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 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.
authors.affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xu
authors.initials: X
authors.lastname: Yang
authors.forename: Zengjin
authors.initials: Z
authors.lastname: Zhang
authors.forename: Qingshun
authors.initials: Q
authors.lastname: Meng
authors.forename: Jun
authors.initials: J
authors.lastname: Zhou
authors.forename: Dawei
authors.initials: D
authors.lastname: Li
authors.forename: Jingjing
authors.initials: J
authors.lastname: Zhang
authors.forename: Peixiang
authors.initials: P
authors.lastname: Ni
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Longhua
authors.initials: L
authors.lastname: Ran
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Jianguo
authors.initials: J
authors.lastname: Zhang
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Shengting
authors.initials: S
authors.lastname: Li
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: Guangyuan
authors.initials: G
authors.lastname: Li
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Wang
authors.forename: Wenming
authors.initials: W
authors.lastname: Zhao
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.forename: Mingtao
authors.initials: M
authors.lastname: Dai
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Yuanzhe
authors.initials: Y
authors.lastname: Li
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.forename: Yunze
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Xiangang
authors.initials: X
authors.lastname: Huang
authors.forename: Wei
authors.initials: W
authors.lastname: Tong
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Jia
authors.initials: J
authors.lastname: Ye
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.forename: Ning
authors.initials: N
authors.lastname: Wei
authors.forename: Guoqing
authors.initials: G
authors.lastname: Li
authors.forename: Le
authors.initials: L
authors.lastname: Dong
authors.forename: Fengdi
authors.initials: F
authors.lastname: Lan
authors.forename: Yongqiao
authors.initials: Y
authors.lastname: Sun
authors.forename: Zhenpeng
authors.initials: Z
authors.lastname: Zhang
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yang
authors.forename: Yingpu
authors.initials: Y
authors.lastname: Yu
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Huang
authors.forename: Dandan
authors.initials: D
authors.lastname: He
authors.forename: Yan
authors.initials: Y
authors.lastname: Xi
authors.forename: Dong
authors.initials: D
authors.lastname: Wei
authors.forename: Qiuhui
authors.initials: Q
authors.lastname: Qi
authors.forename: Wenjie
authors.initials: W
authors.lastname: Li
authors.forename: Jianping
authors.initials: J
authors.lastname: Shi
authors.forename: Miaoheng
authors.initials: M
authors.lastname: Wang
authors.forename: Fei
authors.initials: F
authors.lastname: Xie
authors.forename: Jianjun
authors.initials: J
authors.lastname: Wang
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhang
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Yiqiang
authors.initials: Y
authors.lastname: Zhao
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Ning
authors.initials: N
authors.lastname: Yang
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Changqing
authors.initials: C
authors.lastname: Zeng
authors.forename: Weimou
authors.initials: W
authors.lastname: Zheng
authors.forename: Bailin
authors.initials: B
authors.lastname: Hao
authors.forename: Ladeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Shiaw-Pyng
authors.initials: SP
authors.lastname: Yang
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Mikael
authors.initials: M
authors.lastname: Brandström
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
authors.forename: Richard P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.forename: Jan J
authors.initials: JJ
authors.lastname: van der Poel
authors.forename: Henk
authors.initials: H
authors.lastname: Bovenhuis
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
authors.forename: Laurie
authors.initials: L
authors.lastname: Gordon
authors.forename: Lisa
authors.initials: L
authors.lastname: Stubbs
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Tijana
authors.initials: T
authors.lastname: Glavina
authors.forename: Andrea
authors.initials: A
authors.lastname: Aerts
authors.forename: Pete
authors.initials: P
authors.lastname: Kaiser
authors.forename: Lisa
authors.initials: L
authors.lastname: Rothwell
authors.forename: John R
authors.initials: JR
authors.lastname: Young
authors.forename: Sally
authors.initials: S
authors.lastname: Rogers
authors.forename: Brian A
authors.initials: BA
authors.lastname: Walker
authors.forename: Andy
authors.initials: A
authors.lastname: van Hateren
authors.forename: Jim
authors.initials: J
authors.lastname: Kaufman
authors.forename: Nat
authors.initials: N
authors.lastname: Bumstead
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Lamont
authors.forename: Huaijun
authors.initials: H
authors.lastname: Zhou
authors.forename: Paul M
authors.initials: PM
authors.lastname: Hocking
authors.forename: David
authors.initials: D
authors.lastname: Morrice
authors.forename: Dirk-Jan
authors.initials: DJ
authors.lastname: de Koning
authors.forename: Andy
authors.initials: A
authors.lastname: Law
authors.forename: Neil
authors.initials: N
authors.lastname: Bartley
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.forename: Henry
authors.initials: H
authors.lastname: Hunt
authors.forename: Hans H
authors.initials: HH
authors.lastname: Cheng
authors.forename: Ulrika
authors.initials: U
authors.lastname: Gunnarsson
authors.forename: Per
authors.initials: P
authors.lastname: Wahlberg
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
authors.forename: Ellen
authors.initials: E
authors.lastname: Kindlund
authors.forename: Martti T
authors.initials: MT
authors.lastname: Tammi
authors.forename: Björn
authors.initials: B
authors.lastname: Andersson
authors.forename: Caleb
authors.initials: C
authors.lastname: Webber
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Ian M
authors.initials: IM
authors.lastname: Overton
authors.forename: Paul E
authors.initials: PE
authors.lastname: Boardman
authors.forename: Haizhou
authors.initials: H
authors.lastname: Tang
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Hubbard
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Wilson
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D000829:Animals, Domestic / Q000145:classification / Q000235:genetics; D002645:Chickens / Q000145:classification / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D005260:Female; D016678:Genome; D023281:Genomics; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009954:Ornithine Carbamoyltransferase / Q000737:chemistry; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D009954:Ornithine Carbamoyltransferase