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

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 Lin; Guangyuan 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; Zhenpeng Zhang; Zheng Yang; Yingpu Yu; Yanqing Huang; Dandan He; Yan Xi; Dong Wei; Qiuhui Qi; Wenjie Li; Jianping Shi; Miaoheng Wang; Fei Xie; Jianjun Wang; Xiaowei Zhang; Pei Wang; Yiqiang Zhao; Ning Li; Ning Yang; Wei Dong; Songnian Hu; Changqing Zeng; Weimou Zheng; Bailin Hao; La Deana W. Hillier; Shiaw Pyng Yang; Wesley C. Warren; Richard K. Wilson; Mikael Brandström; Hans Ellegren; Richard P.M.A. Crooijmans; Jan J. van der Poel; Henk Bovenhuis; Martien A.M. Groenen; Ivan Ovcharenko; Laurie Gordon; Lisa Stubbs; Susan Lucas; Tijana Glavina; Andrea Aerts; Pete Kaiser; Lisa Rothwell; John R. Young; Sally Rogers; Brian A. Walker; Andy van Hateren; Jim Kaufman; Nat Bumstead; Susan J. Lamont; Huaijun Zhou; Paul M. Hocking; David Morrice; Dirk Jan de Koning; Andy Law; Neil Bartley; David W. Burt; Henry Hunt; Hans H. Cheng; Ulrika Gunnarsson; Per Wahlberg; Leif Andersson; Ellen Kindlund; Martti T. Tammi; Björn Andersson; Caleb Webber; Chris P. Ponting; Ian M. Overton; Paul E. Boardman; Haizhou Tang; Simon J. Hubbard; Stuart A. Wilson; Jun Yu; Jian Wang; Huan Ming Yang

doi:10.1038/nature03156

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

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 Lin, Guangyuan LiXiaoling 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, Zhenpeng Zhang, Zheng Yang, Yingpu Yu, Yanqing Huang, Dandan He, Yan Xi, Dong Wei, Qiuhui Qi, Wenjie Li, Jianping Shi, Miaoheng Wang, Fei Xie, Jianjun Wang, Xiaowei Zhang, Pei Wang, Yiqiang Zhao, Ning Li, Ning Yang, Wei Dong, Songnian Hu, Changqing Zeng, Weimou Zheng, Bailin Hao, La Deana W. Hillier, Shiaw Pyng Yang, Wesley C. Warren, Richard K. Wilson, Mikael Brandström, Hans Ellegren, Richard P.M.A. Crooijmans, Jan J. van der Poel, Henk Bovenhuis, Martien A.M. Groenen, Ivan Ovcharenko, Laurie Gordon, Lisa Stubbs, Susan Lucas, Tijana Glavina, Andrea Aerts, Pete Kaiser, Lisa Rothwell, John R. Young, Sally Rogers, Brian A. Walker, Andy van Hateren, Jim Kaufman, Nat Bumstead, Susan J. Lamont, Huaijun Zhou, Paul M. Hocking, David Morrice, Dirk Jan de Koning, Andy Law, Neil Bartley, David W. Burt, Henry Hunt, Hans H. Cheng, Ulrika Gunnarsson, Per Wahlberg, Leif Andersson, Ellen Kindlund, Martti T. Tammi, Björn Andersson, Caleb Webber, Chris P. Ponting, Ian M. Overton, Paul E. Boardman, Haizhou Tang, Simon J. Hubbard, Stuart A. Wilson, Jun Yu, Jian Wang, Huan Ming Yang

Research output: Contribution to journal › Article › peer-review

Abstract

We describe a genetic variation map for the chicken genome containing 2.8 miilion 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 test 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 language	English (US)
Pages (from-to)	717-722
Number of pages	6
Journal	Nature
Volume	432
Issue number	7018
DOIs	https://doi.org/10.1038/nature03156
State	Published - Dec 9 2004
Externally published	Yes

