Department of Animal Science



Jessica Lynn Petersen, University of Nebraska-LincolnFollow
James R. Mickelson, University of Minnesota - Twin Cities
E. Gus Cothran, Texas A & M University - College Station
Lisa S. Andersson, Swedish University of Agricultural Sciences
Jeanette Axelsson, Swedish University of Agricultural Sciences
Ernie Bailey, University of Kentucky
Danika L. Bannasch, University of California - Davis
Matthew M. Binns, Equine Analysis
Alexandre S. Borges, University Estadual Paulista
Pieter Brama, University College Dublin
Artur da Câmaro Machado, University of Azores
Ottmar Distl, University of Veterinary Medicine Hannover
Michela Felicetti, University of Perugia
Laura Fox-Clipsham, Animal Health Trust
Kathryn T. Graves, University of Kentucky
Gérard Guérin, French National Institute for Agricultural Research
Bianca Haase, University of SydneyFollow
Telhisa Hasegawa, Nihon Bioresource College
Karin Hemmann, University of Helsinki
Emmeline W. Hill, University College Dublin
Tosso Leeb, University of Bern
Gabriella Lindgren, Swedish University of Agricultural Sciences
Hannes Lohi, University of Helsinki
Maria Susana Lopes, University of Azores
Beatrice A. McGivney, University College Dublin
Sofia Mikko, Swedish University of Agricultural Sciences
Nicholas Orr, Breakthrough Breast Cancer Research Centre
M. Cecilia T. Penedo, University of California - Davis
Richard J. Piercy, Royal Veterinary College, London
Marja Raekallio, University of Helsinki
Stefan Rieder, Agroscope Liebefeld-Posieux Research Station
Knut H. Røed, Norwegian School of Veterinary Science
Maurizio Silvestrelli, University of Perugia
June Swinburne, Animal Health Trust
Teruaki Tozaki, Laboratory of Racing Chemistry
Mark Vaudin, Animal Health Trust
Claire M. Wade, University of Sydney
Molly E. McCue, University of Minnesota - Twin CitiesFollow

Date of this Version



PLoS ONE (January 2013) 8(1): e54997. DOI: 10.1371/journal.pone.0054997.


Copyright 2013, the authors. Used by permission.


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.