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

Richard A. Gibbs; Jeremy F. Taylor; Curtis P. Van Tassell; William Barendse; Kellye A. Eversole; Clare A. Gill; Ronnie D. Green; Debora L. Hamernik; Steven M. Kappes; Sigbjørn Lien; Lakshmi K. Matukumalli; John C. McEwan; Lynne V. Nazareth; Robert D. Schnabel; George M. Weinstock; David A. Wheeler; Paolo Ajmone-Marsan; William Barends; Paul J. Boettcher; Alexandre R. Caetano; Jose Fernando Garcia; OlivierHanotte; Paola Mariani; Loren C. Skow; Tad S. Sonstegard; John L. Williams; Boubacar Diallo; Lemecha Hailemariam; Olivier Hanotte; Mario L. Martinez; Chris A. Morris; Luiz O.C. Silva; Richard J. Spelman; Woudyalew Mulatu; Keyan Zhao; Colette A. Abbey; Morris Agaba; Flábio R. Araujo; Rowan J. Bunch; James Burton; Chiara Gorni; Blair E. Harrison; Bill Luff; Marco A. Machado; Joel Mwakaya; Graham Plastow; Warren Sim; Timothy Smith; Merle B. Thomas; Alessio Valentini; Paul Williams; James Womack; John A. Woolliams; Yue Liu; Xiang Qin; Kim C. Worley; Chuan Gao; Huaiyang Jiang; Stephen S. Moore; Yanru Ren; Xing Zhi Song; Carlos D. Bustamante; Ryan D. Hernandez; Donna M. Muzny; Shobha Patil; Anthony San Lucas; Qing Fu; Matthew P. Kent; Richard Vega; Aruna Matukumalli; Sean McWilliam; Gert Sclep; Katarzyna Bryc; Jungwoo Choi; Hong Gao; John J. Grefenstette; Brenda Murdoch; Alessandra Stella; Rafael Villa-Angulo; Mark Wright; Jan Aerts; Oliver Jann; Riccardo Negrini; Mike E. Goddard; Ben J. Hayes; Daniel G. Bradley; Marcos Barbosa Da Silva; Lilian P.L. Lau; George E. Liu; David J. Lynn; Francesca Panzitta; Ken G. Dodds

doi:10.1126/science.1167936

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

Richard A. Gibbs
, Jeremy F. Taylor
, Curtis P. Van Tassell
, William Barendse
, Kellye A. Eversole
, Clare A. Gill
, Ronnie D. Green
, Debora L. Hamernik
, Steven M. Kappes
, Sigbjørn Lien
, Lakshmi K. Matukumalli
, John C. McEwan
, Lynne V. Nazareth
, Robert D. Schnabel
, George M. Weinstock
, David A. Wheeler
, Paolo Ajmone-Marsan
, William Barends
, Paul J. Boettcher
, Alexandre R. Caetano

Jose Fernando Garcia, OlivierHanotte, Paola Mariani, Loren C. Skow, Tad S. Sonstegard, John L. Williams, Boubacar Diallo, Lemecha Hailemariam, Olivier Hanotte, Mario L. Martinez, Chris A. Morris, Luiz O.C. Silva, Richard J. Spelman, Woudyalew Mulatu, Keyan Zhao, Colette A. Abbey, Morris Agaba, Flábio R. Araujo, Rowan J. Bunch, James Burton, Chiara Gorni, Blair E. Harrison, Bill Luff, Marco A. Machado, Joel Mwakaya, Graham Plastow, Warren Sim, Timothy Smith, Merle B. Thomas, Alessio Valentini, Paul Williams, James Womack, John A. Woolliams, Yue Liu, Xiang Qin, Kim C. Worley, Chuan Gao, Huaiyang Jiang, Stephen S. Moore, Yanru Ren, Xing Zhi Song, Carlos D. Bustamante, Ryan D. Hernandez, Donna M. Muzny, Shobha Patil, Anthony San Lucas, Qing Fu, Matthew P. Kent, Richard Vega, Aruna Matukumalli, Sean McWilliam, Gert Sclep, Katarzyna Bryc, Jungwoo Choi, Hong Gao, John J. Grefenstette, Brenda Murdoch, Alessandra Stella, Rafael Villa-Angulo, Mark Wright, Jan Aerts, Oliver Jann, Riccardo Negrini, Mike E. Goddard, Ben J. Hayes, Daniel G. Bradley, Marcos Barbosa Da Silva, Lilian P.L. Lau, George E. Liu, David J. Lynn, Francesca Panzitta, Ken G. Dodds

