A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

International Chicken Polymorphism Map Consortium, Gane Ka-Shu Wong, Bin Liu, Jun Wang, Yong Zhang, Xu Yang, Zengjin Zhang, Qingshun Meng, Jun Zhou, Dawei Li, Jingjing Zhang, Peixiang Ni, Songgang Li, Longhua Ran, Heng Li, Jianguo Zhang, Ruiqiang Li, Shengting Li, Hongkun Zheng, Wei LinGuangyuan Li, Xiaoling Wang, Wenming Zhao, Jun Li, Chen Ye, Mingtao Dai, Jue Ruan, Yan Zhou, Yuanzhe Li, Ximiao He, Yunze Zhang, Jing Wang, Xiangang Huang, Wei Tong, Jie Chen, Jia Ye, Chen Chen, Ning Wei, Guoqing Li, Le Dong, Fengdi Lan, Yongqiao Sun, Pete Kaiser, Lisa Rothwell, Paul M Hocking, David Morrice, Dirk-Jan de Koning, Andy Law, David W Burt, Chris Ponting, Ian M Overton

Research output: Contribution to journalArticlepeer-review


We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
Original languageEnglish
Pages (from-to)717-22
Number of pages6
Issue number7018
Publication statusPublished - 2004


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