maize ( zea mays l. ) is a species that encompasses 
 the subspecies mays ( commonly called  corn  in the us ) 
 as well as the various teosintes that gave rise to modern maize . maize is an important crop : not only is it one of the most abundant sources of food and feed for 
 people and livestock the world over , it is also an important component of many 
 industrial products . maize byproducts 
 are present in , for example , glue , paint , insecticides , toothpaste , rubber 
 tires , rayon , and molded plastics , among others . maize is also currently the nation 's major 
 source of ethanol , a major biofuel that is more environmentally friendly than 
 gasoline and that may be a more economical fuel alternative in the long 
 run . although it is unlikely that 
 ethanol production from maize directly will be sustainable long - term , maize 's 
 suitability to serve as a model organism for developing fuelstock grasses is 
 apparent . indeed , in addition to its 
 value as a commodity , maize has been a premiere model organism for biological 
 research for over 100 years . many 
 seminal scientific discoveries have first been shown in maize , such as the 
 identification   and cloning   of transposable elements , the correlation between cytological and 
 genetic crossing over , and the discovery of epigenetic phenomena . these exceptional 
 characteristics of maize set this amazing plant apart : no other species serves as both a commodity 
 and a leading model for basic research . today , with the accelerated generation of maize genetic 
 and genomic information maizegdb ( the maize 
 genetics and genomics data base ) ( http://www.maizegdb.org/ ) 
 is the model organism database ( mod ) for maize . stored at maizegdb is comprehensive information on loci ( genes and other 
 genetically defined genomic regions including qtl ) , variations ( alleles and 
 other sorts of polymorphisms ) , stocks , molecular markers and probes , sequences , 
 gene product information , phenotypic images and descriptions , metabolic pathway 
 information , reference data , and contact information for maize 
 researchers . described in the results and discussion section are example workflows that 
 could be followed by researchers to utilize the maizegdb resource for their 
 research . other long - term resources 
 serving maize data include gramene ( http://www.gramene.org/ ) , which 
 specializes in grass comparative genomics , and grin ( the germplasm resources 
 information network ; http://www.ars-grin.gov/npgs/ ) , which provides access to 
 the national plant germplasm system 's germplasm stocks and related breeding 
 data . maizegdb makes an effort to guide 
 researchers to these resources via context - sensitive linkages rather than 
 duplicating data , though some data are shared simply to allow for the 
 context - sensitive linkages to be created . this reduces duplication in effort and allows personnel skilled in 
 comparative genomics and germplasm conservation / plant breeding to interact with 
 maize researchers directly via gramene and grin , respectively . in addition to 
 storing and making maize data available , the maizegdb team also provides 
 services to the community of maize researchers and offers technical support for 
 the maize genetics executive committee and the annual maize genetics 
 conference . also available at the 
 maizegdb website , as a service to the maize research community , are bulletin 
 boards for news items , information of interest to cooperators , lists of 
 websites for projects that focus on the scientific study of maize , the 
 editorial board 's recommended reading list , and educational outreach items . the genetic and 
 genomic data as well as community - related information maintained by maizegdb 
 are highly utilized : maizegdb averages 8620 visitors ( based on unique internet 
 protocol or ip addresses ) and over 160 000 page impressions per month ( july 
 2007 to june 2008 ) . in addition , 
 maizegdb came in fifth 
 out of 170 in a national plant genome initiative grantees poll in which lead 
 principal investigators reported most useful websites for their research . maizegdb is the primary repository for the major genetic and 
 cytogenetic maps and includes details about genes , mutants , qtl ( quantitative 
 trait loci ) , and molecular markers including 2500 rflps ( restriction fragment 
 length polymorphisms ) , 4625 ssrs ( simple sequence repeats ) , 363 snp ( single 
 nucleotide polymorphisms ) , 2500 indels ( insertion / deletion sites ) , and 10 644 overgos ( overlapping oligonucleotides ) . these data 
 are described using 1.27 millions synonyms , 42 000 primer sequences , 16 394 raw 
 scores from mapping based upon 16 panels of stocks , and 323 313 links to 
 genbank   accessions . genbank 
 accessions form the links between the genetic position on a chromosome , the 
 sequence records at maizegdb , and the est ( expressed sequence tag ) and gss 
 ( genome survey sequence ) contig assemblies at plantgdb   and dana farber ( the gene indices at http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=maize , 
 previously at tigr ) . all of the 3 520 247 
 sequences in maizegdb are accessible by blast   and can be filtered to report only mapped loci , including any 
 ssrs and overgos that may not be mapped genetically , but via bacs ( bacterial 
 artificial chromosomes ) in anchored contigs . the inclusion of the public 