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Wong, GKS, Liu, B, Wang, J, Zhang, Y, Yang, X, Zhang, Z, Meng, Q, Zhou, J, Li, D, Zhang, J, Ni, P, Li, S, Ran, L, Li, H, Zhang, J, Li, R, Li, S, Zheng, H, Lin, W, Li, G, Wang, X, Zhao, W, Li, J, Ye, C, Dai, M, Ruan, J, Zhou, Y, Li, Y, He, X, Zhang, Y, Wang, J, Huang, X, Tong, W, Chen, J, Ye, J, Chen, C, Wei, N, Li, G, Dong, L, Lan, F, Sun, Y, Zhang, Z, Yang, Z, Yu, Y, Huang, Y, He, D, Xi, Y, Wei, D, Qi, Q, Li, W, Shi, J, Wang, M, Xie, F, Wang, J, Zhang, X, Wang, P, Zhao, Y, Li, N, Yang, N, Dong, W, Hu, S, Zeng, C, Zheng, W, Hao, B, Hillier, LDW, Yang, SP, Warren, WC, Wilson, RK, Brandström, M, Ellegren, H, Crooijmans, RPMA, van der Poel, JJ, Bovenhuis, H, Groenen, MAM, Ovcharenko, I, Gordon, L, Stubbs, L, Lucas, S, Glavina, T, Aerts, A, Kaiser, P, Rothwell, L, Young, JR, Rogers, S, Walker, BA, van Hateren, A, Kaufman, J, Bumstead, N, Lamont, SJ, Zhou, H, Hocking, PM, Morrice, D, de Koning, DJ, Law, A, Bartley, N, Burt, DW, Hunt, H, Cheng, HH, Gunnarsson, U, Wahlberg, P, Andersson, L, Kindlund, E, Tammi, MT, Andersson, B, Webber, C, Ponting, CP, Overton, IM, Boardman, PE, Tang, H, Hubbard, SJ, Wilson, SA, Yu, J, Wang, J & Yang, HM 2004, 'A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms', Nature, vol. 432, no. 7018, pp. 717-722. https://doi.org/10.1038/nature03156

@article{d47c95108be6415a9abb224c0e0016ed,

title = "A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms",

abstract = "We describe a genetic variation map for the chicken genome containing 2.8 miilion 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 test 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.",

author = "Wong, {Gane Ka Shu} and Bin Liu and Jun Wang and Yong Zhang and Xu Yang and Zengjin Zhang and Qingshun Meng and Jun Zhou and Dawei Li and Jingjing Zhang and Peixiang Ni and Songgang Li and Longhua Ran and Heng Li and Jianguo Zhang and Ruiqiang Li and Shengting Li and Hongkun Zheng and Wei Lin and Guangyuan Li and Xiaoling Wang and Wenming Zhao and Jun Li and Chen Ye and Mingtao Dai and Jue Ruan and Yan Zhou and Yuanzhe Li and Ximiao He and Yunze Zhang and Jing Wang and Xiangang Huang and Wei Tong and Jie Chen and Jia Ye and Chen Chen and Ning Wei and Guoqing Li and Le Dong and Fengdi Lan and Yongqiao Sun and Zhenpeng Zhang and Zheng Yang and Yingpu Yu and Yanqing Huang and Dandan He and Yan Xi and Dong Wei and Qiuhui Qi and Wenjie Li and Jianping Shi and Miaoheng Wang and Fei Xie and Jianjun Wang and Xiaowei Zhang and Pei Wang and Yiqiang Zhao and Ning Li and Ning Yang and Wei Dong and Songnian Hu and Changqing Zeng and Weimou Zheng and Bailin Hao and Hillier, {La Deana W.} and Yang, {Shiaw Pyng} and Warren, {Wesley C.} and Wilson, {Richard K.} and Mikael Brandstr{\"o}m and Hans Ellegren and Crooijmans, {Richard P.M.A.} and {van der Poel}, {Jan J.} and Henk Bovenhuis and Groenen, {Martien A.M.} and Ivan Ovcharenko and Laurie Gordon and Lisa Stubbs and Susan Lucas and Tijana Glavina and Andrea Aerts and Pete Kaiser and Lisa Rothwell and Young, {John R.} and Sally Rogers and Walker, {Brian A.} and {van Hateren}, Andy and Jim Kaufman and Nat Bumstead and Lamont, {Susan J.} and Huaijun Zhou and Hocking, {Paul M.} and David Morrice and {de Koning}, {Dirk Jan} and Andy Law and Neil Bartley and Burt, {David W.} and Henry Hunt and Cheng, {Hans H.} and Ulrika Gunnarsson and Per Wahlberg and Leif Andersson and Ellen Kindlund and Tammi, {Martti T.} and Bj{\"o}rn Andersson and Caleb Webber and Ponting, {Chris P.} and Overton, {Ian M.} and Boardman, {Paul E.} and Haizhou Tang and Hubbard, {Simon J.} and Wilson, {Stuart A.} and Jun Yu and Jian Wang and Yang, {Huan Ming}",

