Skip to main content
Research article - Peer-reviewed, 2013

Genetic diversity in the modern horse illustrated from genome-wide SNP data

Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michaela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.;
Show more authors


Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Published in

2013, volume: 8, number: 1, article number: e54997
Publisher: Public Library of Science

Authors' information

Petersen, Jessica L.
University of Minnesota
Mickelson, James R.
University of Minnesota
Cothran, E. Gus
Andersson, Lisa
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Axelsson, Jeanette
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Bailey, Ernie
University of Kentucky
Bannasch, Danika
Binns, Matthew M.
Equine Analysis
Borges, Alexandre S.
Sao Paulo State University
Brama, Pieter
Trinity College Dublin
da Câmara Machado, Artur
University of Azores
Distl, Ottmar
University of Veterinary Medicine Hannover (TiHo)
Felicetti, Michaela
University of Perugia
Fox-Clipsham, Laura
Animal Health Trust
Graves, Kathryn T.
University of Kentucky
Guérin, Gérard
National Institute of Agricultural Research (INRA)
Haase, Bianca
University of Sydney
Hasegawa, Telhisa
Nihon Bioresource College
Hemmann, Karin
University of Helsinki
Hill, Emmeline W.
Trinity College Dublin
Show more authors

UKÄ Subject classification

Genetics and Breeding

Publication Identifiers


URI (permanent link to this page)