chicken ( gallus gallus ) is an important model organism for biomedical research , the study of embryology and development ( 1,2 ) , aging ( 3 ) , quantitative trait loci ( qtl ) analysis ( 4 ) , in addition to being a major food source . through the comprehensive study of sequence polymorphisms in the chicken , significant progress can be made in understanding the phenotypic differences between individuals / strains and the evolution of populations . towards this end , the beijing genomics institute ( bgi ) led an international team of scientists from china , usa , uk , sweden , the netherlands and germany to identify and characterize extensive dna sequence variation throughout the chicken genome . sequence variation within the genomes of three different breeds of domesticated chickens [ a male broiler ( cornish ) from roslin institute , a female layer ( white leghorn ) from swedish university of agricultural sciences and a female silkie from the chinese agricultural university in beijing ] , was identified by direct comparison with the genome sequence of the red jungle fowl ( rjf ) , assembled by the washington university genome sequencing center ( wugsc ) , as a reference chicken genome sequence ( chicken genome consortium , 2004 ) . from these comparisons 3.1 million unique , high - quality sequence variants were identified , primarily single nucleotide polymorphisms ( snps ) . in order to facilitate the use of this information , we created the  chicken variation database ( chickvd ) , an integrated information system for the storage , retrieval , visualization and analysis of chicken dna sequence variation . to enhance the discovery of relationships between sequence variation and genes , we mapped each variant onto the rjf reference genome sequence in the context of gene annotations and other relevant features , such as genetic markers and qtls . therefore the chickvd database , provides both a powerful information resource and an analysis workbench for applications in biological research , medicine and agriculture . the primary purpose of the chicken snp project was to discover and map extensive sequence variation in the chicken genome , to increase the density of markers on the genetic map , and to facilitate studies on the genetic basis of phenotypic traits . we compared the sequence reads from the three chicken breeds to the 6.6x rjf reference genome sequence ( chicken genome consortium , 2004 ) . for each of the breeds , we sampled 25% of the genome ( a million sequence reads from each breed ) using automated capillary sequencers ( amersham megabace 1000 ) . to minimize sequencing errors , we used the phred quality score ( q - value ) ( 5,6 ) to set minimum thresholds . for base substitutions , we used conservative thresholds of > q25 at the variant site and > q20 for the two flanking 5 bp regions . even more stringent thresholds of q30 and q25 were used to score insertion  deletions ( indels ) . using a genome - wide blastn search , we were able to determine the sequence position on the rjf genome assembly and eliminate confusion between paralogs . a subset of polymorphisms was confirmed by pcr - based resequencing from the lines in which they were initially detected . to display each sequence variant in the context of its physical relationship to the nearest gene or other relevant features , we employed a number of methods to identify these target sequences . these included annotations within public databases , homology searches , prediction programs and information on experimentally derived genes . a non - redundant dataset of genes / cdnas was integrated within chickvd , including ensembl gene annotations ( 7 ) , genbank genes with complete cds ( 8) , full - length cdnas ( 9 ) ( http://pheasant.gsf.de/department/dt40/dt40transcript.html ) and chicken orthologs of human disease genes ( c. webber and c. p. ponting , unpublished data ) . we used blat ( 10 ) to map these sequences using the rjf reference genome , sim4 ( 11 ) to determine the detailed exon intron boundaries and then classified coding snps into synonymous or non - synonymous substitutions . to associate the location of sequence variants with genetically mapped phenotypic traits , we included information on mapped qtls , using data provided by a number of collaborating institutions ( roslin institute , department of medical biochemistry and microbiology of uppsala university , usda - ars avian disease and oncology laboratory , animal breeding and genetics group of wageningen university ) and public resources , such as chickace ( https://acedb.asg.wur.nl/ ) . chickvd contains 3.1 million dna sequence variants ; 2.8 million are categorized as snps and 0.3 million are indels . follow - up experiments indicate that over 90% of these snps are true snps , over 70% are common snps that segregate in many chicken breeds and the mean nucleotide diversity is estimated to be 5 snp / kb ( international chicken polymorphism map consortium , 2004 ) . for the convenience of data display , all types of dna sequence variation ( substitutions , insertions or deletions ) are referred to as snps. snp information is detailed in a  snp report , including type , allelic differences , flanking sequences and pcr - primer designs , location , associated genes and quality scores of sequence reads , functional site in the chicken genome ( e.g. coding region , intron , untranslated regions ) , and details of any predicted or known functional outcomes ( e.g. codon and deduced amino acid changes ) . for additional information to the potential user , 1.5 million contig - covered ( ctgcov ) regions from the broiler , layer and silkie are aligned to the rjf reference genome and 2.5 million raw sequence traces are available within chickvd . for queries about gene - associated polymorphisms , gene report , including gene structure , functional classification , gene ontology ( 12 ) and interpro ( 13 ) annotations , gene - associated snps , and nucleotide / protein sequences . for chicken orthologs of human disease genes , hypertext links to the given ensembl files of human disease genes and omim entries of disease descriptions ( 14 ) a collection of 606 qtls for a wide range of traits are integrated and cross - referenced to markers , genetic maps , genes and snps mapped onto the same chromosomal region , and to pubmed ( 15 ) for literature sources . chickvd also hosts a collection of 884 references , which focus on chicken sequence variation , qtl study and basic chicken biology . a summary of chickvd content is shown in table 1 and all data are freely available from our ftp site ( http://chicken.genomics.org.cn/chicken/jsp/download.jsp ) . all data housed in chickvd are uniquely mapped onto the rjf reference genome and graphically represented in mapview , an efficient visualization tool initially developed in our rice information system ( bgi - ris ) ( 16 ) that allows users to browse snps in genomic and functional context . mapview is composed of four types of subviewers in hierarchical architecture , namely chroview , geneview , snpview and traceview ( figure 1 ) . chroview is based on the reference sequence of rjf with qtls marked along chromosomes , and displays density and statistics of genes and snps . chroview also allows users to center the map onto a specific chromosome location and make options to expand for more detailed views of genes / cdnas , snps via geneview and snpview , respectively . a factual report for each element contained in the visualization system is displayed automatically on demand . q - values for each nucleotide and a position - location function facilitate further investigation of the snps . the chickvd online search tool is the entry point for querying snps and other data types in the database . the results can be further restricted to a specific chicken breed , a certain snp type , a threshold of quality score or to a specific snp functional class , such as a coding non - synonymous snp . blast - based snp search compares a user - supplied sequence against the flanking sequences that immediately surround the sequence variant . advanced search interfaces for other data types ( genes / cdnas , qtls , sequence traces and references ) are also provided . for sequence searches , a key development is the implementation of seqgetter , a search tool that allows extraction of all variations residing within genomic domains , as defined by flanking elements that can be other variants , chromosomal positions , genes , or even specific coding sequences , introns or regulatory domains . chickvd consists of three hardware components , a world wide web server , a database server and a sequence analysis / homology search server . the system is based on an oracle9i relational database , and the front end consists of a set of jsp scripts running on tomcat web server . java applets are applied for traceview functions . to handle the large amount of complex data , we developed the standard sets of snp - centric and qtl - centric xml formats that lay the foundation for our research work and allow chickvd to accommodate the fast - accumulating data and to integrate new data types when they arise . chickvd will also be updated for each new chicken genome update , including annotations and more qtls , markers and references , as soon as they become available . so in the near future , it will be possible for users to retrieve data from different versions , trace up and locate changes of a given entity between different versions . new versions of chickvd will integrate allele frequencies of each variation site from ongoing projects with collaborating institutions . to enhance data utility , our development efforts will extend data structures and establish systems to support haplotype information that is expected to become the principal functional unit for chicken genetics . chickvd continues to make enhancements to user interfaces , improve the functionality of searches and data representation , and evolve the database infrastructure and data model to ensure data quality and consistency . a side - by - side comparative map viewer will make comparative analysis of the snp map and chicken genes easier . we welcome comments and suggestions from the chicken research community to make chickvd a user - friendly knowledge resource . this project was funded by the chinese academy of sciences , commission for economy planning , ministry of science and technology ( 2002aa104250 , 2002aa234011 , 2001aa231061 , 2001aa231011 , 2001aa231101 and 2004aa231050 ) , danish national research foundation ( danish platform for integrative biology ) and the china national grid ( 2002aa104250 ) .
working in parallel with the efforts to sequence the chicken ( gallus gallus ) genome , the beijing genomics institute led an international team of scientists from china , usa , uk , sweden , the netherlands and germany to map extensive dna sequence variation throughout the chicken genome by sampling dna from domestic breeds . using the red jungle fowl genome sequence as a reference , we identified 3.1 million non - redundant dna sequence variants . to facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies 
 , we created the  chicken variation database ( chickvd ) . 
 a graphical mapview shows variants mapped onto the chicken genome in the context of gene annotations and other features , including genetic markers , trait loci , cdnas , chicken orthologs of human disease genes and raw sequence traces . 
 chickvd also stores information on quantitative trait loci using data from collaborating institutions and public resources . 
 our data can be queried by search engine and homology - based blast searches . 
 chickvd is publicly accessible at http://chicken.genomics.org.cn .