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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 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.

SUBMITTER: Wong GK

PROVIDER: S-EPMC2263125 | biostudies-literature | 2004 Dec

REPOSITORIES: biostudies-literature

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

Wong Gane Ka-Shu GK Liu Bin B Wang Jun J Zhang Yong Y Yang Xu X Zhang Zengjin Z Meng Qingshun Q Zhou Jun J Li Dawei D Zhang Jingjing J Ni Peixiang P Li Songgang S Ran Longhua L Li Heng H Zhang Jianguo J Li Ruiqiang R Li Shengting S Zheng Hongkun H Lin Wei W Li Guangyuan G Wang Xiaoling X Zhao Wenming W Li Jun J Ye Chen C Dai Mingtao M Ruan Jue J Zhou Yan Y Li Yuanzhe Y He Ximiao X Zhang Yunze Y Wang Jing J Huang Xiangang X Tong Wei W Chen Jie J Ye Jia J Chen Chen C Wei Ning N Li Guoqing G Dong Le L Lan Fengdi F Sun Yongqiao Y Zhang Zhenpeng Z Yang Zheng Z Yu Yingpu Y Huang Yanqing Y He Dandan D Xi Yan Y Wei Dong D Qi Qiuhui Q Li Wenjie W Shi Jianping J Wang Miaoheng M Xie Fei F Wang Jianjun J Zhang Xiaowei X Wang Pei P Zhao Yiqiang Y Li Ning N Yang Ning N Dong Wei W Hu Songnian S Zeng Changqing C Zheng Weimou W Hao Bailin B Hillier Ladeana W LW Yang Shiaw-Pyng SP Warren Wesley C WC Wilson Richard K RK Brandström Mikael M Ellegren Hans H Crooijmans Richard P M A RP van der Poel Jan J JJ Bovenhuis Henk H Groenen Martien A M MA Ovcharenko Ivan I Gordon Laurie L Stubbs Lisa L Lucas Susan S Glavina Tijana T Aerts Andrea A Kaiser Pete P Rothwell Lisa L Young John R JR Rogers Sally S Walker Brian A BA van Hateren Andy A Kaufman Jim J Bumstead Nat N Lamont Susan J SJ Zhou Huaijun H Hocking Paul M PM Morrice David D de Koning Dirk-Jan DJ Law Andy A Bartley Neil N Burt David W DW Hunt Henry H Cheng Hans H HH Gunnarsson Ulrika U Wahlberg Per P Andersson Leif L Kindlund Ellen E Tammi Martti T MT Andersson Björn B Webber Caleb C Ponting Chris P CP Overton Ian M IM Boardman Paul E PE Tang Haizhou H Hubbard Simon J SJ Wilson Stuart A SA Yu Jun J Wang Jian J Yang Huanming H

Nature 20041201 7018

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 SN ...[more]

PMID: 15592405

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Dataset Information

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

Publications

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

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