Genetic diversity in the modern horse illustrated from genome-wide SNP data
2013
Petersen, Jessica L. | Mickelson, James R. | Cothran, E. Gus | Andersson, Lisa S. | Axelsson, Jeanette | Bailey, Ernie | Bannasch, Danika | Binns, Matthew M. | Borges, Alexandre S. | Brama, Pieter | Machado, Artur da Camara | Distl, Ottmar | Felicetti, Michela | Fox-Clipsham, Laura | Graves, Kathryn T. | Guérin, Gerard | Haase, Bianca | Hasegawa, Telhisa | Hemmann, Karin | Hill, Emmeline W. | Leeb, Tosso | Lindgren, Gabriella | Lohi, Hannes | Lopes, Maria Susana | Mcgivney, Beatrice A. | Mikko, Sofia | Orr, Nicholas | Penedo, M. Cecilia T. | Piercy, Richard J. | Raekallio, Marja | Rieder, Stefan | Roed, Knut H. | Silvestrelli, Maurizio | Swinburne, June | Tozaki, Teruaki | Vaudin, Mark | Wade, Claire M. | Mccue, Molly E. | Coll Vet Med ; University of Minnesota [Twin Cities] (UMN) ; University of Minnesota System (UMN)-University of Minnesota System (UMN) | Coll Vet Med & Biomed Sci ; Texas A&M University System | Department of Animal Bredding and Genetics ; Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet (SLU) | Dept Vet Sci ; University of Kentucky (UK) | Sch Vet Med ; University of California [Davis] (UC Davis) ; University of California (UC)-University of California (UC) | Equine Analysis | Dept Vet Clin Sci ; Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP) | Sch Vet Med ; University College Dublin [Dublin] (UCD) | Inst Biotechnol & Bioengn, Biotechnol Ctr Azores ; University of the Azores | Inst Anim Breeding & Genet ; University of Veterinary Medecine Hannover | Fac Vet Med ; Università degli Studi di Perugia = University of Perugia (UNIPG) | Newmarket ; Anim Hlth Trust | Génétique Animale et Biologie Intégrative (GABI) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | The University of Sydney | Nihon Bioresource College | Fac Vet Med | Coll Agr Food Sci & Vet Med ; University College Dublin [Dublin] (UCD) | Inst Genet ; Universität Bern = University of Bern = Université de Berne (UNIBE) | Coll Agr Food Sci & Vet Med ; University College Dublin [Dublin] (UCD) | Breakthrough Breast Canc Res Ctr ; Institute of Cancer Research (ICR) | Comparat Neuromuscular Dis Lab ; Royal Veterinary College | Agroscope Liebefeld Posieux Res Stn ; Swiss Natl Stud Farm | Dept Basic Sci & Aquat Med ; Norwegian School of Veterinary Science | Anim DNA Diagnost Ltd ; | Dept Mol Genet ; Laboratory of Racing Chemistry | National Research Initiative from the United States Department of Agriculture-National Institute of Food and Agriculture (USDA-NIFA) [2008-35205-18766, 2009-55205-05254, 2012-67015-19432]; Foundation for the Advancement of the Tennessee Walking Show Horse; Tennessee Walking Horse Foundation; National Institutes of Health-National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIHNAIMS) [1K08AR055713-01A2, 2T32AR007612]; American Quarter Horse Foundation; Morris Animal Foundation [D07EQ-500]; Swedish Research Council FORMAS [221-2009-1631, 2008-617]; Swedish-Norwegian Foundation for Equine Research [H0847211, H0947256]; Carl Tryggers Stiftelse [CTS 08: 29]; FCT; DRCT; Science Foundation Ireland [04/Y11/B539]; Volkswagen Stiftung und Niedersa chsisches Ministerium fur Wissenschaft und Kultur, Germany [VWZN2012]; [FRCT/2011/317/005]
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.
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