On March 1, 2004, Beijing Genomics Institute (BGI) of Chinese Academy of Sciences (CAS) announced the construction of a chicken sequence variation map. This project, led by BGI, is complementary to the work of an international consortium that also announced the first sequence map for the chicken genome at the same day. The chicken sequence variation map project was supported by CAS, the Ministry of Science and Technology, the National Natural Science Foundation of China, and the Wellcome Trust, UK. The team has scientists from China, USA, UK, Sweden, Netherlands, and Germany.
The variation map was derived form three different domestic chicken strains,consisting of a broiler strain from the UK, a layer strain from Sweden,and a Silkie strain from China,by using the genome sequence of Red Junglefowl (RJF),believed to be the wild ancestor of domestic chickens, assembled by Washington University Genome Sequencing Center (WUGSC) as a reference framework.. For each of the domestic birds we sampled 1/4 coverage of the genome (a million sequence reads for each)by using Amersham MegaBACE 1000 capillary machines. About 2.8 million non-redundant single-nucleotide polymorphisms (SNPs) and 0.3 million insertion-deletions (Indels) were identified by now. Final analysis results of the chicken variation map project are expected to be published this summer.
In order to facilitate the usage of the most up-to-date knowledge about the chicken sequence variations, we develop the Chicken Variation Database (ChickVD) as an integrated information system for storage, retrieval, visualization and analysis of chicken variation data. ChickVD will assist researchers that are trying to use experimental or computational methods to analyze the functional and phenotypic consequences of sequence variations, and pave the way for discovery of the correlations between genetic, genotype and phenotype. ChickVD continues to make enhancements to its data quality, utility and functionality, aiming at benefiting the biomedical and agricultural researchers around the globe and contributing to the understanding of avian genetics.
We are grateful to Dr Jean M.Buerstedde, Dr Simon Hubbard, Dr Chris P Ponting and Dr Caleb Webber for offering us their unpublished data. We also wish to thank our colleagues from Roslin Institute, Department of Medical Biochemistry and Microbiology of Uppsala University, USDA-ARS Avian Disease and Oncology Laboratory, and Animal Breeding and Genetics Group of Wageningen University for offering us their QTL information. We welcome the chicken research community to make constructive suggestions for our continuous effort in making ChickVD a user-friendly knowledge resource.