PloS one2013; 8(1); e54997; doi: 10.1371/journal.pone.0054997

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

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. 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.
Publication Date: 2013-01-30 PubMed ID: 23383025PubMed Central: PMC3559798DOI: 10.1371/journal.pone.0054997Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • Non-U.S. Gov't
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.


This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research explores the genetic diversity in modern horses using genome-wide Single Nucleotide Polymorphisms (SNPs) data from 814 horses across 36 breeds, providing fresh insights into the relationships and diversity within horse breeds.

Research Methodology and Data

  • The researchers used data from 814 horses from 36 different breeds.
  • This data was represented by a genome-wide set of autosomal SNPs, which are variations at a single position in a DNA sequence among individuals.
  • Through this, they aimed to provide a detailed description of the genetic diversity in different horse breeds.

Results and Findings

  • The study results indicated relationships among breeds which largely reflect geographic origins and known breed histories.
  • It was observed that breeds early in the process of breed development showed low levels of population divergence.
  • This was also seen in breeds with high levels of within-breed diversity due to either large population size, ongoing outcrossing, or large within-breed phenotypic diversity.

Implications of the Findings

  • Low levels of within-breed diversity were observed in populations experiencing population bottlenecks, those under intense selective pressure, or those closed with long breed histories.
  • Understanding these relationships and the extent of diversity can provide new insights into horse breeds.
  • The results can facilitate future genome-wide association studies and investigations into the genomic targets of selection.


  • Overall, the research provides a first detailed look at the genetic diversity among different horse breeds.
  • It uncovers the key factors affecting this diversity and opens up new areas for further study and understanding.

Cite This Article

Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Cu00e2mara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guu00e9rin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Ru00f8ed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. (2013). Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One, 8(1), e54997.


ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 8
Issue: 1
Pages: e54997
PII: e54997

Researcher Affiliations

Petersen, Jessica L
  • University of Minnesota, College of Veterinary Medicine, St Paul, MN, USA.
Mickelson, James R
    Cothran, E Gus
      Andersson, Lisa S
        Axelsson, Jeanette
          Bailey, Ernie
            Bannasch, Danika
              Binns, Matthew M
                Borges, Alexandre S
                  Brama, Pieter
                    da Cu00e2mara Machado, Artur
                      Distl, Ottmar
                        Felicetti, Michela
                          Fox-Clipsham, Laura
                            Graves, Kathryn T
                              Guu00e9rin, Gu00e9rard
                                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
                                                              Ru00f8ed, Knut H
                                                                Silvestrelli, Maurizio
                                                                  Swinburne, June
                                                                    Tozaki, Teruaki
                                                                      Vaudin, Mark
                                                                        M Wade, Claire
                                                                          McCue, Molly E

                                                                            MeSH Terms

                                                                            • Animals
                                                                            • Breeding
                                                                            • Cluster Analysis
                                                                            • Genomics
                                                                            • Horses / classification
                                                                            • Horses / genetics
                                                                            • Polymorphism, Single Nucleotide
                                                                            • Principal Component Analysis

                                                                            Grant Funding

                                                                            • K08 AR055713 / NIAMS NIH HHS
                                                                            • T32 AR007612 / NIAMS NIH HHS
                                                                            • 1K08AR055713-01A2 / NIAMS NIH HHS
                                                                            • 2T32AR007612 / NIAMS NIH HHS

                                                                            Conflict of Interest Statement

                                                                            Matthew M. Binns is employed by Equine Analysis, June Swinburne by Animal DNA Diagnostics Ltd., and Emmeline W. Hill, Nickolas Orr, and Beatrice A. McGivney are associated with Equinome Ltd. There are no competing interests including patents, products in development, or marketed products to declare in relationship to this work. This does not alter the authors‚ adherence to all the PLOS ONE policies on sharing details and materials.


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