Jessica L. Petersen, University of Minnesota - Twin Cities
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, Sweden
Jeanette Axelsson, Swedish University of Agricultural Sciences, Sweden
Ernie Bailey, University of KentuckyFollow
Danika Bannasch, University of California - Davis
Matthew M. Binns, Equine Analysis
Alexandre S. Borges, University Estadual Paulista, Brazil
Pieter Brama, University College Dublin, Ireland
Artur da Câmara Machado, University of Azores, Portugal
Ottmar Distl, University of Veterinary Medicine, Germany
Michela Felicetti, University of Perugia, Italy
Laura Fox-Clipsham, Animal Health Trust, United Kingdom
Kathryn T. Graves, University of KentuckyFollow
Gérard Guérin, French National Institute for Agricultural Research, France
Bianca Haase, University of Sydney, Australia
Telhisa Hasegawa, Nihon Bioresource College, Japan
Karin Hemmann, University of Helsinki, Finland
Emmeline W. Hill, University College Dublin, Ireland
Tosso Leeb, University of Bern, Switzerland
Gabriella Lindgren, Swedish University of Agricultural Sciences, Sweden
Hannes Lohi, University of Helsinki, Finland
Maria Susana Lopes, University of Azores, Portugal
Beatrice A. McGivney, University College Dublin, Ireland
Sofia Mikko, Swedish University of Agricultural Sciences, Sweden
Nicholas Orr, Institute of Cancer Research, United Kingdom
M. Cecilia T. Penedo, University of California - Davis
Richard J. Piercy, Royal Veterinary College, London, United Kingdom
Marja Raekallio, University of Helsinki, Finland
Stefan Rieder, Swiss National Stud Farm, Switzerland
Knut H. Røed, Norwegian School of Veterinary Science, Norway
Maurizio Silvestrelli, University of Perugia, Italy
June Swinburne, Animal Health Trust, United Kingdom
Teruaki Tozaki, Laboratory of Racing Chemistry, Japan
Mark Vaudin, Animal Health Trust, United Kingdom
Claire M. Wade, University of Sydney, Australia
Molly E. McCue, University of Minnesota - Twin Cities


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. F(ST) 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.

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Published in PLoS ONE, v. 8, no. 1, e54997.

© 2013 Petersen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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