 bac fpc ( finger print contig ) information   adds 439 449 bacs together with associated overgo , ssr , and rflp 
 markers , which are used to assemble the contigs and to link contigs onto 
 genetic map coordinates . the order of 
 loci on the bac contigs is represented by over 27 000 sequenced - based loci on 
 the ibm2 fpc057 maps ( http://www.maizegdb.org/cgi-bin/displaymapresults.cgi?term=ibm2+fpc0507 ) 
 in maizegdb , by links to contigs at both the arizona fpc site ( http://www.genome.arizona.edu/ ) and the 
 genome sequencing project ( http://www.maizesequence.org/ ) . as the b73 genome sequence progresses , these 
 bac sequences are added to maizegdb along with links to the sequencing project , 
 both from the bac clones and from genetically mapped loci associated with a 
 bac . the newest maps in maizegdb , 
 ibm snp 2007 ( http://www.maizegdb.org/cgi-bin/displaymapresults.cgi?term=ibm%20snp%202007 ) , 
 are the first of a new generation of genetic maps from the maize diversity 
 project ( http://www.panzea.org/ ) kindly provided 
 pre - publication by dr . mike mcmullen . the snp loci on these maps are associated with allelic sequences from a 
 core set of maize and teosinte germplasm . because the majority of the anticipated 1128 loci have been previously 
 mapped onto bac clones [ 13 , 14 ] , these genetic maps tightly link sequence diversity to the b73 
 genome sequence . maize researchers primarily access maizegdb through the series of interconnected web 
 pages available at http://www.maizegdb.org/ 
 ( see figure 1 ) . these web pages are 
 dynamically generated and are written in php ( the recursive abbreviation for 
 php hypertext preprocessor ) 
 and perl . through this interface , each page shows 
 detailed information on a specific biological entity ( such as a gene ) as well 
 as basic information about data associated with it ( genes are associated with 
 maps , phenotypes , and citations , among others ) . these additional data types are linked to the gene page , enabling quick 
 access to alternative data views . the 
 site also includes links to related resources at other databases ; genes , for 
 example , are linked to gramene . one may access these individual data pages by using either ( 1 ) the 
 search bar located at the top right of every page ( figure 1(a ) ) , or ( 2 ) data 
 type - specific advanced querying tools ( accessible via the  data centers  links ; 
 figure 1(b ) ) on the left side of the home page , or ( 3 ) the bin viewer tool 
 ( figure 1(c ) ) , which is located in the left margin of the home page or via a 
 pull down labeled useful pages  ( figure 1(d ) ) accessible at the top of any 
 maizegdb page . maizegdb 's method of data 
 delivery has three primary goals : placing information within the framework of 
 its scientific meaning , making this information available to the researcher 
 with minimal input ( often only the relevant term ) , and requiring minimal effort 
 from the researcher to comprehend the data displays . by focusing on biological context and ease of 
 use as the primary focus of this interface ( the  production web interface ) , 
 the database is intended to be intuitive to the researcher as their click 
 stream follows a logical path of biological associations . up - to - date site usage statistics can be 
 accessed online at http://www.maizegdb.org / usage/. the production web interface , which most maizegdb users interact with , is only one component of the overall 
 maizegdb infrastructure ( figure 2 ) . the 
 data accessed by the production web interface are typically updated on the 
 first tuesday of each month . prior to being in that production environment , the data are prepared for public 
 accessibility in a staging environment . in the staging environment , the most up - to - date information is 
 available , new data are added to the database , and existing data are updated 
 with new information . in addition to a 
 web interface that appears identical to the one in the production environment , 
 the staging environment offers sql ( structured query language ) read - only access 
 to the community so that researchers interested in interacting with the data in 
 a more direct and customized manner can have access to the most up - to - date 
 information available . in addition , a disaster recovery system has been put 
 in place whereby the curation database is backed up in a compressed format to a 
 separate machine in ames , iowa daily .   once weekly , the ames file is copied to columbia , 
 missouri for off - site storage . to aid in the modeling of new 
 types of data for inclusion in the maizegdb product and to enable programming 
 to be tried out in a safe place , a test 
 environment identical to the staging environment has been created . note that three copies of the database 
 exist . while each environment and server 
 has a specific purpose , all are configured such that they could serve a backup 
 to each other . if any one server was to 
 fail , either of the other two could provide full , unrestricted data access and 
 site functionality . the curation 
 database is backed up on a daily basis and is available for download ( http://goblin1.zool.iastate.edu/~oracle/ ) 
 for those who have oracle relational database management system ( rdbms ) 
 installed locally . also available within the staging environment are community 
 curation tools to enable researchers to add small datasets to the database 
 directly , as well as a set of professional curation tools developed by dr . 