note = "Funding Information: Acknowledgements Gallus gallus SNP discovery and analysis (Beijing Institute of Genomics of Chinese Academy of Sciences and James D. Watson Institute of Genome Sciences of Zhejiang University) was supported by Chinese Academy of Sciences, State Development Planning Commission, Ministry of Science and Technology, National Natural Science Foundation of China, Beijing Municipal Government, Zhejiang Provincial Government, Hangzhou Municipal Government, Zhejiang University, and China National Grid; some equipment and reagents were provided by Wellcome Trust and Sanger Institute of the UK; recent segmental duplications were analysed by G. Cheng and E. E. Eichler; Riken1 cDNAs were provided by R. B. Caldwell and J. M. Buerstedde; non-coding conserved motifs were analysed by J. Taylor and W. Miller. Gallus gallus sequence generation (Washington University School of Medicine) was supported by National Human Genome Research Institute. H.E. (Uppsala University) was supported by Swedish Research Council, Knut and Alice Wallenberg Foundation, and Royal Academy of Sciences; L.A. (Uppsala University) was supported by Wallenberg Consortium North, Foundation for Strategic Research, and Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning. P.K., N.B., J.R.Y. and J.K. (Institute for Animal Health) were supported by BBSRC. S.J.L. (Iowa State University) was supported by Hatch Act and State of Iowa; bone density data for ISU resource population was collected by C. Ashwell and A. Mitchell. P.M.H., A.L., D.J.K. and D.W.B. (Roslin Institute) were supported by BBSRC; SNP genotyping was partially funded by Cobb-Vantress. USDA-ARS Avian Disease and Oncology Laboratory thank J. Kenyon and N. Evenson for technical assistance. C.P.P. (University of Oxford) was supported by UK Medical Research Council. S.J.H. (University of Manchester Institute of Science and Technology) was supported by BBSRC. S.A.W. (University of Sheffield) was supported by BBSRC. This paper is dedicated to Nat Bumstead, who died during the preparation of the manuscript. Nat was a major figure in researching the genetics of disease resistance in poultry; he worked tirelessly to realise the sequence of the chicken genome, which led in part to this consortium.",

year = "2004",

month = dec,

day = "9",

doi = "10.1038/nature03156",

language = "English (US)",

volume = "432",

pages = "717--722",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7018",

}

TY - JOUR

T1 - A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

AU - Wong, Gane Ka Shu

AU - Liu, Bin

AU - Wang, Jun

AU - Zhang, Yong

AU - Yang, Xu

AU - Zhang, Zengjin

AU - Meng, Qingshun

AU - Zhou, Jun

AU - Li, Dawei

AU - Zhang, Jingjing

AU - Ni, Peixiang

AU - Li, Songgang

AU - Ran, Longhua

AU - Li, Heng

AU - Zhang, Jianguo

AU - Li, Ruiqiang

AU - Li, Shengting

AU - Zheng, Hongkun

AU - Lin, Wei

AU - Li, Guangyuan

AU - Wang, Xiaoling

AU - Zhao, Wenming

AU - Li, Jun

AU - Ye, Chen

AU - Dai, Mingtao

AU - Ruan, Jue

AU - Zhou, Yan

AU - Li, Yuanzhe

AU - He, Ximiao

AU - Zhang, Yunze

AU - Wang, Jing

AU - Huang, Xiangang

AU - Tong, Wei

AU - Chen, Jie

AU - Ye, Jia

AU - Chen, Chen

AU - Wei, Ning

AU - Li, Guoqing

AU - Dong, Le

AU - Lan, Fengdi

AU - Sun, Yongqiao

AU - Zhang, Zhenpeng

AU - Yang, Zheng

AU - Yu, Yingpu

AU - Huang, Yanqing

AU - He, Dandan

AU - Xi, Yan

AU - Wei, Dong

AU - Qi, Qiuhui

AU - Li, Wenjie

AU - Shi, Jianping

AU - Wang, Miaoheng

AU - Xie, Fei

AU - Wang, Jianjun

AU - Zhang, Xiaowei

AU - Wang, Pei

AU - Zhao, Yiqiang

AU - Li, Ning

AU - Yang, Ning

AU - Dong, Wei

AU - Hu, Songnian

AU - Zeng, Changqing

AU - Zheng, Weimou

AU - Hao, Bailin

AU - Hillier, La Deana W.

