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PMID: 15592405 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature ·Vol. 432 ·No. 7018 ·2004-12-09 ·Pages 717-22

Wong GK, 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 LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, 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 H, International Chicken Polymorphism Map Consortium

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.

MeSH Terms
Alleles Amino Acid Sequence Animals Animals, Domestic/classification,genetics Chickens/classification,genetics Chromosomes/genetics Female Genome Genomics Haplotypes/genetics Humans Molecular Sequence Data Ornithine Carbamoyltransferase/chemistry Physical Chromosome Mapping Polymorphism, Single Nucleotide/genetics Selection, Genetic
Chemicals
Ornithine Carbamoyltransferase
Authors & Affiliations
115 authors, click to expand affiliations / ORCID
Wong Gane Ka-Shu
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China.
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
Hillier Ladeana W
Yang Shiaw-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 David
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
Yang Huanming
International Chicken Polymorphism Map Consortium
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Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature03156
Published
2004-12-09
Pages
717-22
Language
English
Region
England
NLM ID
0410462
PMCID
PMC2263125
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BBS/B/13497 · United Kingdom
Corrections
CommentIn
PMID: 15592391
CommentIn
PMID: 15602523
External Links
PubMed source DOI: 10.1038/nature03156 PMC Full Text View journal details
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