 marty sachs ' group at the maize genetics cooperation - stock center in urbana - champaign . whereas the community 
 curation tools have many safeguards to help researchers enter data step - wise 
 and with enforced field requirements , the professional curation tools allow 
 maizegdb project members as well as stock center personnel to enter datasets in 
 a more stream - lined and powerful fashion with fewer integrity enforcement rules 
 ( which slow down the data entry process considerably ) . it also should be noted that data added to 
 the database via the community curation tools are first marked as 
  experimental  that must be  activated  by professional curators at 
 maizegdb . the availability of a curation web interface ( within the staging 
 environment ) enables researchers to view the data as they will appear once they 
 are uploaded to production . few 
 researchers ( about 30 at present ) have community curation accounts . to increase the use of these tools , training 
 sessions are being organized ( see section 2.3 , below ) . if researchers wish to deposit complex or 
 large datasets , it would not be reasonable to enter the data via the community 
 curation tools because those tools work via a  bottom - up  approach whereby the 
 records are ( 1 ) built based upon the most basic information included in the 
 dataset and ( 2 ) entered one record at a time ( i.e. , not in bulk ) . for complex or large datasets , researchers 
 are encouraged to submit data files to the curators at maizegdb . those data are added to the database directly 
 by curators and the database administrator . each environment 's server has 
 a perpetual license and is supported by oracle rdbms powered by 2  2.0 ghz 
 xeon processors , 4 gb of ram , 5  73 gb ultra 320 10 k rpm drives with red hat 
 advanced server 2.1 operating system installed . the curation database , 
 either partially or in its entirety , can be moved to mysql , microsoft access , 
 and nearly any other portable data format that a researcher would need . requests to gain read - only sql access to the curation 
 database can be made via the feedback link that appears at the bottom of any 
 maizegdb page . data housed at maizegdb 
 are in the public domain and are freely available for use without a license . one of the strengths of maizegdb is its responsiveness to 
 community input , received either personally or by the feedback forms accessible 
 at the bottom of each page ( figure 1(e ) ) . 
