Article

Nature 432, 717-722 (9 December 2004) | doi:10.1038/nature03156; Received 22 July 2004; Accepted 1 November 2004

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

Gane Ka-Shu Wong1,2,3,25, Bin Liu1,25, Jun Wang1,2,25, Yong Zhang1,4,25, Xu Yang1,25, Zengjin Zhang1, Qingshun Meng1, Jun Zhou1, Dawei Li1, Jingjing Zhang1, Peixiang Ni1, Songgang Li1,4, Longhua Ran5, Heng Li1,6, Jianguo Zhang1, Ruiqiang Li1, Shengting Li1, Hongkun Zheng1, Wei Lin1, Guangyuan Li1, Xiaoling Wang1, Wenming Zhao1, Jun Li1, Chen Ye1, Mingtao Dai1, Jue Ruan1, Yan Zhou2, Yuanzhe Li1, Ximiao He1, Yunze Zhang1, Jing Wang1,4, Xiangang Huang1, Wei Tong1, Jie Chen1, Jia Ye1,2, Chen Chen1, Ning Wei1, Guoqing Li1, Le Dong1, Fengdi Lan1, Yongqiao Sun1, Zhenpeng Zhang1, Zheng Yang1, Yingpu Yu2, Yanqing Huang1, Dandan He1, Yan Xi1, Dong Wei1, Qiuhui Qi1, Wenjie Li1, Jianping Shi1, Miaoheng Wang1, Fei Xie1, Jianjun Wang1, Xiaowei Zhang1, Pei Wang1, Yiqiang Zhao7, Ning Li7, Ning Yang7, Wei Dong1, Songnian Hu1, Changqing Zeng1, Weimou Zheng1,6, Bailin Hao1,6, Genome sequence of red jungle fowl: Washington University School of Medicine, LaDeana W. Hillier8, Shiaw-Pyng Yang8, Wesley C. Warren8, Richard K. Wilson8, Molecular evolution: Uppsala University, Mikael Brandström9, Hans Ellegren9, Population genotyping, BAC sequences and haplotypes: Wageningen University, Richard P. M. A. Crooijmans10, Jan J. van der Poel10, Henk Bovenhuis10, Martien A. M. Groenen10, Lawrence Livermore National Laboratory, Ivan Ovcharenko11,12, Laurie Gordon11,13, Lisa Stubbs11, DOE Joint Genome Institute, Susan Lucas13, Tijana Glavina13, Andrea Aerts13, Examples of application to complex traits: Institute for Animal Health, Pete Kaiser14, Lisa Rothwell14, John R. Young14, Sally Rogers14, Brian A. Walker14, Andy van Hateren14, Jim Kaufman14, Nat Bumstead14, Iowa State University, Susan J. Lamont15, Huaijun Zhou15, Roslin Institute, Paul M. Hocking16, David Morrice16, Dirk-Jan de Koning16, Andy Law16, Neil Bartley16, David W. Burt16, USDA-ARS Avian Disease and Oncology Laboratory, Henry Hunt17, Hans H. Cheng17, Domestication and selection: Uppsala University, Ulrika Gunnarsson18, Per Wahlberg18, Leif Andersson18,19, Karolinska Institutet, Ellen Kindlund20, Martti T. Tammi20,21, Björn Andersson20, Human disease genes: University of Oxford, Caleb Webber22, Chris P. Ponting22, EST-based SNP data: University of Manchester Institute of Science and Technology, Ian M. Overton23, Paul E Boardman23, Haizhou Tang23, Simon J. Hubbard23, University of Sheffield, Stuart A. Wilson24, Scientific management: Beijing Institute of Genomics of Chinese Academy of Sciences, Jun Yu1,2,25, Jian Wang1,2 & HuanMing Yang1,2 for International Chicken Polymorphism Map Consortium(Group contributions are listed by their order of appearance in the manuscript.) Polymorphism discovery and analysis: Beijing Institute of Genomics of Chinese Academy of Sciences and James D. Watson Institute of Genome Sciences of Zhejiang University

  1. Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China;
  2. James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou Genomics Institute, Key Laboratory of Genomic Bioinformatics of Zhejiang Province, Hangzhou 310008, China;
  3. UW Genome Center, Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
  4. College of Life Sciences, Peking University, Beijing 100871, China;
  5. Beijing North Computation Center, Beijing 100091, China;
  6. The Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China;
  7. China Agricultural University, Beijing 100094, China;
  8. Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;
  9. Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 34 Uppsala, Sweden;
  10. Animal Breeding and Genetics Group, Wageningen University, Marijkewg 40, 6709 PG Wageningen, The Netherlands;
  11. Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
  12. Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
  13. DOE Joint Genome Institute, Walnut Creek, California 94598, USA;
  14. Institute for Animal Health, Compton, Berkshire RG20 7NN, UK;
  15. Department of Animal Science, Iowa State Univeristy, Ames, Iowa 50011, USA;
  16. Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK;
  17. USDA-ARS Avian Disease and Oncology Laboratory, 3606 E. Mount Hope Road, East Lansing, Michigan 48823, USA;
  18. Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden;
  19. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-751 24 Uppsala, Sweden;
  20. Center for Genomics and Bioinformatics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
  21. Departments of Biological Sciences and Biochemistry, National University of Singapore, Singapore;
  22. MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK;
  23. Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, PO Box 88, Manchester M60 1QD, UK;
  24. Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
  25. These authors contributed equally to this work

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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.

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