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

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.

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