 to provide outreach and user support as well as to solicit input from 
 researchers in a more active manner , the maizegdb tutorial 
 ( figure 1(f ) ) can be reached from the home page at the top of the left 
 margin . a new user can go through this 
 tutorial , and become familiar with how to use the site quickly . in addition , a  site tour  with an 
 overview with examples can be found under the more 
 specific tutorial examples and other educational materials are available via 
 the  education  link , also within the  useful pages  pull down menu . also , on 
 many of the  data center  pages ( available 
 from the left margin of the front page or via the useful pages  pull down ) a 
 discussion of the topic of the page that is suitable for the general public 
 appears toward the bottom . representatives from maizegdb attend and help 
 researchers at the annual maize genetics conference ( usually in march ) , the 
 international plant and animal genome conference ( january ) , and various other 
 meetings through direct interaction in person . about three times a year , an expert curator travels to various research locations and 
 provides tutorials and support for maize researchers . for these visits , the local maize researchers 
 are asked for a list of specific questions ahead of time . during the one to two day visits , researchers 
 interact in groups and one - on - one with the traveling curator to learn how to 
 utilize maizegdb for their research and to deposit data at maizegdb . two members of the maizegdb team , mls and 
 tes , serve as ex officio 
 members of the maize genetics conference steering committee . they collect electronic abstracts for the 
 annual maize genetics conference and handle the preparation and printing of the 
 program for the conference . maizegdb personnel also manage regular community 
 surveys on behalf of the maize genetics executive committee . these surveys enable the executive committee 
 to summarize the overall research interest of the maize community and to advise 
 funding agencies on future research directions . maizegdb personnel also manage the executive committee 's website ( i.e. , http://www.maizegdb.org/mgec.php ) and 
 conducts the executive committee 's elections . maizegdb houses the mailing list 
 for the annual maize newsletter and project personnel conduct semi - regular 
 mailings to the maize community on behalf of interested researchers by 
 maintaining an electronic list of researchers ' contact information . to demonstrate how researchers utilize maizegdb , three example usage cases are 
 presented here . because researchers with 
 very different goals can all utilize maizegdb to advance their work , the usage 
 cases are classified by research type : basic , translational , and applied . see figure 3 for examples of how these 
 research types fit together . by enabling 
 researchers to carry out workflows that support translational and applied 
 research , although a single researcher might even 
 include all of these three aspects in his / her research simultaneously , here the 
 researcher types are distinguished as follows : basic researchers investigate 
 the fundamental biology of the organism , translational researchers work to 
 determine the application of basic research outcomes for practical purposes , and applied researchers 
 implement proven technologies to improve crops . many basic researchers work with mutants to understand the 
 processes underlying biological phenomena . once a new mutant is found , there are several standard methods used to 
 elucidate normal gene functions . these 
 efforts include determining whether the mutant represents an allele of a 
 previously described gene , and if not , genetic mapping and cloning of the new 
 gene . information stored in maizegdb is 
 useful in all of these steps . in a large screen for mutations that change pericarp pigmentation from red to some other color , 
 researcher 1 has found a plant with a brownish - red pericarp coloration . she first wants search maizegdb to find all 
 known mutants that have red pericarp phenotypes to determine whether this 
 mutation represents a newly discovered gene . 
 because she does not know how others might have described the phenotype , 
 she decides to browse existing phenotype terms and images . from the left margin of the maizegdb 
 homepage , she selects  mutant phenotypes  under  data centers - functional .  on this page ( http://www.maizegdb.org/ ) , 
 she selects pericarp color  from the pull down menu labeled 
  show only phenotypes relating to this trait  in the green search 
 bar . a number of possible mutant phenotypes 
 are returned , including  red pericarp .  clicking on the  red pericarp phenotype 
 link , she finds that the listed mutants are alleles of p1 ( pericarp 
 color1 ) . on this page ( http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id=13818 ) , 
 she scrolls to the bottom and finds that there are many stocks that can be 
 ordered from the maize genetics cooperation - stock center that carry p1-rr ( an allele that causes red pericarp and red cob ) or p1-rw ( red pericarp and white cob ) . having these stocks in hand will enable her 