Baylor College of Medicine
University of Missouri
United States Department of Agriculture
CSIRO
University of New England
Alliance for Animal Genome Research
Texas A&M University
Norwegian University of Life Sciences
George Mason University
AgResearch
Catholic University of the Sacred Heart
International Atomic Energy Agency
Empresa Brasileira de Pesquisa Agropecuária
Universidade Estadual Paulista Júlio de Mesquita Filho
International Livestock Research Institute
Parco Tecnologico Padano
University of Edinburgh
Direction Nationale de l'Élevage
Ethiopian Institute of Agricultural Research
Livestock Improvement Corporation
International Livestock Research Institute Addis Ababa
Cornell University
World Guernsey Cattle Federation
University of Alberta
Tuscia University
Wellcome Trust Sanger Institute
State Government of Victoria
University of Melbourne
Trinity College Dublin
Simon Fraser University

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

703 Citas (Scopus)

Resumen

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.

Idioma original	Inglés
Páginas (desde-hasta)	528-532
Número de páginas	5
Publicación	Science
Volumen	324
N.º	5926
DOI	https://doi.org/10.1126/science.1167936
Estado	Publicada - 24 abr 2009
Publicado de forma externa	Sí

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Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., Lien, S., Matukumalli, L. K., McEwan, J. C., Nazareth, L. V., Schnabel, R. D., Weinstock, G. M., Wheeler, D. A., Ajmone-Marsan, P., Barends, W., Boettcher, P. J., ... Dodds, K. G. (2009). Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324(5926), 528-532. https://doi.org/10.1126/science.1167936

@article{ac6f846e565540fba58a6edc289207d7,

title = "Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds",

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.",

author = "Gibbs, \{Richard A.\} and Taylor, \{Jeremy F.\} and \{Van Tassell\}, \{Curtis P.\} and William Barendse and Eversole, \{Kellye A.\} and Gill, \{Clare A.\} and Green, \{Ronnie D.\} and Hamernik, \{Debora L.\} and Kappes, \{Steven M.\} and Sigbj{\o}rn Lien and Matukumalli, \{Lakshmi K.\} and McEwan, \{John C.\} and Nazareth, \{Lynne V.\} and Schnabel, \{Robert D.\} and Weinstock, \{George M.\} and Wheeler, \{David A.\} and Paolo Ajmone-Marsan and William Barends and Boettcher, \{Paul J.\} and Caetano, \{Alexandre R.\} and Garcia, \{Jose Fernando\} and OlivierHanotte and Paola Mariani and Skow, \{Loren C.\} and Sonstegard, \{Tad S.\} and Williams, \{John L.\} and Boubacar Diallo and Lemecha Hailemariam and Olivier Hanotte and Martinez, \{Mario L.\} and Morris, \{Chris A.\} and Silva, \{Luiz O.C.\} and Spelman, \{Richard J.\} and Woudyalew Mulatu and Keyan Zhao and Abbey, \{Colette A.\} and Morris Agaba and Araujo, \{Fl{\'a}bio R.\} and Bunch, \{Rowan J.\} and James Burton and Chiara Gorni and Harrison, \{Blair E.\} and Bill Luff and Machado, \{Marco A.\} and Joel Mwakaya and Graham Plastow and Warren Sim and Timothy Smith and Thomas, \{Merle B.\} and Alessio Valentini and Paul Williams and James Womack and Woolliams, \{John A.\} and Yue Liu and Xiang Qin and Worley, \{Kim C.\} and Chuan Gao and Huaiyang Jiang and Moore, \{Stephen S.\} and Yanru Ren and Song, \{Xing Zhi\} and Bustamante, \{Carlos D.\} and Hernandez, \{Ryan D.\} and Muzny, \{Donna M.\} and Shobha Patil and Lucas, \{Anthony San\} and Qing Fu and Kent, \{Matthew P.\} and Richard Vega and Aruna Matukumalli and Sean McWilliam and Gert Sclep and Katarzyna Bryc and Jungwoo Choi and Hong Gao and Grefenstette, \{John J.\} and Brenda Murdoch and Alessandra Stella and Rafael Villa-Angulo and Mark Wright and Jan Aerts and Oliver Jann and Riccardo Negrini and Goddard, \{Mike E.\} and Hayes, \{Ben J.\} and Bradley, \{Daniel G.\} and \{Da Silva\}, \{Marcos Barbosa\} and Lau, \{Lilian P.L.\} and Liu, \{George E.\} and Lynn, \{David J.\} and Francesca Panzitta and Dodds, \{Ken G.\}",

