-85%), and only 3.78-6.18% was associated with among-group H and P variation. Global test of differences revealed distinct population structure within bacterial strains isolated from H and P areas only for BOX markers (Fst = 0.05732, P = 0.00275). Phenetic analyses: UPGMA and DCA better discriminated H and P groups based on RAPD data. Both BOX and RAPD methods provided an insight into the genetic complexity of Azotobacter spp. variation in soils of different land-use types. PMID:24798904
Lenart-Boro?, Anna M; Wolny-Ko?adka, Katarzyna A; Boro?, Piotr M; Mitka, J�zef R
Tumor Endothelial Marker Imaging in Melanomas Using Dual-Tracer Fluorescence Molecular Imaging
Purpose Cancer-specific endothelial markers available for intravascular binding are promising targets for new molecular therapies. In this study, a molecular imaging approach of quantifying endothelial marker concentrations (EMCI) is developed and tested in highly light-absorbing melanomas. The approach involves injection of targeted imaging tracer in conjunction with an untargeted tracer, which is used to account for nonspecific uptake and tissue optical property effects on measured targeted tracer concentrations. Procedures Theoretical simulations and a mouse melanoma model experiment were used to test out the EMCI approach. The tracers used in the melanoma experiments were fluorescently labeled anti-Plvap/PV1 antibody (plasmalemma vesicle associated protein Plvap/PV1 is a transmembrane protein marker exposed on the luminal surface of endothelial cells in tumor vasculature) and a fluorescent isotype control antibody, the uptakes of which were measured on a planar fluorescence imaging system. Results The EMCI model was found to be robust to experimental noise under reversible and irreversible binding conditions and was capable of predicting expected overexpression of PV1 in melanomas compared to healthy skin despite a 5-time higher measured fluorescence in healthy skin compared to melanoma: attributable to substantial light attenuation from melanin in the tumors. Conclusions This study demonstrates the potential of EMCI to quantify endothelial marker concentrations in vivo, an accomplishment that is currently unavailable through any other methods, either in vivo or ex vivo.
Tichauer, Kenneth M.; Deharvengt, Sophie J.; Samkoe, Kimberley S.; Gunn, Jason R.; Bosenberg, Marcus W.; Turk, Mary-Jo; Hasan, Tayyaba; Stan, Radu V.; Pogue, Brian W.
Genetic analysis of apomixis in Citrus and Poncirus by molecular markers
Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings
R. Garc�a; M. J. As�ns; J. Forner; E. A. Carbonell
Quantum computations with atoms in optical lattices: Marker qubits and molecular interactions
We develop a scheme for quantum computation with neutral atoms, based on the concept of 'marker' atoms, i.e., auxiliary atoms that can be efficiently transported in state-independent periodic external traps to operate quantum gates between physically distant qubits. This allows for relaxing a number of experimental constraints for quantum computation with neutral atoms in microscopic potential, including single-atom laser addressability. We discuss the advantages of this approach in a concrete physical scenario involving molecular interactions.
Calarco, T. [Institute for Theoretical Physics, University of Innsbruck, and Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); European Centre for Theoretical Studies in Nuclear Physics and Related Areas, I-38050 Villazzano, TN (Italy); CRS BEC-INFM, Dipartimento di Fisica, Universita di Trento, I-38050 Povo, TN (Italy); Dorner, U.; Zoller, P. [Institute for Theoretical Physics, University of Innsbruck (Austria); Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Julienne, P.S.; Williams, C.J. [National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8423 (United States)
Molecular Marker Studies in Riverine Buffaloes, for Characterization and Diagnosis of Genetic Defects
The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural\\u000a traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases\\u000a and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide\\u000a probes showed species-specific bands useful for identification of carcass or
B. R. Yadav
Mapping of quantitative trait loci affecting Drechslera teres resistance in barley with molecular markers
Resistance loci for seedling-stage resistance to net blotch disease (Drechslera teres) in barley were mapped with molecular markers in an F2 population derived from a cross between the susceptible barley cultivar �Arena� and the resistant Ethiopian landrace �Hor\\u000a 9088�. Disease reactions were scored with first and second leaves of 2-week-old plants 7 and 9 days after inoculation with\\u000a a single
K. Richter; J. Schondelmaier; C. Jung
?H2AX: a sensitive molecular marker of DNA damage and repair
Phosphorylation of the Ser-139 residue of the histone variant H2AX, forming ?H2AX, is an early cellular response to the induction of DNA double-strand breaks. Detection of this phosphorylation event has emerged as a highly specific and sensitive molecular marker for monitoring DNA damage initiation and resolution. Further, analysis of ?H2AX foci has numerous other applications including, but not limited to,
L-J Mah; A El-Osta; T C Karagiannis
Development of molecular markers and linkage maps for the Carthamus species C. tinctorius and C. oxyacanthus.
A set of SSR and RFLP markers for safflower (Carthamus tinctorius) and jeweled distaff thistle (C. oxyacanthus) was generated from cDNA and genomic libraries and by mining public and proprietary sequence databases. In total, 1412 PCR-based markers and 75 RFLP markers were screened and polymorphic loci were mapped in an intraspecific F2 population of C. tinctorius and an interspecific BC1 population of C. tinctorius x C. oxyacanthus. The two populations shared one common parent and the resulting linkage maps could be compared for synteny. The level of polymorphism was low in both populations and only 8.2% and 13.7% of the analyzed markers could be mapped in the intraspecific and interspecific maps, respectively. The two maps showed significant colinearity of markers in several regions and an apparent translocation or inversion event on one linkage group. Noticeable segregation distortion was found on one linkage group of the C. tinctorius map and dense clustering of loci occurred on several linkage groups of the C. oxyacanthus map. The two maps represent the first major linkage analysis of Carthamus species. The molecular tools will be useful for a variety of genetic and genomic applications in safflower and its related species and have been used in our laboratory to map a flower color gene in C. tinctorius. PMID:20616858
Mayerhofer, Reinhold; Archibald, Catherine; Bowles, Victoria; Good, Allen G
Molecular Phenotyping of Thyroid Tumors Identifies a Marker Panel for Differentiated Thyroid Cancer Diagnosis
Background��Currently, a large proportion of individuals undergo thyroidectomy as a diagnostic procedure for cancer. The objective of\\u000a this work was to evaluate the molecular phenotype of differentiated thyroid cancer (DTC) and benign thyroid lesions to identify\\u000a molecular markers that allow for accurate thyroid cancer diagnosis.\\u000a \\u000a \\u000a \\u000a Methods��Tissue microarrays consisting of 100 benign and 105 malignant thyroid lesions, plus 24 lymph node
Sam M. Wiseman; Adrienne Melck; Hamid Masoudi; Fariba Ghaidi; Lynn Goldstein; Allen Gown; Steven J. M. Jones; Obi L. Griffith
Multilocus microsatellite signature and identification of specific molecular markers for Leishmania aethiopica
Background Leishmaniasis is a clinically and epidemiologically diverse zoonotic disease caused by obligatory, intracellular protozoan parasites of the genus Leishmania. Cutaneous leishmaniasis is the most widely distributed form of the disease characterized by skin lesions. Leishmania aethiopica is considered the predominant etiological agent in Ethiopia. The current study was aimed at developing multilocus microsatellite markers for L. aethiopica isolated from human cutaneous leishmaniasis patients in Ethiopia. Results L. aethiopica parasites for the study were obtained from Ethiopia and laboratory analysis was conducted at The Ohio State University. DNA was extracted from cultured parasites and an internal transcribed spacer located at the ribosomal region of L. aethiopica genomic DNA was PCR amplified for species identification. Microsatellite markers were identified using multilocus microsatellite typing. We generated an enriched genomic library, and using Primer3 software, designed PCR primers to amplify sequences flanking the detected microsatellites. Subsequent screening of the amplified markers for length variations was performed by gel electrophoresis. Using a variety of molecular methods, 22 different microsatellite markers were identified and tested for typing L. aethiopica strains using a number of clinical isolates. Of the 22 markers tested, 5 were polymorphic and showed distinctive multilocus genotypes, classifying them into four clusters. One marker was found to be specific for L. aethiopica, discriminating it from other species of Leishmania. Conclusion Multilocus microsatellite typing using the markers developed in this study could be useful for epidemiological and population genetic studies of strains of L. aethiopica in order to investigate the structure and dynamics of the corresponding natural foci. It could also help to answer specific clinical questions, such as the occurrence of local and diffuse lesions, strain correlates of parasite persistence after subclinical infection and lesion comparisons from patients suffering from L. aethiopica infections.
DNA marker technologies and their applications in aquaculture genetics
The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in
Z. J. Liu; J. F. Cordes
Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species.
Glaucophytes are the least studied of the three major Archaeplastida (Plantae sensu lato) lineages. It has been largely recognized that comprehensive investigations of glaucophyte genetic and species diversity will shed light on the early evolution of photosynthetic eukaryotes. Here we used molecular phylogenetics and genetic distance estimations of diverse molecular markers to explore strain and species diversity within the glaucophyte genera Cyanophora and Glaucocystis. Single gene and concatenated maximum likelihood analyses of markers from three different genetic compartments consistently recovered similar intrageneric genetic groups. Distance analyses of plastid (psbA and rbcL) and mitochondrial (cob and cox1) genes, and the nuclear internal transcribed spacer (ITS) region, revealed substantial genetic divergence between some Cyanophora paradoxa and Glaucocystis nostochinearum strains. The genetic distances estimated between some glaucophyte strains currently considered the same species are similar or greater than divergence values calculated between different species in other unicellular algae, such as certain green algae and diatoms. The analyzed molecular markers are prospective candidates for future studies of species diversity in glaucophytes. Overall, our results unveil previously unrecognized cryptic diversity within Cyanophora and Glaucocystis species. PMID:24680917
Chong, Jasmine; Jackson, Christopher; Kim, Jong Im; Yoon, Hwan Su; Reyes-Prieto, Adrian
Quantification of the effects of molecular marker oxidation on source apportionment estimates for motor vehicles
NASA Astrophysics Data System (ADS)
Molecular markers are individual organic compounds used in receptor models to apportion fine particulate matter to sources. These models currently assume that molecular markers are chemically stable; however, recent laboratory experiments suggest they may be significantly oxidized on atmospherically relevant time scales. To investigate the effects of photo-oxidation, we extended a 3-D chemical transport model (PMCAMx) to simulate norhopane concentrations over the eastern United States during July 2001. Norhopane is an important molecular marker for motor vehicle exhaust. We examined eight different simulation scenarios, using different combinations of reaction rates and source profiles. The simulations including norhopane oxidation better reproduced the observed spatial patterns of norhopane concentrations than the non-reactive cases. Chemical mass balance (CMB) analysis was performed using the PMCAMx-predicted motor vehicle norhopane and elemental carbon (EC) concentrations to quantify the bias caused by oxidation on source apportionment estimates. Norhopane oxidation caused CMB to underestimate total vehicle OC by 10-50%, with larger biases in rural areas. This underestimation was largely due to changes in the amount of OC apportioned to gasoline vehicles which was reduced by as much as 100%. The OC apportioned to diesel vehicle emissions was relatively insensitive to norhopane reaction. Therefore, oxidation can substantially alter CMB estimates regarding the relative importance of gasoline and diesel vehicle emissions.
Roy, Anirban A.; Wagstrom, Kristina M.; Adams, Peter J.; Pandis, Spyros N.; Robinson, Allen L.
Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.
'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236
Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F
An improved micropropagation of Arnebia hispidissima (Lehm.) DC. and assessment of genetic fidelity of micropropagated plants using DNA-based molecular markers.
An efficient and improved in vitro propagation method has been developed for Arnebia hispidissima, a medicinally and pharmaceutically important plant species of arid and semiarid regions. Nodal segments (3-4 cm) with two to three nodes obtained from field grown plants were used as explants for shoot proliferation. Murashige and Skoog's (MS) medium supplemented with cytokinins with or without indole-3-acetic acid (IAA) or naphthalene acetic acid was used for shoot multiplication. Out of different PGRs combinations, MS medium containing 0.5 mg l(-1) 6-benzylaminopurine and 0.1 mg l(-1) IAA was optimal for shoot multiplication. On this medium, explants produced the highest number of shoots (47.50?�?0.38). About 90 % of shoots rooted ex vitro on sterile soilrite under the greenhouse condition when the base (2-4 mm) of shoots was treated with 300 mg l(-1) of indole-3-butyric acid for 5 min. The plantlets were hardened successfully in the greenhouse with 85-90 % survival rate. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic stability of in vitro-regenerated plants of A. hispidissima. Out of 40 (25 RAPD and 15 ISSR) primers screened, 15 RAPD and 7 ISSR primers produced a total number of 111 (77 RAPD and 34 ISSR) reproducible amplicons. The amplified products were monomorphic across all the micropropagated plants and were similar to the mother plant. To the best of our knowledge, it is the first report on the assessment of the genetic fidelity in micropropagated plants of A. hispidissima. PMID:23645417
Phulwaria, Mahendra; Rai, Manoj K; Shekhawat, N S
Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for oxyuroid species (Nematoda).
Random amplified DNA markers (RAPD; Williams et al., 1990) were used to obtained specific RAPD fragments characterising different species of oxyuroids. We tested six species of worms parasitizing vertebrates or invertebrates: Passalurus ambiguus Rudolphi, 1819, parasite of Leporids; Syphacia obvelata (Rudolphi, 1802) Seurat, 1916, a parasite of rodents; Blatticola blattae (Graeffe, 1860) Chitwood, 1932 parasite of the cockroach Blattella germanica; Hammerschmidtiella diesingi (Hammerschmidt, 1838) Chitwood, 1932 and Thelastoma bulhoesi (Magalhaes, 1990) Travassos, 1929, parasites of the cockroach Periplaneta americana, and an undescribed parasite species of a passalid insect from New Caledonia. Among 15 oligonucleotides tested, nine produced several specific bands allowing the interspecific discrimination. PMID:9754296
Jobet, E; Bougnoux, M E; Morand, S; Rivault, C; Cloarec, A; Hugot, J P
Molecular characterization of Ephedra species found in Pakistan.
Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency. PMID:18273806
Ghafoor, S; Shah, M M; Ahmad, H; Swati, Z A; Shah, S H; Pervez, A; Farooq, U
Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis.
Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity. PMID:24469734
Sudheer Pamidimarri, D V N; Reddy, Muppala P
RAPD based genetic variability among cultivated varieties of Aonla (Indian Gooseberry, Phyllanthus emblica L.)
Aonla, the Indian Gooseberry (Phyllanthus emblica) is widely grown in India due to its neutraceutical properties. Investigations on the use of RAPD markers enabled us to estimate\\u000a genetic variability among commercially cultivated varieties. This study also enabled us to distinguish these varieties using\\u000a a set of four decamer primers, which was otherwise difficult by using morphological markers. Cluster analysis revealed
A. K. Chaurasia; V. R. Subramaniam; Bal Krishna; P. V. Sane
Molecular genetic marker-based approaches to the verification of lilac Syringa vulgaris L. in vitro germplasm collections
RAPD analysis was used to verify the varieties in an in vitro germplasm collection of lilac Syringa vulgaris L. RAPD patterns were obtained with 16 decanucleotide primers for 46 accessions (microclones and corresponding reference\\u000a varieties). The RAPD patterns of a microclone and the corresponding reference variety often differed in composition; consequently,\\u000a it was infeasible to verify the accessions by direct
N. V. Melnikova; E. V. Borhert; S. P. Martynov; I. B. Okuneva; O. I. Molkanova; V. P. Upelniek; A. M. Kudryavtsev
Development of a molecular linkage map of pearl millet integrating DArT and SSR markers.
Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2�נPRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148�cM with an average adjacent-marker interval length of 3.7�cM. The length of individual linkage groups (LGs) ranged from 78�cM (LG 3) to 370�cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available. PMID:21476042
Supriya, A; Senthilvel, S; Nepolean, T; Eshwar, K; Rajaram, V; Shaw, R; Hash, C T; Kilian, A; Yadav, R C; Narasu, M L
Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers.