 to test whether the new mutant represents an allele of the p1 gene , so she decides to order a few for complementation 
 analyses . clicking on the stock links 
 listed on the variation / allele page allows her access to a shopping cart 
 utility ( in the green right hand panel ) , and she orders seed from the stock center 
  directly through the maizegdb interface . she then goes back to the results of 
 her  pericarp color  query and repeats the process for  cherry pericarp ,  
 ordering stocks for r1-ch ( colored1-cherry ) , also to be used in her 
 complementation analyses . ( another way 
 she could have found maize stocks that have red pericarp is the following : from the header of any page , select this pulls up 
 the stock search page http://www.maizegdb.org/stock.php . in the green box , select stocks with the 
 phenotype  red pericarp  from the pull down menu of all phenotype names and 
 submit . a long list of stocks that 
 contain alleles of p1 with red 
 pericarp is returned . alternatively , the stock center catalog is 
 also available from the stocks data center page . ) researcher 1 receives several 
 appropriate stocks and performs allelism tests and determines that her mutant 
 ( which turns out to be recessive ) is not allelic to p1 or r1 . she returns to maizegdb and again looks 
 through  mutant phenotype  results using the  pericarp color  
 query . listed there are brown pericarp , 
 orange pericarp , white pericarp , and lacquer red pericarp phenotypes in 
 addition to the red and cherry phenotypes she focused on initially . she finds that there is no stock available 
 for the brown pericarp phenotype ( the brown 
 pericarp1 mutant has been lost ) , and all the others are alleles that confer 
 colored pericarp in the dominant condition as a result of the presence of p1 alleles . to determine whether the new mutation could 
 be an allele of bp1 maizegdb houses the largest 
 collection of publicly available genetic maps of maize ( currently over 1,337 
 maps ) . these include maps of genes 
 primarily defined by mutants with morphological phenotypes (  genetic 2005  
 is the most current ) , maps based on phenotypic molecular markers , and composite 
 maps where various maps have been integrated . these maps can be easily accessed from the home page , via the left 
 margin link to this page not only allows various map search 
 functions , but also provides information on the most popular maps and a handy 
 reference to explain more about the various composite maps . the maize genome 
 is divided into genetic bins of approximately 20 centimorgans each and boundary 
 markers with nearby ssrs can be used for mapping ( for further explanation see http://www.maizegdb.org/cgi-bin/bin_viewer.cgi ) . researcher 1 decides to utilize ssrs to map 
 her gene to bin resolution . to find the 
 core markers from the home page , she clicks on  tools - bin viewer  in the left margin of the 
 home page this provides a list of the 
 core bin markers and a link to purchase relevant primers to screen her mapping 
 population . she generates a mapping 
 population , performs pcr experiments using the polymorphic markers , and maps 
 her mutant to bin 9.02 . to see what genes 
 are located in bin 9.02 , she goes back to the bin viewer ( from the homepage ) , 
 and holds the curser over the image of chromosome 9 until she sees the result is a 
 long list of genes , other loci , sequences , est contigs , ssrs , bacs , and other data 
 relating to bin 9.02 . searching through 
 this data , she sees that bp1 is 
 listed under  other loci  in bin 9.02 . this is a  lapsed locus  meaning 
 that the stock has been lost , but perhaps she has found a new allele ! to see more 
 specific genetic mapping data on bp1 , 
 she goes to the search bar along the top green bar of every page , selects 
  loci  from the pull down menu , types bp1  into the field 
 provided , and clicks the button marked  go ! this brings her to the bp1 locus page ( http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=61563 ) 
 where she can see that bp1 is placed 
 on three genetic maps . clicking on each 
 map , researcher 1 learns that in 1935 , bp1 was mapped between sh1 and wx1 ( shrunken1 and waxy1 ) , two well - studied 
 genes . to search for molecular markers 
 suitable for fine structure mapping data centers - genetic - maps  from the link on the home page . in the green advanced search box , she 
 enters sh1 and wx1 separately in the  show only maps containing this 
 locus  lines . she finds sh1 at position 80.30 , and wx1 at 185.00 . to choose among several molecular 
 markers , researcher 1 follows the available links leading her to information 
 about suitable primers , a number of variations ( which can help to decide if 
 there may be a polymorphism in her mapping populations ) , gel patterns , and any 
 available genbank accession numbers for sequences as well as sequenced 
 bacs . as she 
 finds markers closer and closer to the gene , she can proceed with positional 
 cloning to determine whether the position is consistent with bp1 ( nice examples of how this is done 
 can be found in [ 1921 ] ) . research to understand the metabolic pathways that produce 
