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PMID: 19390050 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

Science (New York, N.Y.) ·Vol. 324 ·No. 5926 ·2009-04-24 ·Pages 528-32

Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LO, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LP, Liu GE, Lynn DJ, Panzitta F, Dodds KG

Abstract

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.

MeSH Terms

Animals Breeding Cattle/genetics Female Gene Frequency Genetic Variation Genome Male Molecular Sequence Data Mutation Polymorphism, Single Nucleotide Population Density

Authors & Affiliations

92 authors, click to expand affiliations / ORCID

Bovine HapMap Consortium

Gibbs Richard A

Taylor Jeremy F

Van Tassell Curtis P

Barendse William

Eversole Kellye A

Gill Clare A

Green Ronnie D

Hamernik Debora L

Kappes Steven M

Lien Sigbjørn

Matukumalli Lakshmi K

McEwan John C

Nazareth Lynne V

Schnabel Robert D

Weinstock George M

Wheeler David A

Ajmone-Marsan Paolo

Boettcher Paul J

Caetano Alexandre R

Garcia Jose Fernando

Hanotte Olivier

Mariani Paola

Skow Loren C

Sonstegard Tad S

Williams John L

Diallo Boubacar

Hailemariam Lemecha

Martinez Mario L

Morris Chris A

Silva Luiz O C

Spelman Richard J

Mulatu Woudyalew

Zhao Keyan

Abbey Colette A

Agaba Morris

Araujo Flábio R

Bunch Rowan J

Burton James

Gorni Chiara

Olivier Hanotte

Harrison Blair E

Luff Bill

Machado Marco A

Mwakaya Joel

Plastow Graham

Sim Warren

Smith Timothy

Thomas Merle B

Valentini Alessio

Williams Paul

Womack James

Woolliams John A

Liu Yue

Qin Xiang

Worley Kim C

Gao Chuan

Jiang Huaiyang

Moore Stephen S

Ren Yanru

Song Xing-Zhi

Bustamante Carlos D

Hernandez Ryan D

Muzny Donna M

Patil Shobha

San Lucas Anthony

Fu Qing

Kent Matthew P

Vega Richard

Matukumalli Aruna

McWilliam Sean

Sclep Gert

Bryc Katarzyna

Choi Jungwoo

Gao Hong

Grefenstette John J

Murdoch Brenda

Stella Alessandra

Villa-Angulo Rafael

Wright Mark

Aerts Jan

Jann Oliver

Negrini Riccardo

Goddard Mike E

Hayes Ben J

Bradley Daniel G

Barbosa da Silva Marcos

Lau Lilian P L

Liu George E

Lynn David J

Panzitta Francesca

Dodds Ken G

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Article Info

Journal

Science (New York, N.Y.)

Abbr.

Science

ISSN

1095-9203

DOI

10.1126/science.1167936

Published

2009-04-24

Pages

528-32

Language

English

Region

United States

NLM ID

0404511

PMCID

PMC2735092

Subset

Grants

Biotechnology and Biological Sciences Research Council · BBS/E/D/05191130 · United Kingdom

NIGMS NIH HHS · R01 GM083606 · United States

Biotechnology and Biological Sciences Research Council · BBS/B/05710 · United Kingdom

Biotechnology and Biological Sciences Research Council · BBS/E/R/00001610 · United Kingdom

Biotechnology and Biological Sciences Research Council · BBS/E/R/00000673 · United Kingdom

Biotechnology and Biological Sciences Research Council · BBS/E/R/00001618 · United Kingdom

NIGMS NIH HHS · R01 GM083606-02 · United States

Databases

GENBANK

AAFC03000000

Corrections

CommentIn

PMID: 19390037

CommentIn

PMID: 19541976

External Links

PubMed source DOI: 10.1126/science.1167936 PMC Full Text View journal details

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Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

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