Arapaima gigas (Osteoglossidae) is one of the largest fish species in the Amazon Basin, attaining lengths of over 2.5 m and weights of over 100 kg. Its flesh is prized, and it has great potential for production in aquaculture systems. However, live pirarucu cannot be reliably sexed visually, even after sexual development, since this species does not have clear external sexual dimorphism. Simple and inexpensive methods for sexing immature pirarucu based on DNA markers would facilitate production of this species in commercial operations. We analyzed A. gigas male and female DNA pools with 566 RAPD primers, generating 2609 fragments, with an estimated 1341 segregating polymorphic markers, and an estimated average spacing of 714 kb, which corresponds to less than 0.1% of the species' genome. Two putative sex-specific fragments were initially identified in bulked samples; but they were not confirmed in a study of individual male and female samples. We suggest that A. gigas has developed a non-chromosomal system of sex determination or, alternatively, that the species has undergone a recent loss of the chromosome carrying the sex-determining locus. PMID:24338425
Almeida, I G; Ianella, P; Faria, M T; Paiva, S R; Caetano, A R
Inheritance and RAPD tagging of multiple genes for resistance to net blotch in barley.
A doubled haploid barley (Hordeum vulgare L.) population that was created from a cross between cultivars 'L�ger' and 'CI 9831' was characterized by RAPD (random amplified polymorphic DNA) markers for resistance to isolate WRS857 of Pyrenophora teres Drechs. f. sp. maculata Smedeg., the causal agent of the spot form of net blotch. Resistance, which initially appeared to be conferred by a single gene from the approximate 1:1 (resistant : susceptible) segregation ratio of the doubled-haploid (DH) progeny, was found to be associated with three different genomic regions by RAPD analysis. Of 500 RAPD random primers that were screened against the parents, 195 revealed polymorphic bands, seven showed an association to the resistance in bulks, and these seven markers were mapped to three unlinked genomic regions. Two of these regions, one of which was mapped to chromosome 2, have major resistance genes. The third region has some homology to the chromosome 2 region. This study demonstrates the simultaneous location of markers for more than one gene governing a trait by using RAPD and bulked segregant analysis (BSA). PMID:10791809
Molnar, S J; James, L E; Kasha, K J
[Molecular genetic marker-based approaches to the verification of lilac Syringa vulgaris L. in in vitro collections].
RAPD analysis was used to verify the varieties in an in vitro germplasm collection of lilac Syringa vulgaris L. RAPD patterns were obtained with 16 decanucleotide primers for 46 accessions (microclones and corresponding reference varieties). The RAPD patterns of a microclone and the corresponding reference variety often differed in composition; consequently, it was infeasible to verify the accessions by direct comparison of the RAPD patterns. Hence, evaluation of the relative genetic distances between accessions (microclones) and known varieties was proposed as a method to verify lilac in vitro germplasm collections. PMID:19239103
Mel'nikova, N V; Borkhert, E V; Martynov, S P; Okuneva, I B; Molkanova, O I; Upelniek, V P; Kudriavtsev, A M
[Genetic monitoring of populations of Matthiola fragrans (Bunge) using RAPD and AFLP analysis].
The possibility of using RAPD and AFLP methods for genetic monitoring of populations of Matthiola fragrans (Bunge), a species included in the Red Book of the USSR, was shown for the first time. An analysis of inter- and intrapopulation and interspecies genome polymorphism was performed. Differences in the genetic structure of Matthiola populations from various geographical collection points were revealed. A simple method of performing RAPD analysis and the great number of unique markers found in each population compared with the AFLP analysis, as well as the good division of populations under statistical treatment, allow us to draw the conclusion that using the RAPD method in genetic monitoring of rare and insufficiently studied species is well founded. PMID:21874670
Khadeeva, N V; Goriunova, S V; Kochumova, A A; Iakovleva, E Iu; Mel'nikova, N V; Zholobova, O O; Korotkov, O I; Kudriavtsev, A M
A genetic map of cucumber composed of RAPDs, RFLPs, AFLPs, and loci conditioning resistance to papaya ringspot and zucchini yellow mosaic viruses.
The watermelon strain of papaya ringspot virus (PRSV-W) and zucchini yellow mosaic virus (ZYMV) are potyviruses that cause significant disease losses in cucumber. Resistances have been identified primarily in exotic germplasm that require transfer to elite cultivated backgrounds. To select more efficiently for virus resistances, we identified molecular markers tightly linked to PRSV-W and ZYMV resistances in cucumber. We generated F6 recombinant inbred lines (RILs) from a cross between Cucumis sativus L. 'Straight 8' and a line from 'Taichung Mou Gua', TMG1 (susceptible and resistant, respectively, to both viruses), and studied the segregations of amplified fragment length polymorphism (AFLP) markers, randomly amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and resistances to PRSV-W and ZYMV. A 353-point map of cucumber was generated, delineating 12 linkage groups at LOD 3.5. Linkage arrangements among RFLPs were consistent with previously published maps; however linkages among RAPDs in our map did not agree with a previously published map. Resistances to PRSV-W and ZYMV were tightly linked (2.2 cM) and mapped to the end of one linkage group. One AFLP cosegregated with resistance to ZYMV. PMID:11195331
Park, Y H; Sensoy, S; Wye, C; Antonise, R; Peleman, J; Havey, M J
Identification of EZH2 as a Molecular Marker for a Precancerous State in Morphologically Normal Breast Tissues
The discovery of molecular markers to detect the precan- cerous state would have profound implications in the prevention of breast cancer. We report that the expression of the Polycomb group protein EZH2increases in histo- logically normal breast epithelium with higher risk of devel- oping cancer. We identify EZH2as a potential marker for detecting preneoplastic lesions of the breast in vivo
Christine Erdmann; Arul M. Chinnaiyan; Sofia D. Merajver; Celina G. Kleer
Although amplification of source-specific molecular markers from Bacteroidales fecal bacteria can identify several different kinds of fecal contamination in water, it remains unclear how this technique relates to fecal indicator measurements in natural waters. The objectives of t...
Genomic DNA fingerprinting of indigenous chicken breeds with molecular markers designed on interspersed repeats.
In Italy more than fifty different local breeds of chicken (Gallus gallus L.) are known to have been present in the past. The overall situation is now critical since most of these breeds are becoming extinct or threatened and only a few are subject of conservation plans. The use of molecular markers for the analysis of chicken populations could help in characterizing their genetic variation and preserving them from genetic erosion. valuable and irreplaceable sources of chicken germplasm from indigenous populations of the veneto region were analyzed by means of DNA fingerprinting with molecular markers designed on interspersed mini- and microsatellite repeats. The identification of either among-breed discriminant or breed-specific markers was based on the S-SAP and M-AFLP systems derived from the AFLP technology. Genomic DNA fingerprints were generated in 84 individuals belonging to six local breeds (Ermellinata, Padovana, P�poi, Polverara, Robusta Lionata and Robusta Maculata) and one commercial line used as reference standard. A number of variation statistics were computed to assess the genetic variability within and relatedness among breeds: the effective number of alleles per locus (n(e)= 1.570), total and single-breed genetic diversity (H(T)= 0.366 and H(S)= 0.209, respectively) and the fixation index (G(ST)= 0.429). The mean genetic similarity coefficients within and between local breeds were 0.769 and 0.628, respectively. Markers useful for the genetic traceability of breeds revealed significant sequence similarities with either genic or intergenic regions of known chromosome position. Sequence tagged site primers were designed for the most discriminant markers in order to develop multiplex non-radioactive genomic PCR assays. Analysis of the population structure along with individual assignment tests successfully identified all breed clusters and subclusters. The vast majority of animals were correctly allocated to their breed of origin, demonstrating the suitability and reliability of the chosen AFLP-derived marker systems for detecting population structure and tracing individual breeds. The local breeds have been preliminarily identified according to sequence-specific SNPs and haplotypes and the polymorphism information content of genomic AFLP-derived markers is reported and critically discussed. PMID:19891738
Soattin, M; Barcaccia, Gianni; Dalvit, C; Cassandro, M; Bittante, G
Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss).
We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker-trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76�%. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date. PMID:24114565
Allen, M S; Ferguson, M M; Danzmann, R G
Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells
The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. To better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other tissue types, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are enriched in pathways characteristic of CECs, including inorganic anion transmembrane transporter, extracellular matrix structural constituent and cyclin-dependent protein kinase inhibitor activity. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. We also identified stage-specific markers associated with CEC development, such as specific members in the transforming growth factor beta and Wnt signaling pathways only expressed in fetal, but not in adult CECs. Lastly, by the immunohistochemistry of ocular tissues, we demonstrated the unique protein localization for Wnt5a, S100A4, S100A6 and IER3, the four novel markers for fetal and adult CECs. The identification of a new panel of stage-specific markers for CECs would be very useful for characterizing CECs derived from stem cells or ex vivo expansion for cell replacement therapy. GEO accession number: GSE41616.
Chen, Yinyin; Huang, Kevin; Nakatsu, Martin N.; Xue, Zhigang; Deng, Sophie X.; Fan, Guoping
Molecular and biologic markers of progression in monoclonal gammopathy of undetermined significance to multiple myeloma.
Multiple myeloma (MM) is a malignant plasma cell dyscrasia localized in the bone marrow. Recent studies have shown that MM is preceded in virtually all cases by a premalignant state called monoclonal gammopathy of undetermined significance (MGUS). This review focuses on non-IgM MGUS and its progression to MM. Although certain clinical markers of MGUS progression have been identified, it currently is not possible to accurately determine individual risk of progression. This review focuses on the various biologic and molecular markers that could be used to determine the risk of MM progression. A better understanding of the pathogenesis will allow us to define the biological high-risk precursor disease and, ultimately, to develop early intervention strategies designed to delay and prevent full-blown MM. PMID:20958231
Mailankody, Sham; Mena, Esther; Yuan, Constance M; Balakumaran, Arun; Kuehl, W Michael; Landgren, Ola
Evaluation of pharmaceuticals and personal care products as water-soluble molecular markers of sewage.
We examined the utility of 13 pharmaceuticals and personal care products (PPCPs) as molecular markers of sewage contamination in riverine, groundwater, and coastal environments. The PPCPs were crotamiton, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid, thymol, triclosan, propyphenazone, carbamazepine, diethyltoluamide, ethenzamide, and caffeine. Measurements in 37 Japanese rivers showed positive correlations of riverine flux of crotamiton (r2 = 0.85), carbamazepine (r2 = 0.84), ibuprofen (r2 = 0.73), and mefenamic acid (r2 = 0.67) with the population in the catchments. In three surveys in the Tamagawa estuary, crotamiton, carbamazepine, and mefenamic acid behaved conservatively across seasons within a salinity range of 0.4-29 per thousand, suggesting their utility as molecular markers in coastal environments. Removal of ketoprofen and naproxen in the estuary was ascribed to photodegradation. Ibuprofen and thymol were removed from estuarine waters in summer by microbial degradation. Triclosan was removed by a combination of microbial degradation, photodegradation, and adsorption. These results were consistent with those of river water incubated for 8 d at 25 degrees C in the dark in order to examine the effects of biodegradation and photodegradation. Crotamiton was detected in groundwater from the Tokyo metropolitan area (12 out of 14 samples), suggesting wastewater leakage from decrepit sewers. Carbamazepine, ketoprofen, and ibuprofen (5/14), caffeine (4/14), and diethyltoluamide (3/14) were also detected in the groundwater, whereas the other carboxylic and phenolic PPCPs were not detected and were thought to be removed during their passage through soil. All the data demonstrated the utility of crotamiton and carbamazepine as conservative markers in freshwater and coastal environments. We recommend combining these conservative markers with labile PPCPs to detect inputs of poorly treated sewage. PMID:18800500
Nakada, Norihide; Kiri, Kentaro; Shinohara, Hiroyuki; Harada, Arata; Kuroda, Keisuke; Takizawa, Satoshi; Takada, Hideshige
Molecular Markers of Epithelial-to-Mesenchymal Transition Are Associated with Tumor Aggressiveness in Breast Carcinoma
BACKGROUND: Epithelial-to-mesenchymal transition (EMT) is a transient process occurring during developmental stages and carcinogenesis, characterized by phenotypic and molecular alterations, resulting in increased invasive and metastatic capabilities of cancer cells and drug resistance. Moreover, emerging evidence suggests that EMT is associated with increased enrichment of cancer stem-like cells in neoplastic tissues. We interrogated the molecular alterations occurring in breast cancer using proposed EMT markers such as E-cadherin, vimentin, epidermal growth factor receptor (EGFR), platelet-derived growth factor (PDGF) D, and nuclear factor ?B (NF-?B) to decipher their roles in the EMT and breast cancer progression. METHODS: Fifty-seven invasive ductal adenocarcinomas of the breast were assessed for the expression of E-cadherin, vimentin, EGFR, NF-?B, and PDGF-D using immunohistochemical analysis. Tumors were categorized into three groups: A (ER+, and/or PR+, HER-2/neu-), B (ER+, and/or PR+, HER-2/neu+), and C (triple-negative: ER-, PR-, and HER-2/neu-). Immunostained slides were microscopically evaluated and scored using intensity (0, 1+, 2+, and 3+) and percentage of positive cells, and data were statistically analyzed. RESULTS: Membranous E-cadherin was positive in all 57 cases (100%), whereas cytoplasmic E-cadherin was predominantly positive in groups B and C compared with group A (21%, 7%, and 0%, respectively). All group A cases were negative for vimentin and EGFR. There was statistically significant increased expression of vimentin (P < .0002), EGFR (P < .0001), and NF-?B (P < .02) in triple-negative cases when compared with groups A and B. CONCLUSIONS: Vimentin, EGFR, and NF-?B were significantly increased in triple-negative tumors, which is consistent with the aggressiveness of these tumors. These markers could be useful as markers for EMT in breast cancers and may serve as predictive markers for designing customized therapy in the future.
Sethi, Seema; Sarkar, Fazlul H; Ahmed, Quratulain; Bandyopadhyay, Sudeshna; Nahleh, Zeina A; Semaan, Assaad; Sakr, Wael; Munkarah, Adnan; Ali-Fehmi, Rouba
Source apportionment of primary and secondary organic aerosols using positive matrix factorization (PMF) of molecular markers
NASA Astrophysics Data System (ADS)
Monthly average ambient concentrations of more than eighty particle-phase organic compounds, as well as total organic carbon (OC) and elemental carbon (EC), were measured from March 2004 through February 2005 in five cities in the Midwestern United States. A multi-variant source apportionment receptor model, positive matrix factorization (PMF), was applied to explore the average source contributions to the five sampling sites using molecular markers for primary and secondary organic aerosols (POA, SOA). Using the molecular makers in the model, POA and SOA were estimated for each month at each site. Three POA factors were derived, which were dominated by primary molecular markers such as EC, hopanes, steranes, and polycyclic aromatic hydrocarbons (PAHs), and which represented the following POA sources: urban primary sources, mobile sources, and other combustion sources. The three POA sources accounted for 57% of total average ambient OC. Three factors, characterized by the presence of reaction products of isoprene, ?-pinene and ?-caryophyllene, and displaying distinct seasonal trends, were consistent with the characteristics of SOA. The SOA factors made up 43% of the total average measured OC. The PMF-derived results are in good agreement with estimated SOA concentrations obtained from SOA to tracer yield estimates obtained from smog chamber experiments. A linear regression comparing the smog chamber yield estimates and the PMF SOA contributions had a regression slope of 1.01 � 0.07 and an intercept of 0.19 � 0.10 ?g OC m -3 (adjusted R2 of 0.763, n = 58).
Zhang, YuanXun; Sheesley, Rebecca J.; Schauer, James J.; Lewandowski, Michael; Jaoui, Mohammed; Offenberg, John H.; Kleindienst, Tadeusz E.; Edney, Edward O.
[ISSR markers and their applications in plant genetics].
Recently, inter-simple sequence repeat (ISSR) markers have emerged as an alternative system with reliability and advantages of microsatellites (SSR). The technique involves amplification of genomic segments flanked by inversely oriented and closely spaced microsatellite sequences by a single primer or a pair of primers based on SSRs anchored 5' or 3' with 1-4 purine or pyramidine residues. The sequences of repeats and anchor nucleates are arbitrarily selected. Coupled with the separation of amplification products on a polyacrylamide or agarose gels,ISSR amplification can reveal a much larger number of fragments per primer than RAPD. It is concluded that ISSR technique provides a quick, reliable and highly informative system for DNA fingerprinting.ISSR markers are inherited in Mendelin mode and segregated as dominant markers. This technique has been widely used in the studies of cultivar identification, genetic mapping, gene tagging,genetic diversity, evolution and molecular ecology. PMID:16135460
Wang, Jian-bo
Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data.
Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups. PMID:23178877
van Heerwaarden, Joost; Odong, T L; van Eeuwijk, F A
Determination of specific molecular markers of biomass burning in lake sediments
NASA Astrophysics Data System (ADS)
Fire influences regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine interactions between climate and fire activity. One group of these molecular markers is the monosaccharide anhydrides levoglucosan, mannosan and galactosan. Several aerosol studies and recent ice core research use these compounds as a marker for biomass burning, but studies from lake sediment cores are rare. Previous sediment methods used gas chromatography - mass spectrometry and required derivatization of samples. Here, we present a high performance anion exchange chromatography-mass spectrometry method to allow separation and detection of the three monosaccharide anhydrides in lake sediments with implications for reconstructing past biomass burning events. We validated the method by quantifying levoglucosan, mannosan and galactosan in selected sediment core samples from Lake Kirkpatrick, New Zealand. The freeze-dried, milled and homogenized sediment samples were first extracted with methanol by pressurized solvent extraction, pre-concentrated and finally separated and analyzed by high performance anion exchange chromatography-mass spectrometry. We compared these isomers with macroscopic charcoal concentrations, as charcoal is a well-known proxy for biomass burning. In addition, we applied the method to a sediment core from Lake Pet�n Itz�, Guatemala to prove the suitability of these markers for reconstructing biomass burning history over the entire Holocene. In the Lake Kirkpatrick samples, levoglucosan, mannosan and galactosan concentrations significantly correlate with macroscopic charcoal concentrations. The three isomers are present in samples without any macroscopic charcoal, and may reflect the presence of microscopic charcoal. Levoglucosan/mannosan and levoglucosan/(mannosan+galactosan) ratios differ between samples with high macroscopic charcoal concentrations and samples without any charcoal. These ratios may help determine not only when fires occurred, but also past changes in the primary burned vegetation. However, the possibility that these isomer ratios help differentiate changes in burned vegetation needs further evaluation. The preliminary results of the Lake Pet�n Itz� samples demonstrate the occurrence of all three molecular markers in the entire core, covering the past approximately 10,000 years. The three monosaccharide anhydrides levoglucosan, mannosan and galactosan may be an additional tool for reconstructing past fire events over decadal to millennial time scales in sediment cores.
Kirchgeorg, Torben; Sch�pbach, Simon; Kehrwald, Natalie; McWethy, David; Barbante, Carlo
Transcript profiling and identification of molecular markers for early microspore embryogenesis in Brassica napus.
Isolated microspores of Brassica napus are developmentally programmed to form gametes; however, microspores can be reprogrammed through stress treatments to undergo appropriate divisions and form embryos. We are interested in the identification and isolation of factors and genes associated with the induction and establishment of embryogenesis in isolated microspores. Standard and normalized cDNA libraries, as well as subtractive cDNA libraries, were constructed from freshly isolated microspores (0 h) and microspores cultured for 3, 5, or 7 d under embryogenesis-inducing conditions. Library comparison tools were used to identify shifts in metabolism across this time course. Detailed expressed sequence tag analyses of 3 and 5 d cultures indicate that most sequences are related to pollen-specific genes. However, semiquantitative and real-time reverse transcription-polymerase chain reaction analyses at the initial stages of embryo induction also reveal expression of embryogenesis-related genes such as BABYBOOM1, LEAFY COTYLEDON1 (LEC1), and LEC2 as early as 2 to 3 d of microspore culture. Sequencing results suggest that embryogenesis is clearly established in a subset of the microspores by 7 d of culture and that this time point is optimal for isolation of embryo-specific expressed sequence tags such as ABSCISIC ACID INSENSITIVE3, ATS1, LEC1, LEC2, and FUSCA3. Following extensive polymerase chain reaction-based expression profiling, 16 genes were identified as unequivocal molecular markers for microspore embryogenesis in B. napus. These molecular marker genes also show expression during zygotic embryogenesis, underscoring the common developmental pathways that function in zygotic and gametic embryogenesis. The quantitative expression values of several of these molecular marker genes are shown to be predictive of embryogenic potential in B. napus cultivars (e.g. 'Topas' DH4079, 'Allons,' 'Westar,' 'Garrison'). PMID:17384168
Malik, Meghna R; Wang, Feng; Dirpaul, Joan M; Zhou, Ning; Polowick, Patricia L; Ferrie, Alison M R; Krochko, Joan E
Molecular and serum markers in hepatocellular carcinoma: predictive tools for prognosis and recurrence.
With increased understanding of cancer biology, a multitude of pathological, genetic, and molecular events that drive hepatocarcinogenesis, including angiogenesis, invasion, and metastasis, has been identified. Lately, they are being aggressively evaluated due to challenges involved in establishing early diagnosis, optimizing therapy for cancer inducing hepatotrophic viruses, minimizing the emergence of new tumors, and preventing recurrence after surgical resection or liver transplantation. This comprehensive review examines and critiques the evidence from published manuscripts reporting various tissue and serum biomarkers involved in hepatocellular carcinoma. These markers not only help in prediction of prognosis or recurrence, but may also assist in deciding appropriate modality of therapy and represent novel targets for potential therapeutic agents. PMID:21680198
Singhal, Ashish; Jayaraman, Muralidharan; Dhanasekaran, Danny N; Kohli, Vivek
Bulked segregant analysis to develop molecular markers for salt tolerance in Egyptian cotton
Cotton crop plants are considered salt tolerant fibre plants, their adaptive limits range between 7.5 to 27 mmhos\\/cm. Random Amplified Polymorphic DNA (RAPD) analysis was employed to evaluate, the genetic diversity and genetic relationships among the varieties Dendera, Giza 90, Giza 83, Giza 45 and F1, F2 for (G83 * G45) hybrid. Five random 10-mer primers were used to amplify
D. A. El-Kadi; S. A. Afiah; M. A. Aly; A. E. Badran
Identification and authentication of Rosa species through development of species-specific SCAR marker(s).
Roses (Rosa indica) belong to one of the most crucial groups of plants in the floriculture industry. Rosa species have special fragrances of interest to the perfume and pharmaceutical industries. The genetic diversity of plants based on morphological characteristics is difficult to measure under natural conditions due to the influence of environmental factors, which is why a reliable fingerprinting method was developed to overcome this problem. The development of molecular markers will enable the identification of Rosa species. In the present study, randomly amplified polymorphic DNA (RAPD) analysis was done on four Rosa species, Rosa gruss-an-teplitz (Surkha), Rosa bourboniana, Rosa centifolia, and Rosa damascena. A polymorphic RAPD fragment of 391 bp was detected in R. bourboniana, which was cloned, purified, sequenced, and used to design a pair of species-specific sequence-characterized amplified region (SCAR) primers (forward and reverse). These SCAR primers were used to amplify the specific regions of the rose genome. These PCR amplifications with specific primers are less sensitive to reaction conditions, and due to their high reproducibility, these species-specific SCAR primers can be used for marker-assisted selection and identification of Rosa species. PMID:24938705
Bashir, K M I; Awan, F S; Khan, I A; Khan, A I; Usman, M
Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.
Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. PMID:24125952
Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul
Molecular characterization of Anthurium genotypes by using DNA fingerprinting and SPAR markers.
We characterized single primer amplification reaction (SPAR) molecular markers from 20 genotypes of Anthurium andraeanum Lind., including 3 from commercial varieties and 17 from 2 communities in the State of Esp�rito Santo, Brazil. Twenty-four SPAR, consisting of 7 random amplified polymorphic DNA and 17 inter-simple sequence repeat markers were used to estimate the genetic diversity of 20 Anthurium accessions. The set of SPAR markers generated 288 bands and showed an average polymorphism percentage of 93.39%, ranging from 71.43 to 100%. The polymorphism information content (PIC) of the random amplified polymorphic DNA primers averaged 0.364 and ranged from 0.258 to 0.490. Primer OPF 06 showed the lowest PIC, while OPAM 14 was the highest. The average PIC of the inter-simple sequence repeat primers was 0.299, with values ranging from 0.196 to 0.401. Primer UBC 845 had the lowest PIC (0.196), while primer UCB 810 had the highest (0.401). By using the complement of Jaccard's similarity index and unweighted pair group method with arithmetic mean clustering, 5 clusters were formed with a cophenetic correlation coefficient of 0.8093, indicating an acceptable clustering consistency. However, no genotype clustering patterns agreed with the morphological data. The Anthurium genotypes investigated in this study are a germplasm source for conservational research and may be used in improvement programs for this species. PMID:25062412
Souza Neto, J D; Soares, T C B; Motta, L B; Cabral, P D S; Silva, J A
Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma
Background. Carcinomas of the breast with neuroendocrine features are incorporated in the World Health Organization classification since 2003 and include well-differentiated neuroendocrine tumors, poorly differentiated neuroendocrine carcinomas/small cell carcinomas, and invasive breast carcinomas with neuroendocrine differentiation. Neuroendocrine differentiation is known to be more common in certain low-grade histologic special types and has been shown to mainly cluster to the molecular (intrinsic) luminal A subtype. Methods. We analyzed the frequency of neuroendocrine differentiation in different molecular subtypes of breast carcinomas of no histologic special type using immunohistochemical stains with specific neuroendocrine markers (chromogranin A and synaptophysin). Results. We found neuroendocrine differentiation in 20% of luminal B-like carcinomas using current WHO criteria (at least 50% of tumor cells positive for synaptophysin or chromogranin A). In contrast, no neuroendocrine differentiation was seen in luminal A-like, HER2 amplified and triple-negative carcinomas. Breast carcinomas with neuroendocrine differentiation presented with advanced stage disease and showed aggressive behavior. Conclusions. We conclude that neuroendocrine differentiation is more common than assumed in poorly differentiated luminal B-like carcinomas. Use of specific neuroendocrine markers is thus encouraged in this subtype to enhance detection of neuroendocrine differentiation and hence characterize the biological and therapeutic relevance of this finding in future studies.
Wachter, David L.; Hartmann, Arndt; Beckmann, Matthias W.; Fasching, Peter A.; Hein, Alexander; Bayer, Christian M.; Agaimy, Abbas
Identification of Leaf Rust Resistance Genes in Selected Egyptian Wheat Cultivars by Molecular Markers
Leaf rust, caused by Puccinia triticina Eriks., is a common and widespread disease of wheat (Triticum aestivum L.) in Egypt. Host resistance is the most economical, effective, and ecologically sustainable method of controlling the disease. Molecular markers help to determine leaf rust resistance genes (Lr genes). The objective of this study was to identify Lr genes in fifteen wheat cultivars from Egypt. Ten genes, Lr13, Lr19, Lr24, Lr26, Lr34, Lr35 Lr36, Lr37, Lr39, and Lr46, were detected in fifteen wheat cultivars using various molecular markers. The most frequently occurring genes in fifteen Egyptian wheat cultivars were Lr13, Lr24, Lr34, and Lr36 identified in all the cultivars used, followed by Lr26 and Lr35 (93%), Lr39 (66%), Lr37 (53%), and Lr46 (26.6%) of the cultivars, and finally Lr19 was present in 33.3% of cultivars. It is concluded that there was a good variation in Lr genes carried by wheat cultivars commercially grown in Egypt. Therefore, strategies for deploying resistance genes to prolong effective disease resistance are suggested to control wheat leaf rust disease.
Imbaby, I. A.; Mahmoud, M. A.; Hassan, M. E. M.; Abd-El-Aziz, A. R. M.
Molecular Marker Differences Relate to Developmental Position and Subsets of Mesodiencephalic Dopaminergic Neurons
The development of mesodiencephalic dopaminergic (mdDA) neurons located in the substantia nigra compacta (SNc) and ventral tegmental area (VTA) follow a number of stages marked by distinct events. After preparation of the region by signals that provide induction and patterning, several transcription factors have been identified, which are involved in specifying the neuronal fate of these cells. The specific vulnerability of SNc neurons is thought to root in these specific developmental programs. The present study examines the positions of young postmitotic mdDA neurons to relate developmental position to mdDA subset specific markers. MdDA neurons were mapped relative to the neuromeric domains (prosomeres 1-3 (P1-3), midbrain, and hindbrain) as well as the longitudinal subdivisions (floor plate, basal plate, alar plate), as proposed by the prosomeric model. We found that postmitotic mdDA neurons are located mainly in the floorplate domain and very few in slightly more lateral domains. Moreover, mdDA neurons are present along a large proportion of the anterior/posterior axis extending from the midbrain to P3 in the diencephalon. The specific positions relate to some extent to the presence of specific subset markers as Ahd2. In the adult stage more of such subsets specific expressed genes are present and may represent a molecular map defining molecularly distinct groups of mdDA neurons.
Smits, Simone M.; von Oerthel, Lars; Hoekstra, Elisa J.; Burbach, J. Peter H; Smidt, Marten P.
Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori
Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.81050bp was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.51950bp and 825.9710bp showed significant association with floss content and TLD. These markers were segregated in F2 generation and Chi-square test confirmed (?2 = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 � 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight.
Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S
Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori.
Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.8(1050bp) was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.5(1950bp) and 825.9(710bp) showed significant association with floss content and TLD. These markers were segregated in F(2) generation and Chi-square test confirmed (chi(2) = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 +/- 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight. PMID:19662204
Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S
At3g08030 transcript: a molecular marker of seed ageing
Background and Aims Prolonged storage generally reduces seed viability and vigour, although the rate of deterioration varies among species and environmental conditions. Here, we suggest a possible ageing molecular marker: At3g08030 mRNA. At3g08030 is a member of the DUF642 highly conserved family of cell-wall-associated proteins that is specific for spermatophytes. Methods At3g08030 expression was performed by RT-PCR and qRT-PCR analysis in seed samples differing in their rate of germination and final germination following a matrix priming and/or controlled deterioration (rapid ageing) treatment. Key Results The At3g08030 gene transcript was present during the entire Arabidopsis thaliana plant life cycle and in seeds, during maturation, the ripening period and after germination. Matrix priming treatment increased the rate of germination of control seeds and seeds aged by controlled deterioration. Priming treatments also increased At3g08030 expression. To determine whether the orthologues of this gene are also age markers in other plant species, At3g08030 was cloned in two wild species, Ceiba aesculifolia and Wigandia urens. As in A. thaliana, the At3g08030 transcript was not present in aged seeds of the tested species but was present in recently shed seeds. A reduction in germination performance of the aged seeds under salt stress was determined by germination assays. Conclusions At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species.
Garza-Caligaris, Luz Elena; Avendano-Vazquez, Aida Odette; Alvarado-Lopez, Sandra; Zuniga-Sanchez, Esther; Orozco-Segovia, Alma; Perez-Ruiz, Rigoberto V.; Gamboa-deBuen, Alicia
Status of potential PfATP6 molecular markers for artemisinin resistance in Suriname
Background Polymorphisms within the PfATP6 gene have been indicated as potential molecular markers for artemisinin efficacy. Since 2004, the use of artemisinin combination therapy (ACT) was introduced as first-line treatment of the uncomplicated malaria cases in Suriname. The aim of this research was to determine changes in Suriname in the status of the polymorphic markers in the PfATP6 gene before and after the adoption of the ACT-regimen, particularly of the S769N mutation, which was reported to be associated with in vitro Artemether resistance in the neighboring country French Guiana. Methods The PfATP6 gene from Plasmodium falciparum parasites in Suriname was investigated in 28 samples using PCR amplification and restriction enzyme analysis, to assess and determine the prevalence of potentially interesting single nucleotide polymorphisms. The polymorphisms [L263E; A623E; S769N], which may be associated with the artemisinin resistant phenotype were characterized in parasites from three endemic regions before and after the adoption of the ACT-regimen. In addition, the status of these molecular markers was compared in paired P. falciparum isolates from patients with recurring malaria after controlled ACT. Results All the investigated samples exhibit the wild-type genotype at all three positions; L263, A623, S769. Conclusion All investigated isolates before and after the adoption of the ACT-regimen and independent of endemic region harbored the wild-type genotype for the three investigated polymorphisms. The study revealed that decreased artemisinin susceptibility could occur independent from PfATP6 mutations, challenging the assumption that artemisinin resistance is associated with these mutations in the PfATP6 gene.
Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery
Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus.
Use of RAPD for the study of diversity within plant germplasm collections
As part of the development of a molecular toolkit for the study of diversity within large plant germplasm collections, RAPD technology has been applied to accessions of rice (Oryza sativa) obtained from the major world collection held at IRRI (the International Rice Research Institute) which supplies germplasm to breeders. Methods for the speedy extraction of DNA representative of a rice
Parminder S Virk; Brian V Ford-Lloyd; Michael T Jackson; H John Newbury
Angelman syndrome: three molecular classes identified with chromosome 15q11q13-specific DNA markers.
