A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
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.
Wong
Gane Ka-Shu
GK
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China.
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
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
D009954:Ornithine Carbamoyltransferase