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Last Modified 2006-12-16
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    On March 1, 2004 , the National Human Genome Research Institute (NHGRI) announced the accomplishment of the first draft of the chicken genome sequence of Red Junglefowl (RJF), which is believed to be the wild ancestor of domestic chickens. Towards this end, the Beijing Genomics Institute (BGI) led an international team of scientists from China, USA, UK, Sweden, Netherlands, Germany, having created a sequence variation map for three different breeds from domestic chickens (a male broiler (Cornish) from Roslin Institute, a female layer (White Leghorn) from Swedish University of Agricultural Sciences, and a female Silkie from Chinese Agricultural University in Beijing). Using the RJF genome sequence as a reference framework, we identified 3.1 million non-redundant, high-quality sequence variation sites in the genome, primarily as single nucleotide polymorphisms (SNPs).
    To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we implemented the Chicken Variation Database (ChickVD) timely. ChickVD hosts the high-quality sequence variation data, variation analysis in the context of chicken genes, cDNAs, chicken orthologs of human disease genes, genetic markers, quantitative trait loci (QTLs) etc . All data are uniquely mapped onto the RJF draft genome and graphically represented in MapView, an efficient visualization tool that allows users to browse sequence variations in the genomic and functional context. The sub-viewer TraceView assists users to view the vivid graphics of the original traces around the detected SNP. Users may query the data by the online search tool and define concrete limitations to extract records that are best suited to their research needs. For the convenience of data presentation in ChickVD, different types of sequence variations (substitutions, insertions or deletions) are all referred as ???SNPs'. ChickVD is updated constantly as more data generated and is under the continued improvement for its content and functionality.

  More...

•  3,624,831 sequence variation sites identified, including 1,190,072 in the Broiler, 1,009,693 in Layer and 1,425,066 in Silkie.
•  35,647 genes or full length cDNAs, including 2,068 GenBank genes, 28,416 Ensembl gene annotations, 1,825 Riken1 full-length cDNAs, 1,943 BBSRC full-length cDNAs, 995 chicken orthologs of human disease genes etc..
•  1,397,577 SNPs are associated with 33,566 Genes.
•  2,544,985 raw sequence traces, among which 1,205,058 are SNP-associated.
•  606 QTLs are collected from both cooperative institutions and public resources.
•  884 references are collected with focus on chicken variation and QTL study.

  • ChickVD: a sequence variation database for the chicken genome
    Nucleic Acids Research 33, 438-441 (2005)    ( PDF )
  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    Nature 432, 695-716 (2004)    ( PDF    HTML )
  • A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
    Nature 432, 717-722 (2004)    ( PDF    HTML )
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