Angelman syndrome (AS) and Prader-Willi syndrome (PWS) share a cytogenetic deletion of chromosome 15q11q13. To determine the extent of deletion in AS we analyzed the DNA of 19 AS patients, including two sib pairs, with the following chromosome 15q11q13--specific DNA markers: D15S9-D15S13, D15S17, D15S18, and D15S24. Three molecular classes were identified. Class I showed a deletion of D15S9-D15S13 and D15S18; class II showed a deletion of D15S9-D15S13; and in class III, including both sib pairs, no deletion was detected. These molecular classes appear to be identical to those observed in PWS. High-resolution cytogenetic data were available on 16 of the patients, and complete concordance between the presence of a cytogenetic deletion and a molecular deletion was observed. No submicroscopic deletions were detected. DNA samples from the parents of 10 patients with either a class I or a class II deletion were available for study. In seven of the 10 families, RFLPs were informative as to the parental origin of the deletion. In all informative families, the deleted chromosome 15 was observed to be of maternal origin. This finding is in contrast to the paternal origin of the deletions in PWS and is currently the only molecular difference observed between the two syndromes. PMID:1971993
Knoll, J H; Nicholls, R D; Magenis, R E; Glatt, K; Graham, J M; Kaplan, L; Lalande, M
Typing of Salmonella Typhi strains isolated from Egypt by RAPD PCR.
PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) has been used widely for genome identification. In this study, 13 Salmonella Typhi strains were isolated from typhoid patients from Aswan, Cairo, Fayoum, and Monofya Governorates of Egypt. The isolates, along with three reference strains, i.e., O901, H901, and Ty2 were subjected to whole genome typing by RAPD PCR. Three RAPD-PCR 10-mer primers generated a total of 85 RAPD bands (81 polymorphic bands), 12 distinct PCR profiles, and proved to be useful for discriminating the isolates and strains studied. Interestingly, the B(1) and C(1) PCR profile were found only in Cairo and Monofya, respectively; and some PCR types appeared only in certain Governorates of Egypt. By combining the profiles obtained with the primer trio used in this study, an excellent discrimination index (D) of 0.942 was reached. Pairwise comparisons of Jaccard's similarity coefficients calculated among the 12 PCR types identified three major clusters; i.e., O901 branch and Ty2 and H901 sub-branches. Principal component analysis adequately resolved each of these three major clusters. Three principal components accounted for about 72% of the variation, with the first two components accounting for about 62% of the total variance among the genotypes studied. Biclustering improved the display of groups of RAPD amplicons (markers) that cluster similarly across the genomes and could delineate features pertaining to genome structure. In conclusion, RAPD PCR provided a fast method with high potentials in surveillance and epidemiological investigations of Salmonella Typhi infections. PMID:22582153
Rezk, Noha A; Mansour, Hoda; Ghoneim, Nahed H; Rifaat, Mahmoud M
A sex-associated sequence identified by RAPD screening in gynogenetic individuals of turbot (Scophthalmus maximus).
Understanding the genetic basis of sex determination mechanisms is essential for improving the productivity of farmed aquaculture fish species like turbot (Scophthalmus maximus). In culture conditions turbot males grow slower than females starting from eight months post-hatch, and this differential growth rate is maintained until sexual maturation is reached, being mature females almost twice as big as males of the same age. The goal of this study was to identify sex-specific DNA markers in turbot using comparative random amplified polymorphism DNA (RAPD) profiles in males and females to get new insights of the genetic architecture related to sex determination. In order to do this, we analyzed 540 commercial 10-mer RAPD primers in male and female pools of a gynogenetic family because of its higher inbreeding, which facilitates the detection of associations across the genome. Two sex-linked RAPD markers were identified in the female pool and one in the male pool. After the analysis of the three markers on individual samples of each pool and also in unrelated individuals, only one RAPD showed significant association with females. This marker was isolated, cloned and sequenced, containing two sequences, a microsatellite (SEX01) and a minisatellite (SEX02), which were mapped in the turbot reference map. From this map position, through a comparative mapping approach, we identified Foxl2, a relevant gene related to initial steps of sex differentiation, and Wnt4, a gene related with ovarian development, close to the microsatellite and minisatellite markers, respectively. The position of Foxl2 and Wnt4 was confirmed by linkage mapping in the reference turbot map. PMID:24415295
Vale, Luis; Dieguez, Rebeca; S�nchez, Laura; Mart�nez, Paulino; Vi�as, Ana
Apportioning black carbon to sources using highly time-resolved ambient measurements of organic molecular markers in Pittsburgh
We present highly time-resolved measurements of organic molecular markers in downtown Pittsburgh, which are used to investigate sources contributing to atmospheric aerosols in the area. Two-hour average concentrations of condensed-phase and semivolatile organic species were measured using a Thermal Desorption Aerosol GC\\/MS (TAG). Concentrations for mobile source markers like hopanes had regular diurnal and day-of-week patterns. Pairing high time-resolved measurements
Andrew T. Lambe; Jennifer M. Logue; Nathan M. Kreisberg; Susanne V. Hering; David R. Worton; Allen H. Goldstein; Neil M. Donahue; Allen L. Robinson
The semidwarf gene, sd-1, of rice ( Oryza sativa L.). II. Molecular mapping and marker-assisted selection
To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from
Y. G. Cho; M. Y. Eun; S. R. McCouch; Y. A. Chae
Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?
Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies. PMID:21472410
Odong, T L; van Heerwaarden, J; Jansen, J; van Hintum, T J L; van Eeuwijk, F A
Multi-marker Solid Tumor Panels Using Next-generation Sequencing to Direct Molecularly Targeted Therapies
In contemporary oncology practices there is an increasing emphasis on concurrent evaluation of multiple genomic alterations within the biological pathways driving tumorigenesis. At the foundation of this paradigm shift are several commercially available tumor panels using next-generation sequencing to develop a more complete molecular blueprint of the tumor. Ideally, these would be used to identify clinically actionable variants that can be matched with available molecularly targeted therapy, regardless of the tumor site or histology. Currently, there is little information available on the post-analytic processes unique to next-generation sequencing platforms used by the companies offering these tests. Additionally, evidence of clinical validity showing an association between the genetic markers curated in these tests with treatment response to approved molecularly targeted therapies is lacking across all solid-tumor types. To date, there is no published data of improved outcomes when using the commercially available tests to guide treatment decisions. The uniqueness of these tests from other genomic applications used to guide clinical treatment decisions lie in the sequencing platforms used to generate large amounts of genomic data, which have their own related issues regarding analytic and clinical validity, necessary precursors to the evaluation of clinical utility. The generation and interpretation of these data will require new evidentiary standards for establishing not only clinical utility, but also analytical and clinical validity for this emerging paradigm in oncology practice.
Marrone, Michael; Filipski, Kelly K; Gillanders, Elizabeth M; Schully, Sheri D; Freedman, Andrew N
Caracterizaci�n de la diversidad gen�tica en el pez Brycon henni (Characiformes: Characidae) en Colombia central por medio de marcadores RAPD
Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae) in central Colombia with RAPD markers. Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished
Hermes Pineda Santis; Lucy Arboleda Chac�n; Amparo Echeverry Echavarria; Silvio Urcuqui Inchima; Diego Pareja Molina; Martha Olivera �ngel; Juan Builes G�mez
Association of molecular markers with cold tolerance and green period in zoysiagrass (Zoysia Willd.)
Cold tolerance and the green period are key traits in the breeding of zoysiagrass (Zoysia Willd.). Identification of molecular markers associated with cold tolerance and the green period of zoysiagrass will contribute to efficient selection of elite cultivars. These two traits were measured in 96 zoysiagrass accessions in 2004 and 2005�2006, respectively. The mapping population was screened with 29 pairs of simple sequence repeat (SSR) primers and 54 pairs of sequence-related amplified polymorphism (SRAP) primers. A multi-loci in silico mapping approach implemented with an empirical Bayes method was applied for association mapping of cold tolerance and green period. We detected 254 SSR polymorphic loci and 338 SRAP polymorphic loci, among which three SSR loci (Xgwm131-3B-187, Xgwm469-6D-194 and Xgwm234-5B-244) and one SRAP locus (Me11Em7-406) were significantly associated with cold tolerance with effect values of 57.83%, 38.05%, 36.92% and 37%, respectively. Three SSR loci (Xgwm132-6B-225, Xgwm111-7D-34 and Xgwm102-2D-97) and two SRAP loci (Me19Em5-359 and Me16Em8-483) were significantly associated with the green period with effect values of 79.54%, 62.59%, 99.04%, 49.01% and 82.57%. These markers will be useful for genetic improvement of the cold tolerance and green period of zoysiagrass by marker-assisted breeding.
Guo, Hai-Lin; Xuan, Ji-Ping; Liu, Jian-Xiu; Zhang, Yuan-Ming; Zheng, Yi-Qi
Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers.
The genus Astreopora is a small but ancestral group in Acroporidae, which is one of the most diverse and dominant families of scleractinian coral in Indo-Pacific reefs. We estimated the species boundaries of Astreopora corals using two molecular markers: a mitochondrial non-coding region and a nuclear ribosomal 5.8S region. Seven species (59 specimens) commonly observed around Japan (Astreopora expansa, A. gracilis, A. incrustans, A. listeri, A. myriophthalma, A. cf. suggesta, and Astreopora sp.1) were investigated, and we observed no genetic divergence in the mitochondrial marker, suggesting that these species are closely related, consistent with a species complex or recent divergence, although genotyping by the marker is not so sensitive. In the nuclear 5.8S region, 121 clones consisted of six species were divided into the four major genetic groups. Although there were no monophyletic clades, the two dominant species A. myriophthalma and A. gracilis rarely shared the same haplotypes, suggesting that gene flow is limited between them. However, A. incrustans frequently shared the same haplotypes with A. gracilis although the distributions do not overlap. We found that the ancestral genus Astreopora in Acroporidae shows less genetic variation than traditionally identified morphospecies. Although further research on fertilization rate among these species is required to determine if there are reproductive barriers, the low level of genetic diversification in this genus hints that some ecological differences among acroporid corals play a role in the evolution of scleractinian corals, considering that the other members of this family, Acropora and Montipora, are highly diversified. PMID:23915155
Suzuki, Go; Nomura, Keiichi
Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.
The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods. PMID:21867972
C�rdenas, Leyla; S�nchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Esc�rate, Cristi�n; Tanguy, Arnaud
Molecular marker analysis as a guide to the sources of fine organic aerosols
The molecular composition of fine particulate (D[sub p] [ge] 2 [mu]m) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available.
Rogge, W.F.; Cass, G.R. (California Inst. of Tech., Pasadena, CA (United States)); Hildemann, L.M. (Stanford Univ., CA (United States). Dept. of Civil Engineering); Mazurek, M.A. (Brookhaven National Lab., Upton, NY (United States)); Simoneit, B.R.T. (College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group)
Molecular marker analysis as a guide to the sources of fine organic aerosols
The molecular composition of fine particulate (D{sub p} {ge} 2 {mu}m) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available.
Rogge, W.F.; Cass, G.R. [California Inst. of Tech., Pasadena, CA (United States); Hildemann, L.M. [Stanford Univ., CA (United States). Dept. of Civil Engineering; Mazurek, M.A. [Brookhaven National Lab., Upton, NY (United States); Simoneit, B.R.T. [College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group
Efficacy, safety, and selection of molecular markers of drug resistance by two ACTs in Mali.
We conducted a randomized single-blinded trial comparing the efficacy and safety of artesunate (AS) + amodiaquine (AQ, 3 days) versus AS (3 days) + sulfadoxine-pyrimethamine (SP, single dose) versus AS monotherapy (5 days) in Southern Mali. Uncomplicated malaria cases were followed for 28 days. Molecular markers of drug resistance were determined. After identification of recrudescences by genotyping, both artemisinin-based combination therapies (ACTs) reached nearly 100% efficacy at Day 14 and Day 28 versus 98.3% and 96.5% for AS, respectively (P > 0.05). AS + SP significantly selected DHFR and DHPS mutations associated with sulfadoxine and pyrimethamine resistance (P < 0.001), and AS + AQ equally selected PfCRT and PfMDR1 point mutations associated with chloroquine and AQ resistance (P < 0.001). No significant adverse event attributable to any of the study drugs was found. The ACTs were efficacious and safe, but the selection of markers for resistance to the partner drugs raises concerns over their lifespan in areas of intense malaria transmission. PMID:18337343
Djimd�, Abdoulaye A; Fofana, Bakary; Sagara, Issaka; Sidibe, Bakary; Toure, Sekou; Dembele, Demba; Dama, Souleymane; Ouologuem, Dinkorma; Dicko, Alassane; Doumbo, Ogobara K
Identification of the sources of primary organic aerosols at urban schools: A molecular marker approach.
Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children's exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools. PMID:24842381
Crilley, Leigh R; Qadir, Raeed M; Ayoko, Godwin A; Schnelle-Kreis, J�rgen; Abbaszade, G�lcin; Orasche, J�rgen; Zimmermann, Ralf; Morawska, Lidia
2007 EORTC-NCI-ASCO Annual Meeting: Molecular Markers in Cancer
The recent EORTC-NCI-ASCO Annual Meeting on �Molecular Markers in Cancer� was held on 15�17 November 2007 in Brussels, Belgium. It was the largest meeting to date and marked the first year in which the American Association of Clinical Oncology (ASCO) joined in the efforts of the European Organisation for Research and Treatment of Cancer (EORTC) and the National Cancer Institute (NCI) in organizing this annual event. More than 300 clinicians, pathologists, laboratory scientists and representatives from regulatory agencies and the pharmaceutical industry came together for three days of intense discussion, debate and reflection on the latest biomarker therapeutic discoveries, strategies and clinical applications. The poster discussion sessions featured 79 research abstracts. The three most outstanding abstracts, all authored by young female researchers, were selected for presentation during the main meeting sessions. Highlights of each scientific session are presented.
Lukan, C
Triazole-based Zn(2+)-specific molecular marker for fluorescence bioimaging.
Fluorescence bioimaging potential, both in vitro and in vivo, of a yellow emissive triazole-based molecular marker has been investigated and demonstrated. Three different kinds of cells, viz Bacillus thuringiensis, Candida albicans, and Techoma stans pollen grains were used to investigate the intracellular zinc imaging potential of 1 (in vitro studies). Fluorescence imaging of translocation of zinc through the stem of small herb, Peperomia pellucida, having transparent stem proved in vivo bioimaging capability of 1. This approach will enable in screening cell permeability and biostability of a newly developed probe. Similarly, the current method for detection and localization of zinc in Gram seed sprouts could be an easy and potential alternative of the existing analytical methods to investigate the efficiency of various strategies applied for increasing zinc-content in cereal crops. The probe-zinc ensemble has efficiently been applied for detecting phosphate-based biomolecules. PMID:24725748
Sinha, Sougata; Mukherjee, Trinetra; Mathew, Jomon; Mukhopadhyay, Subhra K; Ghosh, Subrata
Constancy of RAPD primer amplification strength among distantly related taxa of flowering plants
A survey of 480 10-mer primers for RAPD markers revealed general consistency in primer amplification strength among the flowering\\u000a plant generaDatisca, Helianthus andYucca. Six characteristics of primer base sequences were analyzed: total (G+C) content; the amounts of G, A, C, and T taken separately;\\u000a and the (G+C) content in the last four bases of the 3? end. Of these, total
Peter Fritsch; Michael A. Hanson; Chrystal D. Spore; Phillip E. Pack; Loren H. Rieseberg
Relationships among some cornelian cherry genotypes ( Cornus mas L.) based on RAPD analysis
Turkey is an important producer of cornelian cherries (Cornus mas L.), especially in northern Anatolia. Seed propagation and long-term human selection has given rise to a great diversity\\u000a of trees. Twenty-six cornelian cherry genotypes (CC1�CC26) from the Coruh Valley in northern Anatolia were evaluated for genetic\\u000a relationships by using Randomly Amplified Polymorphic DNA (RAPD) markers, based on 56 decamer random
Sezai Ercisli; Emine Orhan; Ahmet Esitken; Nalan Yildirim; Guleray Agar
UHRF1 is a novel molecular marker for diagnosis and the prognosis of bladder cancer
Background: Bladder cancer is the second most common cancer of the urinary system. Early diagnosis of this tumour and estimation of risk of future progression after initial transuretherial resection have a significant impact on prognosis. Although there are several molecular markers for the diagnosis and prognosis for this tumour, their accuracy is not ideal. Previous reports have shown that UHRF1 (ubiquitin-like with PHD and ring-finger domains 1) is essential for cellular proliferation. In this study, we examined whether UHRF1 can be a novel molecular marker of bladder cancer. Methods: We performed real-time TaqMan quantitative reverse transcription�PCR and immunohistochemistry to examine expression levels of UHRF1 in bladder and kidney cancers. Results: Significant overexpression of UHRF1 was observed in bladder cancer. The overexpression was correlated with the stage and grade of the cancer. Although UHRF1 expression in muscle-invasive cancer was greater than in non-invasive (pTa) or superficially invasive (pT1) cancers, UHRF1 could still be detected by immunohistochemistry in these early-stage cancers. Overexpression of UHRF1 in bladder cancer was associated with increased risk of progression after transurethral resection. High expression of UHRF1 in kidney cancer was also observed. But the increased levels of UHRF1 in kidney cancer were less significant compared with those in bladder cancer. Conclusion: Our result indicates that an immunohistochemistry-based UHRF1 detection in urine sediment or surgical specimens can be a sensitive and cancer-specific diagnostic and/or prognosis method, and may greatly improve the current diagnosis based on cytology.
