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

Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyun, Wang, Xioaling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mmingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xingang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, LaDeana W., Yang, Shuaw-Pyng, Warren, Wesley C., Wilson, Richard K., Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P. M. A., van der Poel, Jan J., Bovenhuis, Henk, Groenen, Martien A. M., Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R., Rogers, Sally, Walker, Brian A., van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J., Zhou, Huaijun, Hocking, Paul M., Morrice, Dvaid, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W., Hunt, Henry, Cheng, Hans H., Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T., Andersson, Björn, Webber, Caleb, Ponting, Chris P., Overton, Ian M., Boardman, Paul E., Tang, Haizhou, Hubbard, Simon J., Wilson, Stuart A., Yu, Jun, Wang, Jian and Yang, HuanMing 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432 (7018) , pp. 717-722. 10.1038/nature03156

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Abstract

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.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Medicine
Publisher: Nature Research
ISSN: 0028-0836
Date of Acceptance: 1 November 2004
Last Modified: 21 Oct 2020 15:00
URI: http://orca-mwe.cf.ac.uk/id/eprint/135817

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