 pigmentation ( like those outlined in section 3.1 ) are well studied in maize . one example of a 
 well - characterized gene that confers pigmentation is p1 , which encodes a transcription factor that regulates synthesis 
 of flavones such as anthocyanins . the p1 gene , along with its adjacent duplicate pericarp color2 ( p2 ) , 
 controls pericarp and cob coloration and causes silks to brown when cut . one flavone produced by the pathway is 
 maysin , a compound which has been shown to be antinutritive to the corn ear 
 worm at concentrations above 0.2% fresh weight if husks limit access to the ear 
 such that feeding on silks is required for the insect to enter . many qtl for resistance 
 to corn earworm map near loci in the flavone synthesis pathway that are either 
 regulatory genes ( such as p1 and p2 ) , or at rate - limiting enzymatic 
 steps , such as c1 ( chalcone synthase1 ) that contribute 
 maysin accumulation in silks . understanding how maysin 
 functions and how this information could be used for production agriculture is 
 researcher 2 's area of expertise . researcher 2 has investigated 
 maysin synthesis for some time , and has decided to clone an uncharacterized 
 maysin qtl near umc105a , in the bin 
 9.02 , which is bounded by bz1 and wx1 . he believes that the qtl 
 may be a previously described , but lost , bp1 mutant thought to be involved in maysin synthesis . in the first step , he must first find 
 molecular markers to more finely map the region ( his preference would be to use 
 ssrs , since members of the lab are already using them successfully ) . he plans to follow the strategy of chromosome 
 walking to narrow down the region of interest [ 1921 ] followed by association mapping to identify the actual qtl 
 sequence [ 26 , 27 ] . knowing this sequence 
 would enable plant breeders to track the qtl for marker assisted selection . to find ssr data 
 for mapping to a bin region , researcher 2 goes to the maizegdb home page and clicks 
 on  data centers - genomic - molecular markers / probes  in the left margin , 
 then clicks the  ssr link at the top of the page ( the link is located in  specific 
 information is available on bacs , ests , overgos , and ssrs . a report is returned that lists the available 
 ssrs for bin 9.02 , complete with primers , gel patterns for different germplasm , 
 and related maps . by going back to the 
 ssr page , he also downloads tabular reports of map locations of all ssrs on 
 chromosome 9 , including those that have been anchored to a bac contig . using this information in the laboratory , members of his research group perform mapping experiments using several ssrs in 
 bin 9.02 along with some others in the more distal part of bin 9.03 . they discover that the mid - region peak for 
 the qtl is very near an ssr for bnlg1372 , 
 which is anchored to a bac contig . to find sequenced 
 bacs that may harbor the earworm resistance qtl , researcher 2 uses the search 
 bar at the top of each maizegdb page to find the locus bnlg1372 . at the top of the bnlg1372 page , he follows a link to the 
 contig 373 display at the maize sequencing project site ( http://www.maizesequence.org/ ) . this is a rather large contig with many 
 sequenced bacs and assigned markers . at 
 the maize sequencing project site , he uses the export function ( a button at the 
 left margin ) to view a text list of all the markers and sequenced bac clones 
 that are available on the finger print contig physical map . this information provides coordinates for viewing the region on a large 
 contig associated with bnlg1372 , the 
 sequence of bac c0324e10 , and any other bacs nearby . researcher 2 sequences 
 candidate regions in diverse germplasm and conducts association analysis using 
 silk maysin levels as a trait . this may 
 require other information about nearby markers , which also are accessible via 
 maizegdb [ 28 , 29 ] . although these investigations 
 may require the development of further sequenced - based markers , researcher 2 
 hopes that useful markers already exist and decides to explore maizegdb for any 
 other sequences or primer - based markers already assigned to the region of 
 interest including snps and indels . to 
 do this from the locus page for bnlg1372 , 
 he clicks on the link to the most current ibm neighbors map listed , then 
 explores the  sequence  and  primer  view versions of the map by clicking on 
 the relevant links at the top of the page just under the map name . the primer view shows primers associated with 
 mapping probes along with the name of the probes  just what he needs to get going with the 
 association mapping work . interested in breeding plants for organic sweet corn production , 
 researcher 3 has decided to use molecular markers to select for high maysin 
 content , which would increase resistance to the corn earworm  a cause of significant damage to sweet corn . although plants could be 
 genetically modified to carry the genes that confer high maysin levels in silks 
 ( e.g. , see ) , researcher 3 's farming clients require that their product be 
 certified as both organic and  gmo - free .  