Unoki, M; Kelly, J D; Neal, D E; Ponder, B A J; Nakamura, Y; Hamamoto, R
Genetic variation of Usnea filipendula (Parmeliaceae) populations in western Germany investigated by RAPDs suggests reinvasion from various sources.
Random amplified polymorphic DNA (RAPD) markers were characterized for 25 specimens of Usnea filipendula to evaluate the genetic diversity of populations reinvading formerly uninhabited regions in Northrhine-Westphalia due to decreasing sulfur dioxide levels. With six 10-mer randomly amplified polymorphic DNA (RAPD) primers, a 66 character by 25 specimens matrix was generated. Phenetic analysis (UPGMA) showed no obvious groupings. The reinvading populations are distributed over the phenogram and are not genetically closely related. The results suggest that the reinvading populations of this usually sterile species are derived from different sources and do not consist of a particular clone capable of re-entering the area. PMID:10330079
Heibel, E; Lumbsch, H T; Schmitt, I
Molecular markers from three organellar genomes unravel complex taxonomic relationships within the coralline algal genus Chiharaea (Corallinales, Rhodophyta).
The use of molecular markers in taxonomic studies has become a standard practice in biology. However, consensus on which markers to use at the species level is lacking because evolutionary lineages show differences in divergence rates between organellar genomes. Ideally, researchers use multiple lines of evidence when first describing a species, such as the incorporation of several molecular markers from varied genomes (mitochondrion, plastid and nucleus). This study examined species boundaries in the red algal genus Chiharaea. We used five molecular markers, with at least one marker from each genome, coupled with thorough morphological analyses. We recognized three species in Chiharaea (C.americana, C. rhododactyla sp. nov., C. silvae) and two forms (C. americana f. americana and C. americana f. bodegensis (H.W. Johansen) stat. nov.). For C. americana f. americana and C. americana f. bodegensis differentiation based on morphological data was reflected in the plastid-encoded large subunit of RuBisCO (rbcL), but was not concordant with either the mitochondrial cytochrome c oxidase subunit 1 (COI-5P) or nuclear internal transcribed spacer (ITS) sequence data. We suggest that this discordance is indicative of ongoing hybridization and introgression between populations of C. americana f. americana and C. americana f. bodegensis. In addition, we used a PCR assay with ITS specific primers to amplify multiple ITS variants for collections assignable to C. americana indicating that there is genetic variability within ITS copies most likely due to introgression, crossing over and/or the retention of ancestral variants. PMID:23467004
Hind, Katharine R; Saunders, Gary W
Survivin as a prognostic/predictive marker and molecular target in cancer therapy.
Evasion from apoptotic cell death is reported to be a pivotal mechanism by which tumor cells acquire resistance to therapeutic treatment. Targeting the apoptotic pathways may constitute a promising strategy to counteract therapy resistance and to re-sensitize cancer cells. Expression of survivin, the smallest and structurally unique member of the inhibitor of apoptosis protein (IAP) family, has been shown to be associated with poor clinical outcome, more aggressive clinicopathologic features and resistance to both, conventional chemo and radiation therapy. Moreover, survivin detection in cancer tissue, in circulating tumor cells and in patient's serum has prognostic and predictive relevance and may display a prerequisite for marker based molecular therapies. Indeed, due to its universal over expression in malignant tissue, and its prominent role at disparate networks of cellular division, intracellular signaling, apoptosis and adaption to unfavorable surroundings, survivin has been shown to be a suitable target for a targeted therapy. The applicability of survivindriven strategies in clinical practice is currently under investigation as the first survivin antagonists (small molecule inhibitors, antisense oligonucleotides and immunotherapy) successfully entered phase I/II trials. Taken together, these data provide a rationale for the implementation of both, survivin as a molecular diagnostic tool and survivin targeted therapies, within future clinical practice. PMID:22680927
R�del, F; Sprenger, T; Kaina, B; Liersch, T; R�del, C; Fulda, S; Hehlgans, S
Transcriptomic molecular markers for screening human colon cancer in stool and tissue.
There is a need for sensitive and specific diagnostic molecular markers that can be used to monitor early patterns of gene expression in non-invasive exfoliated colonocytes shed in the stool, and in situ in adenoma-carcinoma epithelium of the colon. RNA-based detection methods are more comprehensive than either DNA-, protein- or methylation-based screening methods. By routinely and systematically being able to perform quantitative gene expression studies on these samples using less than ten colon cancer genes selected by the enormous resources of the National Cancer Institute's Cancer Genome Anatomy Project, we were able to monitor changes at various stages in the neoplastic process, allowing for reliable diagnostic screening of colon cancer particularly at the early, pre-malignant stages. Although the expression of some of the genes tested in tissue showed less variability in normal or cancerous patients than in stool, the stool by itself is suitable for screening. Thus, a transcriptomic approach using stool or tissue samples promises to offer more sensitivity and specificity than currently used molecular screening methods for colon cancer. A larger prospective clinical study utilizing stool and tissue samples derived from many control and colon cancer patients, to allow for a statistically valid analysis, is now urgently required to determine the true sensitivity and specificity of the transcriptomic screening approach for this preventable cancer. PMID:17726236
Ahmed, Farid E; Vos, Paul; iJames, Stephanie; Lysle, Donald T; Allison, Ron R; Flake, Gordon; Sinar, Dennis R; Naziri, Wade; Marcuard, Stefan P; Pennington, Rodney
[Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].
Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic passports. PMID:21446184
Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V
High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding.
A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. A BAC clone anchoring Bn-FAE1.1 from a B. rapa BAC library and a BAC clone anchoring Bn-FAE1.2 from a B. oleracea BAC library were used in this research. After sequencing the gene flanking regions, it was found that the dissimilarity of the flanking sequences of these two FAE1 homologs facilitated the design of genome-specific primers that could amplify the corresponding genome in allotetraploid B. napus. The two-base deletion in the C genome gene was detected as a sequence-characterized amplified region (SCAR) marker. To increase the throughput, one genome-specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. Eventually, a super pool of 80 samples was detected simultaneously. This dramatically reduces the cost of marker detection. The single base change in the Bn-FAE1.1 gene was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5' primer end to increase SNP detection throughput through sample pooling. Furthermore, the Bn-FAE1.1 and Bn-FAE1.2 were integrated into the N8 and N13 linkage groups of our previously reported high-density sequence-related amplified polymorphism (SRAP) map, respectively. There were 124 SRAP markers in a N8 bin in which the Bn-FAE1.1 gene-specific SCAR marker was located and 46 SRAP markers in a N13 bin into which the Bn-FAE1.2 SNP marker was integrated. These three kinds of high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. PMID:18633592
Rahman, Mukhlesur; Sun, Zudong; McVetty, Peter B E; Li, Genyi
Ribosomal DNA as molecular markers and their applications in the identification of fish parasites (Platyhelminthes: Monogenea) from India
The development of molecular techniques for taxonomic analysis of monogenean parasites has led to a great increase for proper identification and factualness. These molecular techniques, in particular the use of molecular markers, have been used to identify and validate the monogenean parasites. Although, improvements in marker detection systems particularly of elements of rDNA like 18S, ITS and 28S used in monogeneans parasites have enabled great advances to be made in recent years in India. However, the molecular sequence analysis and phylogenetic relationships among the parasitic helminthes is unconventional in India. Many workers have been always questioned the validity of Indian species of monogeneans and emphasized the need to ascertain the status of species from Indian fish. Here we would like to provide additional resolution for the interpretation of use of molecular markers in study of monogeneans in India. This review provides an overview of current stage of studies in India that have been used in applying molecular techniques to monogenean.
Chaudhary, Anshu; Verma, Chandni; Singh, Hridaya Shanker
Molecular markers predictive of the capacity of expanded human articular chondrocytes to form stable cartilage in vivo
Objective. To establish a model and associated molecular markers for monitoring the capacity of in vitro-expanded chondrocytes to generate stable carti- lage in vivo. Methods. Adult human articular chondrocytes (AHAC) were prepared by collagenase digestion of samples obtained postmortem and were expanded in monolayer. Upon passaging, aliquots of chondrocyte suspensions were either injected intramuscularly into nude mice, cultured in agarose,
Francesco Dell'Accio; Cosimo De Bari; Frank P. Luyten
Molecular Markers for Detection and Differentiation of Plasmodium falciparum and Plasmodium vivax in Human Blood Samples by Pyrosequencing
PCR amplification coupled with pyrosequencing was used to measure molecular markers that could be used to detect and differentiate Plasmodium falciparum and Plasmodium vivax in human blood samples. The detection rates were in agreement with the results of Giemsa-stained film microscopy, which is the current gold standard for detection. This method provides an exciting alternative for malaria diagnosis.
Lulitanond, Viraphong; Intapan, Pewpan M.; Tantrawatpan, Chairat; Sankuntaw, Nipaporn; Sanpool, Oranuch; Janwan, Penchom
Prevalence, Morphologic Features and Proliferation Indices of Breast Carcinoma Molecular Classes Using Immunohistochemical Surrogate Markers
There is dearth of studies that provide a practical working formulation of breast cancer gene expression analysis for the surgical pathologist. ER, PR, HER2 were used as surrogate markers to classify 205 breast carcinomas into molecular classes. Ki-67 labeling index was calculated using an image analysis system. The data was analyzed for molecular class prevalence, and inter-relationships amongst morphologic parameters, Ki-67 index, and molecular classes. Of the 205 tumors, 113 (55%) were classified as luminal A (strong ER+, HER2 negative), 34 (17%) as luminal B (weak to moderate ER+, HER2 negative), 32 (15%) as triple negative (negative for ER/PR and HER2), 8 (4%) as ERBB2 (negative for ER/PR but HER2+), 10 (5%) as luminal A-HER2 hybrid (strong ER+ and HER2+), and 8 (4%) as luminal B-HER2 hybrid (weak to moderate ER+ and HER2+). The average Ki-67 index was lowest in luminal A (15.8%), intermediate for ERBB2 (27.8%) and highest for triple negative tumors (>50%). Multivariate logistic regression analyses found the following associations: ERBB2 tumors with apocrine differentiation (p=0.0031); Triple negative tumors with high Ki-67 index (p<0.0001) and CK5 positivity (p<0.0001); HER2 negative-low receptor positive tumors (luminal B) with increased lymph node involvement (p=0.0141). The immunohistologic criteria were validated on a different set of 359 cases treated with neoadjuvant chemotherapy, which showed a pathologic complete response predominantly in ERBB2 and triple negative tumors. Immunohistochemistry is a reliable surrogate tool to classify breast carcinoma according to the gene expression profile classification.
Bhargava, Rohit; Striebel, Joan; Beriwal, Sushil; Flickinger, John C.; Onisko, Agnieszka; Ahrendt, Gretchen; Dabbs, David J.
Laboratory studies of oxidation of primary emissions: Oxidation of organic molecular markers and secondary organic aerosol production
NASA Astrophysics Data System (ADS)
Particulate matter (PM) is solid particles and liquid droplets of complex composition suspended in the atmosphere. In 1997, the National Ambient Air Quality Standards (NAAQS) for PM was modified to include new standards for fine particulate (particles smaller than 2.5mum, PM2.5) because of their association with adverse health effects, mortality and visibility reduction. Fine PM may also have large impacts on the global climate. Chemically, fine particulate is a complex mixture of organic and inorganic material, from both natural and anthropogenic sources. A large fraction of PM2.5 is organic. The first objective was to investigate heterogeneous oxidation of condensed-phase molecular markers for two major organic source categories, meat-cooking emissions and motor vehicle exhaust. Effective reaction rate constants of key molecular markers were measured over a range of atmospherically relevant experimental conditions, including a range of concentrations and relative humidities, and with SOA condensed on the particles. Aerosolized meat grease was reacted with ozone to investigate the oxidation of molecular markers for meat-cooking emissions. Aerosolized motor oil, which is chemically similar to vehicle exhaust aerosol and contains the molecular markers used in source apportionment, was reacted with the hydroxyl radical (OH) to investigate oxidation of motor vehicle molecular markers. All molecular markers of interest - oleic acid, palmitoleic acid, and cholesterol for meat-cooking emissions, and hopanes and steranes for vehicle exhaust - reacted at rates that are significant for time scales on the order of days assuming typical summertime oxidant concentrations. Experimental conditions influenced the reaction rate constants. For both systems, experiments conducted at high relative humidity (RH) had smaller reaction rate constants than those at low RH. SOA coating slowed the reaction rate constants for meat-cooking markers, but had no effect on the oxidation of vehicle markers. Aerosol composition is a key influence on reaction rate constants, perhaps more significant than external influences. Alkenoic acid concentrations in the meat grease particles appear to influence cholesterol oxidation rates. Also, the reaction rate constants for new motor oil were faster than those of the more viscous used motor oil. The measured reaction rate constants were used to oxidize source profiles that were subsequently run in the Chemical Mass Balance (CMB) model. Oxidizing the molecular markers in the meat-cooking profile led to unrealistically high meat-cooking aerosol contributions to the total organic carbon (OC), often more than 100%. This suggests that there is either unaccounted for sources of meat-cooking molecular markers in the ambient samples, or there is some property of atmospheric aerosols that significantly inhibits reaction that was not captured in this study. Oxidation of motor vehicle profiles led to both higher estimates of total vehicle OC and a quadrupling of gasoline OC, while the diesel contribution changed very little. The increase in gasoline OC changes gasoline vehicle emissions from a relatively minor source to a major one. Thus, oxidation of molecular markers can have a significant impact on receptor model predictions. The second objective was to investigate SOA formation from the photo-oxidation of whole diesel exhaust. Diluted exhaust from a diesel engine was photo-oxidized in a smog chamber to investigate SOA production. Photochemical oxidation rapidly produced significant SOA, almost doubling the organic aerosol contribution of primary emissions after several hours of processing. Less than 10% of the SOA mass could be explained using a SOA model and the measured oxidation of known precursors, such as light aromatics. However, the ultimate yield of SOA is uncertain because it is sensitive to treatment of particle and vapor losses to the chamber walls. Aerosol Mass Spectrometer (AMS) mass spectra reveal that the organic aerosol becomes progressively more oxidized throughout the experiments. The data provide str
Weitkamp, Emily A.
Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties.
Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively. The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of 153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift, sampling of loci and unknown relationships among supposedly unrelated ancestors. PMID:11294614
Davierwala, A P; Chowdari, K V; Kumar, S; Reddy, A P; Ranjekar, P K; Gupta, V S
Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.
Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330
Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui
Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.
We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars. PMID:24301792
�z, M H; Vurgun, H; Bakir, M; B�y�k, ?; Y�ksel, C; �nl�, H M; �ukadar, K; Karado?an, B; K�se, �; Erg�l, A
Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori.
In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed. PMID:15931240
Nagaraja, G M; Mahesh, G; Satish, V; Madhu, M; Muthulakshmi, M; Nagaraju, J
Analysis of Segregation Distortion of Molecular Markers in F 2 Population of Rice
A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers (33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male
Bing ZHAO; Qi-Ming DENG; Qi-Jun ZHANG; Jie-Qin LI; Shao-Ping YE; Yong-Shu LIANG; Yong PENG; Ping LI
Evaluation of RAPD-PCR and protein profile analysis to differentiate Vibrio harveyi strains prevalent along the southwest coast of India
Sixty five isolates of Vibrio harveyi were subjected to random amplified polymorphic DNA (RAPD)-PCR analysis and protein profiling to investigate the genetic variability\\u000a among V. harveyi prevalent along the coast and also assess the discriminating ability of these two molecular methods. A total of 10 RAPD primers\\u000a were assayed for their specificity in detecting V. harveyi, of which only two
Biswajit Maiti; Malathi Shekar; Rekha Khushiramani; Iddya Karunasagar; Indrani Karunasagar
Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp.
