A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
Ka-Shu Wong, Gane; 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, Guangyuan; Wang, Xiaoling; Zhao, Wenming; Li, Jun; Ye, Chen; Dai, Mingtao; Ruan, Jue; Zhou, Yan; Li, Yuanzhe; He, Ximiao; Zhang, Yunze; Wang, Jing; Huang, Xiangang; 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; sequence of red jungle fowl: Washington University School of Medicine, Genome; Hillier, LaDeana W.; Yang, Shiaw-Pyng; Warren, Wesley C.; Wilson, Richard K.; evolution: Uppsala University, Molecular; Brandström, Mikael; Ellegren, Hans; genotyping, BAC sequences and haplotypes: Wageningen University, Population; Crooijmans, Richard P. M. A.; van der Poel, Jan J.; Bovenhuis, Henk; Groenen, Martien A. M.; Livermore National Laboratory, Lawrence; Ovcharenko, Ivan; Gordon, Laurie; Stubbs, Lisa; Joint Genome Institute, DOE; Lucas, Susan; Glavina, Tijana; Aerts, Andrea; of application to complex traits: Institute for Animal Health, Examples; Kaiser, Pete; Rothwell, Lisa; Young, John R.; Rogers, Sally; Walker, Brian A.; van Hateren, Andy; Kaufman, Jim; Bumstead, Nat; State University, Iowa; Lamont, Susan J.; Zhou, Huaijun; Institute, Roslin; Hocking, Paul M.; Morrice, David; de Koning, Dirk-Jan; Law, Andy; Bartley, Neil; Burt, David W.; Avian Disease and Oncology Laboratory, USDA-ARS; Hunt, Henry; Cheng, Hans H.; and selection: Uppsala University, Domestication; Gunnarsson, Ulrika; Wahlberg, Per; Andersson, Leif; Institutet, Karolinska; Kindlund, Ellen; Tammi, Martti T.; Andersson, Björn; disease genes: University of Oxford, Human; Webber, Caleb; Ponting, Chris P.; SNP data: University of Manchester Institute of Science and Technology, EST-based; Overton, Ian M.; Boardman, Paul E; Tang, Haizhou; Hubbard, Simon J.; of Sheffield, University; Wilson, Stuart A.; management: Beijing Institute of Genomics of Chinese Academy of Sciences, Scientific; Yu, Jun; Wang, Jian; Yang, HuanMing; International Chicken Polymorphism Map Consortium; Ka-Shu Wong, Gane; ;;; Wang, Jun; ;; Zhang, Yong; ;; Yu, Jun; ;
Журнал:
Nature
Дата:
2004
Аннотация:
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 linesâ 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 100â kilobases.
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