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Home / Equine Research Bank / PLoS Genet / Genome-wide analysis reveals selection for important traits ...
PLoS genetics2013; 9(1); e1003211; doi: 10.1371/journal.pgen.1003211

Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Abstract: Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.
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Publication Date: 2013-01-17 PubMed ID: 23349635PubMed Central: PMC3547851DOI: 10.1371/journal.pgen.1003211Google Scholar: Lookup
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  • Journal Article
  • Research Support
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  • Extramural
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  • Non-U.S. Gov't
  • Research Support
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Summary

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 study delves into the genetics of various horse breeds, identifying specific patterns of selection for traits such as size, gait, and muscle fiber composition. Particularly, it looks into two genes–MSTN and DMRT3–which respectively influence muscle fiber and gait in horses. These genes have been selected for in different breeds leading to diverse physical attributes.

Genome-Wide Analysis and Selection Traits

  • The research utilized a pool of 744 individual horses from 33 different breeds and a 54,000 SNP genotyping array. Selection pressures applied over a short evolutionary time have caused homogeneity within breeds but considerable variation between them.
  • The study focused on identifying breed-specific selection targets by using an F(ST)-based statistic calculated across 500-kb windows of the genome. This approach identifies areas of the genome where there is a statistically significant amount of variation between the selected populations.

The Role of MSTN and DMRT3 Genes

  • The MSTN gene positioned on the ECA18 chromosome exhibited a significant signature of selection in both the Paint and Quarter Horse breeds.
  • Sequencing of this gene and histological analysis of muscle biopsies revealed that variations of MSTN were significantly associated with changes in muscle fiber composition. Specifically, certain variations were linked with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse. This shows that selection at this locus had tangible effects on the muscle composition of certain horse breeds.
  • On chromosome ECA23, strong signatures of selection were spotted in all gaited breeds involved in the study and it led to the discovery of a shared, 186-kb haplotype including two genes related to the “doublesex” mab transcription factor genes (DMRT2 and DMRT3).
  • A mutation in the DMRT3 gene within this haplotype appears necessary for alternative gaits. The recent identification of this mutation adds further evidence of selection happening at this locus.

Identification of Loci influencing Size

  • The researchers also identified potential loci for the determination of size in draft breeds and the Miniature horse on chromosome ECA11.
  • Other loci that were potentially under selection surrounding candidate genes were also examined, providing more details on how selection has been shaping diverse horse phenotypes.

In summary, this research underscores the importance of the MSTN gene in racing breeds, shows strong evidence for the selection of gait and size, and demonstrates the potential of population-based techniques to find genomic regions influencing crucial phenotypes in modern horses.

Cite This Article

APA
Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Capomaccio S, Cappelli K, Cothran EG, Distl O, Fox-Clipsham L, Graves KT, Guérin 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, Røed KH, Swinburne J, Tozaki T, Vaudin M, Wade CM, McCue ME. (2013). Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet, 9(1), e1003211. https://doi.org/10.1371/journal.pgen.1003211

Publication

PLoS genetics
ISSN: 1553-7404
NlmUniqueID: 101239074
Country: United States
Language: English
Volume: 9
Issue: 1
Pages: e1003211

Researcher Affiliations

Petersen, Jessica L
  • College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA. jlpeters@umn.edu
Mickelson, James R
    Rendahl, Aaron K
      Valberg, Stephanie J
        Andersson, Lisa S
          Axelsson, Jeanette
            Bailey, Ernie
              Bannasch, Danika
                Binns, Matthew M
                  Borges, Alexandre S
                    Brama, Pieter
                      da Câmara Machado, Artur
                        Capomaccio, Stefano
                          Cappelli, Katia
                            Cothran, E Gus
                              Distl, Ottmar
                                Fox-Clipsham, Laura
                                  Graves, Kathryn T
                                    Guérin, Gérard
                                      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
                                                                    Røed, Knut H
                                                                      Swinburne, June
                                                                        Tozaki, Teruaki
                                                                          Vaudin, Mark
                                                                            Wade, Claire M
                                                                              McCue, Molly E

                                                                                MeSH Terms

                                                                                • Animals
                                                                                • Biological Evolution
                                                                                • Breeding
                                                                                • Genome-Wide Association Study
                                                                                • Genotype
                                                                                • Haplotypes
                                                                                • Horses / genetics
                                                                                • Myostatin / genetics
                                                                                • Phenotype
                                                                                • Polymorphism, Single Nucleotide
                                                                                • Selection, Genetic

                                                                                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

                                                                                Equinome Ltd. (EWH, Director) has been granted a license for commercial use of MSTN data as contained within patent applications: U.S. Provisional Serial Number 61/136553; Irish Patent Application Numbers 2008/0735 and 2010/0151; and Patent Cooperation Treaty number PCT/IE2009/000062. The PCT publication WO2010/029527A published 18 March 2010. Title: “A method for predicting athletics performance potential” and U.S. publication US2011/0262915 published 27 October 2011. Title: “Method for predicting the athletic performance potential of a subject.” EWH, NO, and BAM are named on the applications. MMB works for The Genetic Edge, previously published a paper on the association between SNPs in the MSTN region and best racing distance for elite Thoroughbred horses [46], and uses these markers in commercial tests. LSA and GL are co-applicants on a patent application concerning the commercial utilization of the DMRT3 mutation. These commercial ventures had no influence on the interpretation of the results relating to myostatin or gait presented in the paper.

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