Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.
The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.
Gibbs
Richard A
RA
Taylor
Jeremy F
JF
Van Tassell
Curtis P
CP
Barendse
William
W
Eversole
Kellye A
KA
Gill
Clare A
CA
Green
Ronnie D
RD
Hamernik
Debora L
DL
Kappes
Steven M
SM
Lien
Sigbjørn
S
Matukumalli
Lakshmi K
LK
McEwan
John C
JC
Nazareth
Lynne V
LV
Schnabel
Robert D
RD
Weinstock
George M
GM
Wheeler
David A
DA
Ajmone-Marsan
Paolo
P
Boettcher
Paul J
PJ
Caetano
Alexandre R
AR
Garcia
Jose Fernando
JF
Hanotte
Olivier
O
Mariani
Paola
P
Skow
Loren C
LC
Sonstegard
Tad S
TS
Williams
John L
JL
Diallo
Boubacar
B
Hailemariam
Lemecha
L
Martinez
Mario L
ML
Morris
Chris A
CA
Silva
Luiz O C
LO
Spelman
Richard J
RJ
Mulatu
Woudyalew
W
Zhao
Keyan
K
Abbey
Colette A
CA
Agaba
Morris
M
Araujo
Flábio R
FR
Bunch
Rowan J
RJ
Burton
James
J
Gorni
Chiara
C
Olivier
Hanotte
H
Harrison
Blair E
BE
Luff
Bill
B
Machado
Marco A
MA
Mwakaya
Joel
J
Plastow
Graham
G
Sim
Warren
W
Smith
Timothy
T
Thomas
Merle B
MB
Valentini
Alessio
A
Williams
Paul
P
Womack
James
J
Woolliams
John A
JA
Liu
Yue
Y
Qin
Xiang
X
Worley
Kim C
KC
Gao
Chuan
C
Jiang
Huaiyang
H
Moore
Stephen S
SS
Ren
Yanru
Y
Song
Xing-Zhi
XZ
Bustamante
Carlos D
CD
Hernandez
Ryan D
RD
Muzny
Donna M
DM
Patil
Shobha
S
San Lucas
Anthony
A
Fu
Qing
Q
Kent
Matthew P
MP
Vega
Richard
R
Matukumalli
Aruna
A
McWilliam
Sean
S
Sclep
Gert
G
Bryc
Katarzyna
K
Choi
Jungwoo
J
Gao
Hong
H
Grefenstette
John J
JJ
Murdoch
Brenda
B
Stella
Alessandra
A
Villa-Angulo
Rafael
R
Wright
Mark
M
Aerts
Jan
J
Jann
Oliver
O
Negrini
Riccardo
R
Goddard
Mike E
ME
Hayes
Ben J
BJ
Bradley
Daniel G
DG
Barbosa da Silva
Marcos
M
Lau
Lilian P L
LP
Liu
George E
GE
Lynn
David J
DJ
Panzitta
Francesca
F
Dodds
Ken G
KG
D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D016678:Genome; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D011156:Population Density