The genus Rhipicephalus (Acari: Ixodidae) comprises a large number of vectors of pathogens of substantial medical and veterinary concern; however, species identification based solely on morphological features is often challenging. In the present study, genetic distance within selected Rhipicephalus species (i.e., Rhipicephalus bursa, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus), were investigated based on molecular and phylogenetic analyses of fragments of the mitochondrial 16S, 12S and cytochrome c oxidase subunit 1 (cox1) genes, as well as of the whole sequences of the ribosomal internal transcribed spacer-2 (ITS-2) region. Mean values of inter-specific genetic distance (e.g., up to 12.6%, 11.1% and 15.2%), as well as of intra-specific genetic distance (e.g., 0.9%, 0.9% and 1%), calculated using the Kimura-2 parameter substitution model with uniform rates among sites for 16S, 12S and cox1 genes, respectively, confirmed the differentiation of the rhipicephaline species herein examined. The molecular identification was also supported by the distinct separation of species-specific clades inferred from the phylogenetic analyses of all mitochondrial sequences. Conversely, little interspecific divergence was detected amongst ribosomal ITS-2 sequences (i.e., up to 2.8%) for species belonging to the R. sanguineus complex, which resulted in the ambiguous placement of selected R. sanguineus s.l. and R. turanicus sequences in the corresponding phylogenetic tree. Results from this study confirm the suitability of mtDNA markers for the reliable identification of ticks within the Rhipicephalus genus and provide a framework for future studies of taxonomy, speciation history and evolution of this group of ticks. PMID:24103336
Latrofa, Maria S; Dantas-Torres, Filipe; Annoscia, Giada; Cantacessi, Cinzia; Otranto, Domenico
Differentiation of beauveria bassiana isolates from the darkling beetle, alphitobius diaperinus, using isozyme and RAPD analyses
Two natural genetic markers, isozymes and RAPD, were utilized to differentiate 24 strains of Beauveria bassiana (Deuteromycotina: Hyphomycetes) collected from the darkling beetle, Alphitobius diaperinus (Coleoptera: Tenebrionidae), from poultry houses in North Carolina and West Virginia. Nine enzyme systems were screened, of which alkaline phosphatase, alpha- and beta-esterase, and glucose phosphate isomerase gave well-resolved, scorable bands. A total of 26 isozyme bands was generated by these four enzymes which partitioned the 24 strains into 14 classes. Three classes were shared by two or more strains while the rest of the strains had distinct electrophoretic profiles. Ten RAPD primers, selected from 72 that were screened, produced 141 bands from the 24 strains and separated each as a unique class. While both systems were able to detect variation present among the 24 strains from different regions in North Carolina and West Virginia, RAPD markers provided better resolution of the differences between strains. Variation was detected not only within and among strains from different regions but also among strains collected from a given insect host. Copyright 1998 Academic Press. PMID:9784340
Castrillo; Brooks
New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).
Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop. PMID:17546067
Patzak, Josef; Vrba, Luk�s; Matousek, Jaroslav
Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis.
In traditional medicine, Lonicera japonica (Thunb.) has a notable place, and it has been used for thousands of years in China, Japan, Korea and other East-Asian countries for treating cancer, inflammation, hepatic complications, influenza and wounds. However, the molecular or genetic characteristic of this plant is not well defined. In this study, improved random amplified polymorphic DNA (RAPD) has been employed for the genetic characterization of five varieties of L. japonica collected from different geographic locations of Southern China. A total of 147 bands of DNA fragments were obtained in RAPD-PCR by using 18 primers, and the band sizes ranged from approximately 300-2,000 bp, with 3-11 amplified bands for each primer. Based on the RAPD amplification profiles, cluster dendrogram was obtained, which showed that the similarity coefficients among five varieties of L. japonica ranged from 0.59 to 0.77. To our knowledge, this is the first report of genetic characterization of L. japonica using improved RAPD analysis which has been validated by ISSR analysis, and this characterization may be useful for the preservation of genetic diversity and Lonicera population identification. Moreover, as an option, the improved method could be employed for a variety of applications in genetic diversity and fingerprinting analyses. PMID:24057241
Fu, Junjiang; Yang, Luquan; Khan, Md Asaduzzaman; Mei, Zhiqiang
Protamine mRNA as molecular marker for spermatozoa in semen stains.
Cytological detection of spermatozoa with subsequent DNA analysis is the most important biological evidence in sexual crimes when suitable samples are available. Immunological and enzymatic detection of semen-specific proteins may be helpful but cannot replace specific identification of spermatozoa. We have recently shown that detection of cell-specific gene expression can be used to identify menstrual blood. In this paper we demonstrate that the basic nucleoproteins protamine 1 and 2 are suitable markers for spermatozoa because they are exclusively expressed in the haploid genome and that protamine mRNA can be detected in semen stains by the highly sensitive reverse transcriptase-polymerase chain reaction (RT-PCR). With semi-nested PCR, 10-100 spermatozoa are theoretically sufficient to provide positive amplification results, with hot-start PCR at least 100-1,000 cells are required corresponding to an average semen volume of 0.01-0.1 microl. This new method thus allows specific identification of spermatozoa with molecular biology tools and may broaden the spectrum of investigations in the forensic laboratory. PMID:12799737
Bauer, M; Patzelt, D
Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers
Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.
Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming
Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design
Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning.
Diaz-Cano, Salvador J.
Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers.
The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a atisfactory agreement with increased tolerance to environmental stress conditions of winter rape. PMID:24840830
Amosova, Alexandra V; Zemtsova, Lyudmila V; Grushetskaya, Zoya E; Samatadze, Tatiana E; Mozgova, Galina V; Pilyuk, Yadviga E; Volovik, Valentina T; Melnikova, Natalia V; Zelenin, Alexandr V; Lemesh, Valentina A; Muravenko, Olga V
The androgen receptor as a surrogate marker for molecular apocrine breast cancer subtyping.
The Androgen Receptor (AR) is a potential prognostic marker and therapeutic target in breast cancer. We evaluated AR protein expression in high-risk breast cancer treated in the adjuvant setting. Tumors were subtyped into luminal (ER+/PgR�/AR�), molecular apocrine (MAC, [ER-/PgR-/AR+]) and hormone receptor negative carcinomas (HR-negative, [ER-/PgR-/AR-]). Subtyping was evaluated with respect to prognosis and to taxane therapy. High histologic grade (p�<�0.001) and increased proliferation (p�=�0.001) more often appeared in MAC and HR-negative than in luminal tumors. Patients with MAC had outcome comparable to the luminal group, while patients with HR-negative disease had increased risk for relapse and death. MAC outcome was favorable upon taxane-containing treatment; this remained significant upon multivariate analysis for overall survival (HR 0.31, 95%CI 0.13-0.74, interaction p�=�0.035) and as a trend for time to relapse (p�=�0.15). In conclusion, AR-related subtyping of breast cancer may be prognostic and serve for selecting optimal treatment combinations. PMID:24703723
Lakis, Sotiris; Kotoula, Vassiliki; Eleftheraki, Anastasia G; Batistatou, Anna; Bobos, Mattheos; Koletsa, Triantafyllia; Timotheadou, Eleni; Chrisafi, Sofia; Pentheroudakis, George; Koutras, Angelos; Zagouri, Flora; Linardou, Helena; Fountzilas, George
Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).
Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A.�microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae. PMID:22004100
Derocles, Stephane A P; LE Ralec, Anne; Plantegenest, Manuel; Chaubet, Bernard; Cruaud, Corinne; Cruaud, Astrid; Rasplus, Jean-Yves
Conservation of wild animals by assisted reproduction and molecular marker technology.
Wild animals are an integral component of the ecosystem. Their decimation due to abrupt natural calamities or due to gradual human intervention would be disastrous to the ecosystem and would alter the balance in nature between various biotic components. Such an imbalance could have an adverse effect on the ecosystem. Therefore, there is an urgent need to put an end to the ever increasing list of endangered species by undertaking both in situ and ex situ conservation using tools of modern biology, to ascertain the degree of genetic variation and reproductive competence in these animals. This review highlights the development and use of molecular markers such as microsatellites, minisatellites, mitochondrial control region, cytochrome b and MHC loci to assess the genetic variation in various Indian wild animals such as the lion, tiger, leopard and deer. The review also presents data on the semen profile of the big cats of India. Reproductive technologies such as cryopreservation of semen and artificial insemination in big cats are also highlighted. PMID:15255374
Shivaji, S; Kholkute, S D; Verma, S K; Gaur, Ajay; Umapathy, G; Singh, Anju; Sontakke, Sadanand; Shailaja, K; Reddy, Anuradha; Monika, S; Sivaram, V; Jyotsna, B; Bala, Satyare; Ahmed, M Shakeel; Bala, Aruna; Chandrashekar, B V N; Gupta, Sandeep; Prakash, Surya; Singh, Lalji
Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers.
Citrus production with its many varieties is of importance since it provides economically important products for Turkish exports. Sour orange is a rootstock commonly used for propagating the different scion varieties. Knowledge of the genetic diversity of the rootstock accessions would be useful in order to improve citrus breeding programs. We studied genetic relationships and diversity of 51 accessions of sour orange (Citrus aurantium) and their relatives using SSR (simple sequence repeat) and SRAP (sequence-related amplified polymorphism) molecular markers. Twenty-one SRAP primer combinations were tested on these accessions and relatives, producing 167 polymorphic fragments, with a mean of 8.0 and a mean polymorphism information content value of 0.47. Seventeen SSR primers also produced 30 polymorphic fragments, with a mean of 1.4 per primer and a mean polymorphism information content value of 0.39. The unweighted pair-group method with arithmetic average analysis using combined SSR and SRAP data showed a similarity range from 0.71 to 1.00 among the accessions. In the cluster analysis, sour orange relatives were indicated as a separate group from sour orange. 'Macrophylla' and 'Mexican lime' were the accessions most distinct (0.71) from the others. We conclude that genetic diversity in these sour orange accessions is lower and some of them were identical. PMID:23079821
Polat, I; Kacar, Y A; Yesiloglu, T; Uzun, A; Tuzcu, O; Gulsen, O; Incesu, M; Kafa, G; Turgutoglu, E; Anil, S
Development of genomic SSR markers and molecular characterization of magnaporthe oryzae isolates from wheat in Brazil.
Magnaporthe oryzae, the causal agent of wheat blast, was characterized on a molecular level with 38 newly isolated genomic SSR loci. Among the 31 wheat isolates analyzed, 15 polymorphic loci were detected, with an average of 1.7 alleles per locus, 28.9% of them being highly or reasonably informative. The number of polymorphic loci was higher in isolates from Londrina in the Brazilian state of Paran� and Coromandel in Minas Gerais compared with Goi�nia in Goi�s and S�o Borja in Rio Grande do Sul. The rice isolate was clearly different from the wheat isolates, and the size difference in polymorphic SSR loci between one isolate from wheat and one isolate from rice was associated with the number of repeats. Some isolates collected from different states and in different years demonstrated similarities of 100%. The markers developed here are useful for the genetic analysis of M. oryzae isolated from wheat, and isolates representing the variability detected in the field can be used to search for better wheat blast resistance. PMID:24271825
Pereira, Jorge Fernando; Consoli, Luciano; de Souza Bombonatto, Estevon Alexandre; Bonato, Ana L�dia Variani; Maciel, Jo�o Leodato Nunes
Molecular diversity analysis of eggplant (Solanum melongena) genetic resources.
Eggplant (Solanum melongena), a vegetable that is cultivated worldwide, is of considerable importance to agriculture in China. We analyzed the diversity of this plant using inter-simple sequence repeat (ISSR) and RAPD procedures to subdivide 143 Chinese-cultivated eggplants based on coefficient of parentage, genetic diversity index (GDI) and canonical discriminant analysis. ISSR markers were more effective than RAPD markers for detecting genetic diversity, which ranged from 0.10-0.51, slightly lower than what is known from other crops. Our ISSR/RAPD data provide molecular evidence that coincides with morphological-based classification into three varieties and further subdivision into eight groups, except for two groups. Intensive use of elite parents and extensive crossing within groups have resulted in increased coefficient of parentage and proportional contribution but decreased GDI during the past decades. The mean coefficient of parentage and proportional contribution increased from 0.05 to 0.10% and from 3.22 to 6.46% during 1980-1991 and 1992-2003, respectively. The GDI of landraces was 0.21, higher than the 0.09 and 0.08 calculated for the hybrid cultivars released during the two periods. The recent introduction of alien genotypes into eggplant breeding programs may broaden the genetic base. PMID:21710466
Ali, Z; Xu, Z L; Zhang, D Y; He, X L; Bahadur, S; Yi, J X
Identification of sex in Simmondsia chinensis (Jojoba) using RAPD markers
Simmondsia chinensis (Link) Schneider, a multipurpose dioecious shrub of arid zones, has emerged as a cash crop. It is being cultivated for its\\u000a seeds which store liquid wax whose properties are similar to spermaceti (Sperm whale oil), a substitute for petro products\\u000a and precious high-priced lubricants. Jojoba is a slow-growing desert shrub having a male biased (5:1; male:female ratio) population.
Veena Agrawal; Kuldeep Sharma; Sarika Gupta; Ravindra Kumar; Manoj Prasad
Efficient Molecular Marker Design Using the MaizeGDB Mo17 SNPs and Indels Track
Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion�deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize.
Settles, A. Mark; Bagadion, Alyssa M.; Bai, Fang; Zhang, Junya; Barron, Brady; Leach, Kristen; Mudunkothge, Janaki S.; Hoffner, Cassandra; Bihmidine, Saadia; Finefield, Erin; Hibbard, Jaime; Dieter, Emily; Malidelis, I. Alex; Gustin, Jeffery L.; Karoblyte, Vita; Tseung, Chi-Wah; Braun, David M.
Analysis of segregation distortion of molecular markers in F2 population of rice.
A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers(33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male parent indica GuangLuAi-4 and 13 markers toward heterozygote, but none toward the female parent Nipponbare. It was found that the segregation distortion might be caused by gametophyte and zygote. Since most gametophyte loci and sterility loci were mapped in segregation distortion regions, it indicated that the segregation distortion may be caused by these gametophyte loci and sterility loci. Finally, this research also analyzed the skewed segregation of some markers, which had not been mapped on chromosome. PMID:16722340
Zhao, Bing; Deng, Qi-Ming; Zhang, Qi-Jun; Li, Jie-Qin; Ye, Shao-Ping; Liang, Yong-Shu; Peng, Yong; Li, Ping
Characterization of alien chromosomes in backcross derivatives of Triticum aestivum�� Elymus rectisetus hybrids by using molecular markers and sequential multicolor FISH/GISH.
Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Based on DNA sequences of genome-specific RAPD markers, sequence-tagged site (STS) markers specific for W and Y genomes have been obtained. Coupling with the use of genomic in situ hybridization, these STS markers enabled the identification of the W- and Y-genome chromosomes in backcross derivatives from hybrids of bread wheat Triticum aestivum L. (2n=42; AABBDD) and Elymus rectisetus (Nees in Lehm.) �. L�ve & Connor (2n=42; StStWWYY). The detection of six different alien chromosomes in five of these derivatives was ascertained by quantitative PCR of STS markers, simple sequence repeat markers, rDNA genes, and (or) multicolor florescence in situ hybridization. Disomic addition line 4687 (2n=44) has the full complement of 42 wheat chromosomes and a pair of 1Y chromosomes that carry genes for resistance to tan spot (caused by Pyrenophora tritici-repentis (Died.) Drechs.) and Stagonospora nodorum blotch (caused by Stagonospora nodorum (Berk.) Castellani and Germano). The disomic addition line 4162 has a pair of 1St chromosomes and 21 pairs of wheat chromosomes. Lines 4319 and 5899 are two triple substitution lines (2n=42) having the same chromosome composition, with 2A, 4B, and 6D of wheat substituted by one pair of W- and two pairs of St-genome chromosomes. Line 4434 is a substitution-addition line (2n=44) that has the same W- and St-genome chromosomes substituting 2A, 4B, and 6D of wheat as in lines 4319 and 5899 but differs by having an additional pair of Y-genome chromosome, which is not the 1Y as in line 4687. The production and identification of these alien cytogenetic stocks may help locate and isolate genes for useful agronomic traits. PMID:22494709
Dou, Quan-Wen; Lei, Yunting; Li, Xiaomei; Mott, Ivan W; Wang, Richard R-C
Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers
The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a diploid mosquito, Aedes aegypti. RAPD-SSCP analysis revealed segregation of codominant alleles at markers that appeared to segregate as dominant (band presence/band absence) markers or appeared invariant on agarose gels. Our SSCP protocol uses silver staining to detect DNA fractionated on large thin polyacrylamide gels and reveals more polymorphic markers than agarose gel electrophoresis. In B. hebetor, 79 markers were mapped with 12 RAPD primers in six weeks; in A. aegypti, 94 markers were mapped with 10 RAPD primers in five weeks. Forty-five percent of markers segregated as codominant loci in B. hebetor, while 11% segregated as codominant loci in A. aegypti. SSCP analysis of RAPD-PCR markers offers a rapid and inexpensive means of constructing intensive linkage maps of many species.