 to meet the producers ' needs , he has decided to pursue a marker - assisted 
 selection program to create high maysin sweet inbred lines , which he will use 
 to generate single - cross hybrids . to get 
 started with the work , he searches maizegdb to find references , markers , and 
 stocks for the project . described here 
 are the details on how he could use maizegdb to ( 1 ) access stocks known to have 
 high maysin content directly and ( 2 ) locate relevant stocks based upon 
 associated data with no prior knowledge of which stocks he wants to find . an outline of how he uses maizegdb to 
 identify relevant selectable markers for tracking the various qtl associated 
 with maysin accumulation also is described . in the instance 
 of looking for particular stocks , researcher 3 has identified gt114 as a high 
 maysin line from . using the green search 
 bar at the top of any maizegdb page , he searches at that page , he sees a brief annotation 
 stating that gt114 is a poor pollen producer and makes a note of that 
 observation and plans to cross by ia453 and ia5125 , sweet lines that produce pollen 
 well , to ameliorate this potential difficulty . clicking the link to gt114 , he sees that it is an inbred line derived 
 from gt - ddsa ( dd syn a ) in georgia , and it is made available via grin . 
 selecting the link for grin , listed there are the crop science registration data , availability ( noted as currently 
 unavailable , but a call to mark millard , maize curator at the maintenance site 
 indicates that he could access that stock in limited quantities if current 
 resources allow ) , and an image of bulk kernels among other information . the image of bulked kernels is especially 
 revealing : the kernels are yellow and the cob fragments appear red . aware that 
 a red cob would be unacceptable for breeding sweet corn ( the red pigment could 
 cause quite a mess for those cooking and eating corn on then cob ) , he decides 
 to search maizegdb for other available high maysin stocks . after a literature search of breeding stocks with a white cob that might still produce 
 maysin in the silks , researcher 3 starts searching stocks for those known to 
 carry the p1-wwb allele , a dominant 
 allele of the p1 locus that confers 
 white pericarp , white cob , and browning silks . 
 by clicking the  data centers - genetic - stocks  link from the maizegdb homepage , he 
 arrives at the stocks data center 
  page ( which is also accessible via the  useful pages  pull down at the top of 
 every maizegdb page ) . he uses the 
 advanced search box to limit the query by variation to those stocks associated 
 with the allele p1-wwb . a number of the stocks returned on the 
 results page have been evaluated for silk maysin accumulation ( per associated 
 publications ) and could be further investigated as potential breeding stocks . although the p1 gene accounts for much of the 
 variability in maysin accumulation , association and qtl analyses for candidate genes for maysin 
 accumulation also have identified anthocyaninless1 ( a1 ) , colorless2 ( c2 ) , and white pollen1 ( whp1 ) as contributing significantly [ 32 , 33 ] . researcher 3 can track 
 the dominant p1-wwb allele visually by selecting for browning silks given that the sweet 
 lines he will be using in the breeding program have silks that do not brown , 
 but tracking the other factors will require the use of molecular markers . to find molecular markers to select for 
 desirable alleles of , for example , a1 , 
 researcher 3 uses the search menu at the top of any page at maizegdb to find 
  loci  using the query  a1 . the results 
 page ( http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=a1 ) lists many loci with a1 as a substring , but shows the exact match 
 ( the a1 locus ) at the top of the 
 list . clicking on that link shows the a1 locus page ( http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=12000 ) , 
 which lists useful information including six probes / molecular markers that 
 could be used for tracking useful a1 alleles . using the same process , he also 
 finds markers for the c2 and whp1 loci and sets to work determining 
 which markers to use for his selections . because maizegdb stores and makes accessible data of use for a 
 variety of applications , it is a resource of interest to maize researchers 
 spanning many disciplines . the fact that 
 basic research outcomes are tied to translational and applied data enables all 
 researcher types to utilize the maizegdb resource to further their research 
 goals , and connections to external resources like gramene , ncbi , and grin make 
 it possible for researchers to find relevant resources quickly , irrespective of 
 storage location . at present , maize geneticists are at the cusp of a milestone : the 
 genome of the maize inbred b73 is being sequenced in the u.s . , with 
 anticipated completion in 2008 . in addition , scientists working in mexico at langebio ( the national genomics for 
