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

Jessica L Petersen, James R Mickelson, Aaron K Rendahl, Stephanie J Valberg, Lisa S Andersson, Jeanette Axelsson, Ernie Bailey, