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

Jessica L Petersen ,Richard J Piercy,James R Mickelson,Telhisa Hasegawa,Hannes Lohi,Teruaki Tozaki,Artur Da Câmara Machado,Molly E Mccue,E Gus Cothran,Gérard Guérin,Claire M Wade,Karin Hemmann,June Swinburne,Bianca Haase,Tosso Leeb,Nicholas Orr,Sofia Mikko,Maurizio Silvestrelli,Stefan Rieder,Marja Raekallio,Michela Felicetti,Gabriella Lindgren,Beatrice A Mcgivney,Danika L Bannasch ,P A J Brama ,Knut Røed ,E Bailey ,E W Hill ,J Axelsson ,O Distl ,M S Lopes ,M M Binns ,Lisa Andersson ,M C T Penedo ,Mark D Vaudin ,Kathryn Graves ,Laura Y Fox-Clipsham ,Alexandre Secorun Borges

doi:10.1371/journal.pone.0054997

Abstract

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.

Highlights

With a world-wide population greater than 58 million [1], and as many as 500 different breeds, horses are economically important and popular animals for agriculture, transportation, and recreation
Prior genetic work aimed at understanding horse domestication has shown that a significant proportion of the diversity observed in modern maternal lineages was present at the time of domestication [2,8,16]
Samples Of the 38 populations sampled, two breeds were represented by geographically distinct populations: the Thoroughbred was sampled in the both the United States (US) and the United Kingdom and Ireland (UK/Ire), and the Standardbred was sampled in the US as well as in Norway

Summary

Introduction

With a world-wide population greater than 58 million [1], and as many as 500 different breeds, horses are economically important and popular animals for agriculture, transportation, and recreation. The question of mitochondrial DNA (mtDNA) diversity was further addressed by recent sequencing of the entire mtDNA genome These studies estimate that, minimally, 17 to 46 maternal lineages were used in the founding of the modern horse [2,17]; those data were unable to support prior studies suggesting geographic structure among maternal lineages [9,18]. Recent nuclear DNA analyses have utilized ‘‘non-breed’’ horses sampled across Eurasia to attempt to understand the population history of the horse These microsatellite-based studies suggest a weak pattern of isolation by distance with higher levels of diversity in, and population expansion originating from Eastern Asia [13,19]. While significant diversity is observed in maternal lineages, paternal input into modern horse breeds appears to have been extremely limited as shown by a lack of variation at the Y-chromosome [20,21]

Methods

Results

Discussion

Conclusion