Antolin, M. F.; Bosio, C. F.; Cotton, J.; Sweeney, W.; Strand, M. R.; Black-IV, W. C.
Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers
Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics\\u000a on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development\\u000a of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats\\u000a (ISSR)
Hui-Zhong Wang; Zhen-Xing Wu; Jiang-Jie Lu; Nong-Nong Shi; Yan Zhao; Zhi-Tao Zhang; Jun-Jun Liu
Genetic relations among basil taxa ( Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number
Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the\\u000a nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into
Klaudija Carovi?-Stanko; Zlatko Liber; Vi�nja Besendorfer; Branka Javornik; Borut Bohanec; Ivan Kolak; Zlatko Satovic
Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Miscanthus
A survey of Gramineae markers was carried out with the aim of developing cost-effective methods for the molecular analysis\\u000a of Miscanthus species. Ten out of twenty Gramineae RFLP probes from �anchor� sets hybridized well to Miscanthus DNA while all 15 maize probes tested cross-hybridized successfully, showing similar patterns in both species. Cross-taxa\\u000a amplification of maize microsatellite primers was then tested.
P. Hern�ndez; G. Dorado; D. A. Laurie; A. Mart�n; J. W. Snape
Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea
Publicly available genomic tools help researchers integrate information and make new discoveries. In this paper, we describe\\u000a the development of immortal mapping populations of rapid cycling, self-compatible lines, molecular markers, and linkage maps\\u000a for Brassica rapa and B. oleracea and make the data and germplasm available to the Brassica research community. The B. rapa population consists of 160 recombinant inbred
Federico Luis Iniguez-Luy; Lewis Lukens; Mark W. Farnham; Richard M. Amasino; Thomas C. Osborn
Temporal trends of molecular markers associated with artemether-lumefantrine tolerance\\/resistance in Bagamoyo district, Tanzania
BACKGROUND: Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance\\/resistance before
M. Malmberg; B. Ngasala; P. E. Ferreira; E. Larsson; I. Jovel; A. Hjalmarsson; M. Petzold; Z. Premji; J. P. Gil; A. Bjorkman; A. Martensson
Cryptic Diversity within the Major Trypanosomiasis Vector Glossina fuscipes Revealed by Molecular Markers
Background The tsetse fly Glossina fuscipes s.l. is responsible for the transmission of approximately 90% of cases of human African trypanosomiasis (HAT) or sleeping sickness. Three G. fuscipes subspecies have been described, primarily based upon subtle differences in the morphology of their genitalia. Here we describe a study conducted across the range of this important vector to determine whether molecular evidence generated from nuclear DNA (microsatellites and gene sequence information), mitochondrial DNA and symbiont DNA support the existence of these taxa as discrete taxonomic units. Principal Findings The nuclear ribosomal Internal transcribed spacer 1 (ITS1) provided support for the three subspecies. However nuclear and mitochondrial sequence data did not support the monophyly of the morphological subspecies G. f. fuscipes or G. f. quanzensis. Instead, the most strongly supported monophyletic group was comprised of flies sampled from Ethiopia. Maternally inherited loci (mtDNA and symbiont) also suggested monophyly of a group from Lake Victoria basin and Tanzania, but this group was not supported by nuclear loci, suggesting different histories of these markers. Microsatellite data confirmed strong structuring across the range of G. fuscipes s.l., and was useful for deriving the interrelationship of closely related populations. Conclusion/Significance We propose that the morphological classification alone is not used to classify populations of G. fuscipes for control purposes. The Ethiopian population, which is scheduled to be the target of a sterile insect release (SIT) programme, was notably discrete. From a programmatic perspective this may be both positive, given that it may reflect limited migration into the area or negative if the high levels of differentiation are also reflected in reproductive isolation between this population and the flies to be used in the release programme.
Choi, Kwang-Shik; Darby, Alistair C.; Causse, Sandrine; Kapitano, Berisha; Hall, Martin J. R.; Steen, Keith; Lutumba, Pascal; Madinga, Joules; Torr, Steve J.; Okedi, Loyce M.; Lehane, Michael J.; Donnelly, Martin J.
Molecular markers of trichloroethylene-induced toxicity in human kidney cells
Difficulties in evaluation of trichloroethylene (TRI)-induced toxicity in humans and extrapolation of data from laboratory animals to humans are due to the existence of multiple target organs, multiple metabolic pathways, sex-, species-, and strain-dependent differences in both metabolism and susceptibility to toxicity, and the lack or minimal amount of human data for many target organs. The use of human tissue for mechanistic studies is thus distinctly advantageous. The kidneys are one target organ for TRI and metabolism by the glutathione (GSH) conjugation pathway is responsible for nephrotoxicity. The GSH conjugate is processed further to produce the cysteine conjugate, S-(1,2-dichlorovinyl)-L-cysteine (DCVC), which is the penultimate nephrotoxic species. Confluent, primary cultures of human proximal tubular (hPT) cells were used as the model system. Although cells in log-phase growth, which are undergoing more rapid DNA synthesis, would give lower LD{sub 50} values, confluent cells more closely mimic the in vivo proximal tubule. DCVC caused cellular necrosis only at relatively high doses (>100 {mu}M) and long incubation times (>24 h). In contrast, both apoptosis and enhanced cellular proliferation occurred at relatively low doses (10-100 {mu}M) and early incubation times (2-8 h). These responses were associated with prominent changes in expression of several proteins that regulate apoptosis (Bcl-2, Bax, Apaf-1, Caspase-9 cleavage, PARP cleavage) and cellular growth, differentiation and stress response (p53, Hsp27, NF-{kappa}B). Effects on p53 and Hsp27 implicate function of protein kinase C, the mitogen activated protein kinase pathway, and the cytoskeleton. The precise pattern of expression of these and other proteins can thus serve as molecular markers for TRI exposure and effect in human kidney.
Lash, Lawrence H. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)]. E-mail: firstname.lastname@example.com; Putt, David A. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Hueni, Sarah E. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Horwitz, Beth P. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)
Molecular markers of Plasmodium falciparum drug resistance in southern highland Rwanda.
In Rwanda, frequent mutations in the pfdhfr and pfdhps genes of Plasmodium falciparum have suggested intense sulfadoxine-pyrimethamine resistance. However, data on pfmdr1 are not available but might be important in the context of the first-line treatment with artemether-lumefantrine. During a survey among 749 children under five years of age in southern highland Rwanda, 104 P. falciparum isolates were obtained. Parasite polymorphisms associated with drug sensitivity were typed including the genes pfdhfr, pfdhps, pfmdr1, and pfcrt. Plasma concentrations of chloroquine and pyrimethamine were measured by ELISA. Treatment with artemether-lumefantrine within the preceding two weeks was stated by 12.5% of the respondents; chloroquine in plasma was detected in 17.6%, pyrimethamine in none. Isolates with pfdhfr triple and pfdhps double/triple mutations occurred in 75% and 93%, respectively; 69% of the isolates comprised pfdhfr/pfdhps quintuple or sextuple mutations associated with high-grade sulfadoxine-pyrimethamine resistance. Pfdhfr L164 was absent. The pfmdr1 pattern revealed more than 50% of the F184 polymorphism and almost 40% of the N86-F184-D1246 allele combination known to be selected in infections reappearing following artemether-lumefantrine treatment. Molecular markers demonstrate intense antifolate drug resistance of P. falciparum in southern Rwanda. The present, first-time data on pfmdr1 alleles from Rwanda reveal a pattern which might reflect a predominance of wild types for some alleles or, alternatively, substantial artemether-lumefantrine pressure on the local parasite population. PMID:21996622
Zeile, Irene; Gahutu, Jean-Bosco; Shyirambere, Cyprien; Steininger, Christian; Musemakweri, Andre; Sebahungu, Fid�le; Karema, Corine; Harms, Gundel; Eggelte, Teunis A; Mockenhaupt, Frank P
Molecular mapping of resistance to Leptosphaeria maculans in Australian cultivars of Brassica napus.
Doubled haploid (DH) lines together with a cotyledon bioassay were employed for the molecular analysis of resistance to the blackleg fungus Leptosphaeria maculans in the Australian Brassica napus cultivars Shiralee and Maluka. We used bulked segregant analysis to identify 13 RAPD and two RFLP markers linked to the resistance phenotype and mapped these markers in the segregating DH population. Our data suggest the presence of a single major locus controlling resistance in the cultivar Shiralee, confirming our previous results obtained from Mendelian genetic analyses. In addition, preliminary mapping data for the cultivar Maluka also support a single locus model for resistance and indicate that the resistance genes from 'Shiralee' and 'Maluka' are either linked or possibly identical. The molecular markers identified in this study should be a useful tool for breeding blackleg resistant varieties using marker-assisted selection, and are the essential first step towards the map-based cloning of this resistance gene. PMID:18464830
Mayerhofer, R; Good, A G; Bansal, V K; Thiagarajah, M R; Stringam, G R
Assessment of genetic diversity in a highly valuable medicinal plant Catharanthus roseus using molecular
Genetic diversity was evaluated among 14 cultivars of Catharanthus roseus using RAPD and ISSR markers. The RAPD primers resulted in the amplification of 56 bands, among which 46 (82%) bands were polymorphic Four ISSR primers amplified 31 loci out of which 17 were polymorphic and 14 are monomorphic. The Jaccard's similarity derived from the combined marker system showed that the
Ranjan Kumar Shaw; Laxmikanta Acharya; Arup Kumar Mukherjee
Long-range transport of biomass burning emissions based on organic molecular markers and carbonaceous thermal distribution.
Semi-continuous organic carbon (OC), elemental carbon (EC), and organic molecular markers were analyzed using the thermal optical transmittance method at the Gosan supersite (on Jeju Island, Korea), which has been widely used as a regional background site for East Asia. The Carbonaceous Thermal Distribution (CTD) method, which can provide detailed carbon signature characteristics relative to analytical temperature, was used to improve the carbon fractionation of the analytical method. Ground-based measurements were conducted from October 25 to November 5, 2010. During the sampling period, one high OC concentration event and two characteristic periods were observed. Considering the thermal distribution patterns, the relationship between the EC and black carbon (BC) by optical measurements, the backward trajectories, the aerosol optical thickness, the PM10 concentrations from the 316 PM-network sites that were operated by the Ministry of Environment in Korea, and the organic molecular markers, such as levoglucosan, PAHs, and organic acids, we concluded that the event was influenced by long-range transport from biomass burning emissions. This study discusses the CTD analysis with organic molecular marker concentrations, extracts and interprets additional carbon fractions from a semi-continuous data set, and provides knowledge regarding the origin of carbon sources and their behaviors. PMID:23892024
Bae, Min-Suk; Shin, Ju-Seon; Lee, Kwang-Yul; Lee, Kwon-Ho; Kim, Young J
Do Molecular Markers Predict Survival in Non-Small-Cell Lung Cancer?
Patients with non-small-cell lung cancer (NSCLC) survive for variable lengths of time, even when ad- justment is made for pathological stage. Numerous reports suggest that biological markers predict survival in patients undergoing surgery for NSCLC with curative intent, but many of these claims are unconfirmed or conflicting. We postulated that the use of multiple putative markers might provide greater power
Genetic relationships of Japanese potato cultivars assessed by RAPD analysis
Seventy-three breeding lines and cultivars, which included all Japanese cultivars, were assessed by random amplified polymorphic\\u000a DNA (RAPD) analysis. Thirty-one of 40 decamer primers revealed 84 scorable RAPDs. Using these RAPDs, 67 of 73 cultivars were\\u000a distinguished from each other. One of the cultivars released as a protoclonal variant was able to distinguish from the parent\\u000a by increasing the number
K. Hosaka; M. Mori; K. Ogawa
[RAPD analysis of plant pathogenic coryneform bacteria].
RAPD analysis was used for the taxonomy of plant pathogenic coryneform bacteria, especially for the classification of two new pathogens (Curtobacterium flaccumfaciens pv. basellae pv. nov. and Curtobacterium flaccumfaciens pv. beticola pv. nov.). 20 random primers were screened from 50 ones to detect polymorphism among the total strains used. 80.4% were polymorphic bands among the 225 ones produced. The results of pairwise similarity and UPGMA cluster analysis suggest that the two new pathovars of sugar beet (Beta vulgaris var. saccharifera) and malabar spinach (Basella rubra) are genetically close related with Curtobacterium flacumfaciens, and the minimal similarity coefficient is 0.6511. According to the RAPD analysis and previous research, some newly made taxonomic changes of the plant pathogenic coryneform bacteria are discussed. PMID:16496687
Yin, Yan-Ni; Chen, Yong-Fang; Li, Shi-Mo; Guo, Jian-Hua
The potential of hypoxia markers as target for breast molecular imaging - a systematic review and meta-analysis of human marker expression
Background Molecular imaging of breast cancer is a promising emerging technology, potentially able to improve clinical care. Valid imaging targets for molecular imaging tracer development are membrane-bound hypoxia-related proteins, expressed when tumor growth outpaces neo-angiogenesis. We performed a systematic literature review and meta-analysis of such hypoxia marker expression rates in human breast cancer to evaluate their potential as clinically relevant molecular imaging targets. Methods We searched MEDLINE and EMBASE for articles describing membrane-bound proteins that are related to hypoxia inducible factor 1? (HIF-1?), the key regulator of the hypoxia response. We extracted expression rates of carbonic anhydrase-IX (CAIX), glucose transporter-1 (GLUT1), C-X-C chemokine receptor type-4 (CXCR4), or insulin-like growth factor-1 receptor (IGF1R) in human breast disease, evaluated by immunohistochemistry. We pooled study results using random-effects models and applied meta-regression to identify associations with clinicopathological variables. Results Of 1,705 identified articles, 117 matched our selection criteria, totaling 30,216 immunohistochemistry results. We found substantial between-study variability in expression rates. Invasive cancer showed pooled expression rates of 35% for CAIX (95% confidence interval (CI): 26-46%), 51% for GLUT1 (CI: 40-61%), 46% for CXCR4 (CI: 33-59%), and 46% for IGF1R (CI: 35-70%). Expression rates increased with tumor grade for GLUT1, CAIX, and CXCR4 (all p < 0.001), but decreased for IGF1R (p < 0.001). GLUT1 showed the highest expression rate in grade III cancers with 58% (45-69%). CXCR4 showed the highest expression rate in small T1 tumors with 48% (CI: 28-69%), but associations with size were only significant for CAIX (p < 0.001; positive association) and IGF1R (p = 0.047; negative association). Although based on few studies, CAIX, GLUT1, and CXCR4 showed profound lower expression rates in normal breast tissue and benign breast disease (p < 0.001), and high rates in carcinoma in situ. Invasive lobular carcinoma consistently showed lower expression rates (p < 0.001). Conclusions Our results support the potential of hypoxia-related markers as breast cancer molecular imaging targets. Although specificity is promising, combining targets would be necessary for optimal sensitivity. These data could help guide the choice of imaging targets for tracer development depending on the envisioned clinical application.
Bladder Cancer 2000: Molecular Markers for the Diagnosis of Transitional Cell Carcinoma
The search continues for better tumor markers to improve the rate of detection of transitional cell carcinoma (TCC) more quickly in larger populations and to predict the possibility of disease recurrence. Among several new tests currently being screened, telomerase and hyaluronic acid/hyaluronidase (HA/HAase) have shown sensitivity and specificity equal to or better than cytology, and other promising tumor markers are being investigated. Although no marker has yet replaced the need to perform cystoscopy and cytology, the new tests can minimize the cost and difficulty of screening and long-term surveillance of patients who have or are at risk for bladder cancer.
Chao, Debby; Freedland, Stephen J; Pantuck, Allan J; Zisman, Amnon; Belldegrun, Arie S
Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus.
Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D(2) statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F2 population of cross, BR11�Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model. PMID:23643394
Latif, Mohammad Abdul; Rahman, Mohammad Mahfuzur; Ali, Mohammad Eaqub; Ashkani, Sadegh; Rafii, Mohd Yusop
Low RAPD Variation and Female-Biased Sex Ratio Indicate Genetic Drift in Small Populations of the Dioecious Conifer Taxus Baccata in Switzerland
Small populations are prone to genetic drift as a consequence of random sampling effects. We investigated whether we could detect such random sampling effects in the English yew (Taxus baccata), a dioecious conifer species occurring in scattered populations in Switzerland. Seven pairs of small and large populations were analyzed using random amplified polymorphic DNA (RAPD) marker bands from 20 individuals
Karin Hilfiker; Felix Gugerli; Jean-Philippe Sch�tz; Peter Rotach; Rolf Holderegger
The genome of the Mediterranean fruitfly ceratitis capitata : Localization of molecular markers by in situ hybridization to salivary gland polytene chromosomes
We hybridized cloned DNA segments to salivary gland polytene chromosomes of the medfly,Ceratitis capitata, and thus established molecular markers for 24 sites on 6 out of 10 autosomal arms. An additional marker identified a medfly repetitive element that hybridizes to approximately 100 autosomal sites as well as a granular network that is thought to represent theX chromosome. Some of the
A. Zacharopoulou; M. Frisardi; C. Savakis; A. S. Robinson; P. Tolias; M. Konsolaki; K. Komitopoulou; F. C. Kafatos
An update of the Courtot � Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat
We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars 'Courtot' and 'Chinese Spring'. This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes
P. Sourdille; T. Cadalen; H. Guyomarc'h; J. Snape; M. Perretant; G. Charmet; C. Boeuf; S. Bernard; M. Bernard
Molecular Marker Approach on Characterizing and Quantifying Charcoal in Environmental Media
NASA Astrophysics Data System (ADS)
Black carbon (BC) is widely distributed in natural environments including soils, sediments, freshwater, seawater and the atmosphere. It is produced mostly from the incomplete combustion of fossil fuels and vegetation. In recent years, increasing attention has been given to BC due to its potential influence in many biogeochemical processes. In the environment, BC exists as a continuum ranging from partly charred plant materials, charcoal residues to highly condensed soot and graphite particles. The heterogeneous nature of black carbon means that BC is always operationally-defined, highlighting the need for standard methods that support data comparisons. Unlike soot and graphite that can be quantified with well-established methods, it is difficult to directly quantify charcoal in geologic media due to its chemical and physical heterogeneity. Most of the available charcoal quantification methods detect unknown fractions of the BC continuum. To specifically identify and quantify charcoal in soils and sediments, we adopted and validated an innovative molecular marker approach that quantifies levoglucosan, a pyrogenic derivative of cellulose, as a proxy of charcoal. Levoglucosan is source-specific, stable and is able to be detected at low concentrations using gas chromatograph-mass spectrometer (GC-MS). In the present study, two different plant species, honey mesquite and cordgrass, were selected as the raw materials to synthesize charcoals. The lab-synthesize charcoals were made under control conditions to eliminate the high heterogeneity often found in natural charcoals. The effects of two major combustion factors, temperature and duration, on the yield of levoglucosan were characterized in the lab-synthesize charcoals. Our results showed that significant levoglucosan production in the two types of charcoal was restricted to relatively low combustion temperatures (150-350 degree C). The combustion duration did not cause significant differences in the yield of levoglucosan in the two charcoals. Interestingly, the low temperature charcoals are undetectable by the acid dichromate oxidation method, a popular soot/charcoal analytical approach. Our study demonstrates that levoglucosan can serve as a proxy of low temperature charcoals that are undetectable using other BC methods. Moreover, our study highlights the limitations of the common BC quantification methods to characterize the entire BC continuum.
Kuo, L.; Herbert, B. E.; Louchouarn, P.
ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma
Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. Methods First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR) treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP). Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. Results The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR) demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM); tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC) was 76.2% compared with 25.5% in invasive ductal carcinoma (IDC), and this difference was statistically significant (p = 0.0002). Conclusion ADAM33 gene silencing may be related to the discohesive histological appearance of ILCs. We suggest that ADAM33 promoter methylation may be a useful molecular marker for differentiating ILC and IDC.
Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology
Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions.
Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Herve; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M
Applications of the green fluorescent protein as a molecular marker in environmental microorganisms
In this review, we examine numerous applications of the green fluorescent protein (GFP) marker gene in environmental microbiology research. The GFP and its variants are reviewed and applications in plant�microbe interactions, biofilms, biodegradation, bacterial�protozoan interactions, gene transfer, and biosensors are discussed. Methods for detecting GFP-marked cells are also examined. The GFP is a useful marker in environmental microorganisms, allowing new
D. Errampalli; K. Leung; M. B. Cassidy; M. Kostrzynska; M. Blears; H. Lee; J. T. Trevors
Molecular marker-assisted sex control in half-smooth tongue sole ( Cynoglossus semilaevis)
Half-smooth tongue sole females grow larger and faster than males. An all-female population would be of significant benefit for tongue sole aquaculture. In the present study, a female-specific AFLP marker (CseF305) was isolated from female genomic DNA of the tongue sole and sequenced. One pair of SCAR primers was designed based on the sequences of the female-specific marker. A PCR
Song-Lin Chen; Si-Ping Deng; Hong-Yu Ma; Yong-Sheng Tian; Jian-Yong Xu; Jing-Feng Yang; Qing-Yin Wang; Xiang-Shan Ji; Chang-Wei Shao; Xian-Li Wang; Peng-Fei Wu; Han Deng; Jie-ming Zhai
Epithelioid Sarcoma and Unclassified Sarcoma with Epithelioid Features: Clinicopathological Variables, Molecular Markers, and a New Experimental Model
Background. Epithelioid sarcoma (ES) and unclassified sarcoma with epithelioid features (USEF) are clinically and therapeutically unresolved. We compared ES and USEF patients' clinical behavior, treatment, outcome, and molecular marker expression. Furthermore, preclinical ES study models were developed to enable comprehensive benchside investigations. Patients and Methods. A database of ES and USEF patients (n = 116) treated since 1992 was created. A clinically annotated ES�USEF tissue microarray (TMA) was assayed for tumor-related markers. Newly established human and commercially available ES cell lines were characterized and tested in vivo. Results. ES and USEF patients presenting with localized disease exhibited 22% and 25% local recurrence rates, 35% and 19% nodal metastasis rates, and 41% and 53% distant metastasis rates (median follow-up, 54 months and 39 months, respectively). The 5- and 10-year disease-specific survival rates were 88% and 43% and 52% and 42% (ES and USEF, respectively). TMA immunohistochemistry identified integrase interactor (INI)-1 loss, cancer antigen 125, and p53 nuclear expression as significantly more common in ES than USEF cases. Both cell lines preserved ES morphological and biochemical characteristics in vitro and in vivo; loss of INI-1 was shown to occur in both lines. Conclusions. Enhanced knowledge of ES and USEF clinical behavior, marker expression, and molecular determinants, extended via experimental models, will hopefully accelerate development of urgently needed effective targeted therapies for ES and USEF.
Sakharpe, Aniket; Lahat, Guy; Gulamhusein, Taher; Liu, Ping; Bolshakov, Svetlana; Nguyen, Theresa; Zhang, Pingyu; Belousov, Roman; Young, Eric; Xie, Xianbiao; Rao, Priya; Hornick, Jason L.; Lazar, Alexander J.; Pollock, Raphael E.
Random amplified polymorphic DNA (RAPD) detection of dwarf off-types inmicropropagated Cavendish (Musa spp. AAA) bananas
A RAPD marker specific to the dwarf off-type (hereafter known as dwarf) from micropropagation of Cavendish banana (Musa spp. AAA) cultivars New Guinea Cavendish and Williams was identified following an analysis of 57 normal (true-to-type) and 59 dwarf plants generated from several different micropropagation events. Sixty-six random decamer primers were used in the initial screen, of which 19 (28.8%) revealed
Olivia P. Damasco; Glenn C. Graham; Robert J. Henry; Steve W. Adkins; Mike K. Smith; Ian D Godwin
Evaluation of chemical, molecular, and traditional markers of fecal contamination in an effluent dominated urban stream.
In this paper we present a quantitative sanitary survey of the Middle Santa Ana River, in southern California, utilizing a variety of source tracking tools, including traditional culture-dependent fecal markers (Enterococcus and Escherichia coli by IDEXX), speciation of enterococci isolates, culture-independent fecal markers (human-specific HF183 Bacteroides and Enterococcus by quantitative polymerase chain reaction, qPCR), and chemical markers of sewage and wastewater (nutrients, enantiomeric fraction (EF) of propranolol and ethylenediaminetetraacetic acid). To facilitate comparison of these different methods, data are interpreted in a loading (i.e., mass per time) framework that enables a quantitative apportionment of fecal markers and nutrients to specific source waters in the Middle Santa Ana River. Multiple lines of evidence support the hypothesis that Enterococcus in the Middle Santa Ana River originates primarily from in situ growth in streambed sediments, not from significant and persistent sources of untreated human waste. The EF of propranolol of tertiary treated wastewater effluent is in the range (0.42 to 0.71) previously reported for raw sewage, making EF of propranolol an unsuitable marker for fecal pollution, at least at this site. The human fecal marker HF183 Bacteroides was detected at a few sites, although not in a source of disinfected and tertiary treated wastewater effluent. Based on the results presented here and prior experience at other sites in southern California, HF183 Bacteroides would appear to be a candidate marker of fecal contamination for inland waters, although more qPCR measurements in disinfected wastewater effluent are needed to account for variations due to treatment plant performance and other factors. More generally, our results support the notion that regrowth of fecal indicator bacteria (FIB) in river sediments may lead to a decoupling between FIB and pathogen concentrations in the water column and thus limit the utility of FIB as an indicator of recreational waterborne illness in inland waters. PMID:20839837
Litton, Rachel M; Ahn, Jong Ho; Sercu, Bram; Holden, Patricia A; Sedlak, David L; Grant, Stanley B
Cytology, RAPD, and seed colour of progeny plants from Brassica rapa-alboglabra aneuploids and development of monosomic addition lines.
Progeny plants from Brassica rapa-alboglabra aneuploids were characterized genetically by scoring random amplified polymorphic DNA (RAPD) markers and seed colour and cytologically as to chromosome number and pairing. Sets of RAPD markers specific for each of the encountered eight alien Brassica alboglabra chromosomes were defined. The finding of subsets of markers associated with the presence or absence of alien chromosomes inferred the frequent occurrence of intergenomic genetic recombination and introgression. The chromosome numbers were in the range 2n = 20-28, with a maximum of seven alien B. alboglabra chromosomes and one trisomic B. rapa chromosome. Five types of monosomic addition lines were obtained, two of which have not been developed before. Differences in chromatin condensation patterns made it possible to differentiate between the B. rapa and B. alboglabra chromosomes at diakinesis, and to detect intergenomic homoeological pairing. In addition to the frequent formation of trivalents by homoeologous pairing of an alien B. alboglabra chromosome and a background B. rapa pair, occasional heteromorphic intergenomic bivalents and B. rapa univalents were encountered. Homoeological intergenomic pairing occurred between chromosomes with similar centromeric and karyotypic positions. Plants with structurally changed alien chromosomes were found. The RAPD and cytological data substantiated each other. Observations of the colour of sown and harvested seeds indicated that B. alboglabra chromosome 4 carries a gene for brown seed colour. It exerts its control embryonically, and thus it differs from chromosome 1 which controls seed colour maternally. PMID:11768204
Heneen, W K; J�rgensen, R B
Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica.
Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30-40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100-150 AFLP loci and 150-200 individuals appear sufficient for adequately estimating SGS in our analysis, 150-200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species. PMID:17305851
Jump, Alistair S; Pe�uelas, Josep
Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers
NASA Astrophysics Data System (ADS)
The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and ?-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and ?-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the ?-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.
Hu, Xiaoyan; Hu, Xiaozhong; Al-Rasheid, Khaled A. S.; Al-Farraj, Saleh A.; Song, Weibo
Expression and prognostic role of molecular markers in 99 KIT-positive gastric stromal tumors in Taiwanese
AIM: To elucidate the prognostic role and relationship of three molecular markers such as tumor suppressor gene p53, proliferating cell nuclear antigen (PCNA) and Ki-67 in gastric stromal tumor. METHODS: A total of 108 surgically resected gastric smooth muscle tumor specimens were collected from January 1987 to December 1999. Immunohistochemical studies were performed on the paraffin sections of 99 of 108 CD117-positive tumors with antibodies of p53, PCNA, and Ki-67. Immunoreactivity of three molecular markers was recorded by labeling index (LI, %) and was analyzed for clinicopathologic and survival correlation. RESULTS: Of the 99 cases, immunostaining revealed that 52 patients (52.5%) had p53, and 37 patients (37.3%) had Ki-67 immunoreactivity (defined as >10% of LI). All patients (100%) had PCNA immunoreactivity ranging from 12% to 93% of LI, divided into high or low by median. Statistics revealed that LI of three markers positively correlate to each other (P<0.01) and to microscopic tumor mitotic counts (P <0.001). By combination, patients with ?2 markers (positive or high) in tumors had early tumor recurrence (P <0.001) and unfavorable outcome (P <0.001). Univariate analysis indicated that patients with tumor size >5 cm (P =?0.003), tumor mitosis >5/50 HPF (P 0.001), p53 immunoreactivity (P ?=?0.001), Ki-67 immunoreactivity (P =0.026), high PCNA LI (P =0.015) and male gender (P =0.036) were six predictors for early disease recurrence. Subsequent multivariate analysis revealed that mitotic counts, tumor size, and p53 immunoreactivity were three independent prognostic factors for both disease free and overall survival of patients. By combination of three independent prognostic factors for grouping, we found higher tumor recurrence rate (P <0.001) and shorter survival (P <0.001) existed in groups with increasing factors. CONCLUSION: We first provide the prognostic value and linkage of three molecular markers in GISTs. The combination of three factors (p53, tumor size, and tumor mitosis) provides a more powerful prediction of prognosis than any single factor does.
Hu, Tsung-Hui; Chuah, Seng-Kee; Lin, Jui-Wei; Chiu, Yi-Chun; Changchien, Chi-Sin; Wang, Chih-Chi; Chen, Yaw-Sen; Yi, Li-Na; Chiu, King-Wah; Lee, Chuan-Mo
Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.
Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants. PMID:20083169
Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma
Identification of Single-Copy Orthologous Genes between Physalis and Solanum lycopersicum and Analysis of Genetic Diversity in Physalis Using Molecular Markers
The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei�s genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.
Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai
Can neutral molecular markers be used to determine the success of an introduction of a "better" strain into an established population of a biocontrol parasitoid?
Neutral molecular markers are gene sequences where variants are considered to confer no fitness advantage, such as microsatellites and mitochondrial haplotypes. Several types of neutral marker are easy to develop, cheap to use, and have found extensive application for addressing ecological questions. In biocontrol, these markers are used to simplify identification of cryptic species and of prey remains in predators. Here, we address the potential of neutral molecular markers for determining the relative performance of a "superior" strain of a species after release into an already established conspecific population. We used modeling to show that only under very limited conditions can traditional neutral markers be used to demonstrate that beneficial genetic variation was successfully introgressed into the existing population. However, new population genomic methods do make it possible to track alleles at a large number of loci and consequently make it possible to show if alleles from a superior strain spread in an already established conspecific population. PMID:24772526
Stouthamer, Richard; Nunney, Leonard
A potential species-specific molecular marker suggests interspecific hybridization between sibling species Littorina arcana and L. saxatilis (Mollusca, Caenogastropoda) in natural populations.
Three sister species of rough periwinkles, viz. Littorina saxatilis (Olivi 1792), L. arcana (Hannaford Ellis 1978) and L. compressa (Jeffreys 1865) from the Barents Sea (Russia), the White Sea (Russia) and the Norwegian Sea (Norway) were studied. The identification of two sibling species L. saxatilis and L. arcana is often difficult as both species have extremely similar shell morphology and reproductive systems. Only mature females can be unambiguously distinguished, with a jelly gland present in female L. arcana, but which is replaced by a brood pouch containing developing embryos in L. saxatilis. No clear-cut diagnostic features have been found to discriminate between males or juveniles of the two species. The very first diagnostic DNA marker (DNA fragment A2.8, 271 bp length) for L. arcana and L. saxatilis separation was developed. The marker was derived from apparently species-specific L. arcana DNA fragments obtained via Random Amplified Polymorphic DNA (RAPD) analysis. This fragment was cloned and sequenced, whereupon specific primers were designed and the amplification was surveyed in a large number of morphologically well-identified females of both species. Subsequently, the specific DNA marker was us