AU - Yang, Shiaw Pyng

AU - Warren, Wesley C.

AU - Wilson, Richard K.

AU - Brandström, Mikael

AU - Ellegren, Hans

AU - Crooijmans, Richard P.M.A.

AU - van der Poel, Jan J.

AU - Bovenhuis, Henk

AU - Groenen, Martien A.M.

AU - Ovcharenko, Ivan

AU - Gordon, Laurie

AU - Stubbs, Lisa

AU - Lucas, Susan

AU - Glavina, Tijana

AU - Aerts, Andrea

AU - Kaiser, Pete

AU - Rothwell, Lisa

AU - Young, John R.

AU - Rogers, Sally

AU - Walker, Brian A.

AU - van Hateren, Andy

AU - Kaufman, Jim

AU - Bumstead, Nat

AU - Lamont, Susan J.

AU - Zhou, Huaijun

AU - Hocking, Paul M.

AU - Morrice, David

AU - de Koning, Dirk Jan

AU - Law, Andy

AU - Bartley, Neil

AU - Burt, David W.

AU - Hunt, Henry

AU - Cheng, Hans H.

AU - Gunnarsson, Ulrika

AU - Wahlberg, Per

AU - Andersson, Leif

AU - Kindlund, Ellen

AU - Tammi, Martti T.

AU - Andersson, Björn

AU - Webber, Caleb

AU - Ponting, Chris P.

AU - Overton, Ian M.

AU - Boardman, Paul E.

AU - Tang, Haizhou

AU - Hubbard, Simon J.

AU - Wilson, Stuart A.

AU - Yu, Jun

AU - Wang, Jian

AU - Yang, Huan Ming

N1 - Funding Information: Acknowledgements Gallus gallus SNP discovery and analysis (Beijing Institute of Genomics of Chinese Academy of Sciences and James D. Watson Institute of Genome Sciences of Zhejiang University) was supported by Chinese Academy of Sciences, State Development Planning Commission, Ministry of Science and Technology, National Natural Science Foundation of China, Beijing Municipal Government, Zhejiang Provincial Government, Hangzhou Municipal Government, Zhejiang University, and China National Grid; some equipment and reagents were provided by Wellcome Trust and Sanger Institute of the UK; recent segmental duplications were analysed by G. Cheng and E. E. Eichler; Riken1 cDNAs were provided by R. B. Caldwell and J. M. Buerstedde; non-coding conserved motifs were analysed by J. Taylor and W. Miller. Gallus gallus sequence generation (Washington University School of Medicine) was supported by National Human Genome Research Institute. H.E. (Uppsala University) was supported by Swedish Research Council, Knut and Alice Wallenberg Foundation, and Royal Academy of Sciences; L.A. (Uppsala University) was supported by Wallenberg Consortium North, Foundation for Strategic Research, and Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning. P.K., N.B., J.R.Y. and J.K. (Institute for Animal Health) were supported by BBSRC. S.J.L. (Iowa State University) was supported by Hatch Act and State of Iowa; bone density data for ISU resource population was collected by C. Ashwell and A. Mitchell. P.M.H., A.L., D.J.K. and D.W.B. (Roslin Institute) were supported by BBSRC; SNP genotyping was partially funded by Cobb-Vantress. USDA-ARS Avian Disease and Oncology Laboratory thank J. Kenyon and N. Evenson for technical assistance. C.P.P. (University of Oxford) was supported by UK Medical Research Council. S.J.H. (University of Manchester Institute of Science and Technology) was supported by BBSRC. S.A.W. (University of Sheffield) was supported by BBSRC. This paper is dedicated to Nat Bumstead, who died during the preparation of the manuscript. Nat was a major figure in researching the genetics of disease resistance in poultry; he worked tirelessly to realise the sequence of the chicken genome, which led in part to this consortium.

PY - 2004/12/9

Y1 - 2004/12/9

N2 - We describe a genetic variation map for the chicken genome containing 2.8 miilion 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 test 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.

AB - We describe a genetic variation map for the chicken genome containing 2.8 miilion 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 test 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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U2 - 10.1038/nature03156

DO - 10.1038/nature03156

M3 - Article

C2 - 15592405

AN - SCOPUS:10644271562

SN - 0028-0836

VL - 432

SP - 717

EP - 722

JO - Nature

JF - Nature

IS - 7018

ER -

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

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