year = "2009",

month = apr,

day = "24",

doi = "10.1126/science.1167936",

language = "English",

volume = "324",

pages = "528--532",

journal = "Science",

issn = "0036-8075",

number = "5926",

}

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, Barends, W, Boettcher, PJ, Caetano, AR, Garcia, JF, OlivierHanotte, Mariani, P, Skow, LC, Sonstegard, TS, Williams, JL, Diallo, B, Hailemariam, L, Hanotte, O, Martinez, ML, Morris, CA, Silva, LOC, Spelman, RJ, Mulatu, W, Zhao, K, Abbey, CA, Agaba, M, Araujo, FR, Bunch, RJ, Burton, J, Gorni, C, 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, Lucas, AS, 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, Da Silva, MB, Lau, LPL, Liu, GE, Lynn, DJ, Panzitta, F & Dodds, KG 2009, 'Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds', Science, vol. 324, n.º 5926, pp. 528-532. https://doi.org/10.1126/science.1167936

TY - JOUR

T1 - Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

AU - Gibbs, Richard A.

AU - Taylor, Jeremy F.

AU - Van Tassell, Curtis P.

AU - Barendse, William

AU - Eversole, Kellye A.

AU - Gill, Clare A.

AU - Green, Ronnie D.

AU - Hamernik, Debora L.

AU - Kappes, Steven M.

AU - Lien, Sigbjørn

AU - Matukumalli, Lakshmi K.

AU - McEwan, John C.

AU - Nazareth, Lynne V.

AU - Schnabel, Robert D.

AU - Weinstock, George M.

AU - Wheeler, David A.

AU - Ajmone-Marsan, Paolo

AU - Barends, William

AU - Boettcher, Paul J.

AU - Caetano, Alexandre R.

AU - Garcia, Jose Fernando

AU - OlivierHanotte,

AU - Mariani, Paola

AU - Skow, Loren C.

AU - Sonstegard, Tad S.

AU - Williams, John L.

AU - Diallo, Boubacar

AU - Hailemariam, Lemecha

AU - Hanotte, Olivier

AU - Martinez, Mario L.

AU - Morris, Chris A.

AU - Silva, Luiz O.C.

AU - Spelman, Richard J.

AU - Mulatu, Woudyalew

AU - Zhao, Keyan

AU - Abbey, Colette A.

AU - Agaba, Morris

AU - Araujo, Flábio R.

AU - Bunch, Rowan J.

AU - Burton, James

AU - Gorni, Chiara

AU - Harrison, Blair E.

AU - Luff, Bill

AU - Machado, Marco A.

AU - Mwakaya, Joel

AU - Plastow, Graham

AU - Sim, Warren

AU - Smith, Timothy

AU - Thomas, Merle B.

AU - Valentini, Alessio

AU - Williams, Paul

AU - Womack, James

AU - Woolliams, John A.

AU - Liu, Yue

AU - Qin, Xiang

AU - Worley, Kim C.

AU - Gao, Chuan

AU - Jiang, Huaiyang

AU - Moore, Stephen S.

AU - Ren, Yanru

AU - Song, Xing Zhi

AU - Bustamante, Carlos D.

AU - Hernandez, Ryan D.

AU - Muzny, Donna M.

AU - Patil, Shobha

AU - Lucas, Anthony San

AU - Fu, Qing

AU - Kent, Matthew P.

AU - Vega, Richard

AU - Matukumalli, Aruna

AU - McWilliam, Sean

AU - Sclep, Gert

AU - Bryc, Katarzyna

AU - Choi, Jungwoo

AU - Gao, Hong

AU - Grefenstette, John J.

AU - Murdoch, Brenda

AU - Stella, Alessandra

AU - Villa-Angulo, Rafael

AU - Wright, Mark

AU - Aerts, Jan

AU - Jann, Oliver

AU - Negrini, Riccardo

AU - Goddard, Mike E.

AU - Hayes, Ben J.

AU - Bradley, Daniel G.

AU - Da Silva, Marcos Barbosa

AU - Lau, Lilian P.L.

AU - Liu, George E.

AU - Lynn, David J.

AU - Panzitta, Francesca

AU - Dodds, Ken G.

PY - 2009/4/24

Y1 - 2009/4/24

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/65449132092

U2 - 10.1126/science.1167936

DO - 10.1126/science.1167936

M3 - Article

C2 - 19390050

AN - SCOPUS:65449132092

SN - 0036-8075

VL - 324

SP - 528

EP - 532

JO - Science

JF - Science

IS - 5926

ER -

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

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