 biodiversity laboratory ) and cinvestav ( centro de investigacion y estudios 
 avanzados ) have announced through a press release ( july 12 , 2007 ) that they 
 completely sequenced 95% of the genes with 4x coverage in a native mexican 
 popcorn called palomero , though the data have not yet been released and the quality 
 of the data is unknown ( see http://www.bloomberg.com/apps/news?pid=20601086&sid=ao.xj8ybaexi&refer=latin_america ) . at present and as more maize sequence becomes 
 available relating sequences to the existing compendium of maize data is the primary need that must be met for maize 
 researchers in the immediate future . creating and conserving relationships among the data will enable 
 researchers to ask and answer questions about the structure and function of the 
 maize genome that previously could not be addressed . to address this need , maizegdb personnel genome view  by adopting and customizing a genome browser that could 
 be used to integrate the outcomes of the maize genome sequencing project . for genome browser functionality , basic 
 researchers have an interest in visualizing genome structure , gene models , 
 functional data , and genetic variability . translational researchers would like to be able to assign values to 
 genomic and genetic variants ( e.g. , the value of a particular allele in a given 
 population ) and to view those values within a genomic context . applied researchers are interested in tagging 
 variants for use as selectable markers and retrieving tags for particular 
 regions of the genome . will allow researchers to visualize 
 a gene within its genomic context and a soon to be created  pathway view will 
 enable the visualization of a gene product within the context of relevant 
 metabolic pathways annotated with plant ontology ( http://www.plantontology.org/ )   and gene ontology ( http://www.geneontology.org/index.shtml ) 
  terms . by making sequence information 
 more easily accessible and fully integrated with other data stored at maizegdb , it will become possible for researchers to begin to investigate how sequence 
 relates to the architecture of the maize chromosome complement . is it possible to relate the genetic and 
 cytological maps to the assembled genome sequence ? are there sequences present at centromeres 
 that signal the cell to construct kinetochores , the machines that ensure proper 
 chromosome segregation to occur , at the correct site ? maizegdb aims to enable researchers to 
 discover answers to such queries that will enhance the quality of basic maize 
 research and ultimately the value of maize as a crop . it will become possible to interrogate the 
 database to find answers to these and other complex questions , and the content 
 of the genome can better be related to its function , both within the cell and 
 to the plant as a whole . convergence of traditional 
 biological investigation with the knowledge of genome content and organization 
 is currently lacking , and is a new area of research that will open up once a 
 complete genome sequence and a method for searching through the whole of the 
 data are both in place . it is the ability to investigate and answer 
 such basic research questions that will serve as the basis for devising sound 
 methods to breed better plants . once the 
 relationships among sequence data and more traditional maize data like 
 genotypes , phenotypes , stocks , and so forth have been captured , it is important that 
 those data be presented to researchers in a way that can be easily understood 
 without requiring that they have any awareness of how the data are actually 
 stored within a database . it is these 
 needs  creating connections between sequence and 
 traditional genetic data , improving the interface to those data , and 
 determining how sequence data relate to the overall architecture of the maize 
 chromosome complement  that the maizegdb team seeks to fulfill in the 
 very near future .
in 2001 maize became the number one production crop in the world with the food and agriculture organization of the united nations reporting over 614 million tonnes produced . 
 its success is due to the high productivity per acre in tandem with a wide variety of commercial uses . 
 not only is maize an excellent source of food , feed , and fuel , but also 	  its by - products are used in the production of various commercial products . 
 maize 's unparalleled success in agriculture stems from basic research , the outcomes of which drive breeding and product development .   in order for basic , translational , and applied researchers to benefit from others ' investigations , 
 newly generated data must be made freely and easily accessible . 
 maizegdb is the maize research community 's central repository for genetics and genomics information . 
 the overall goals of maizegdb are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities .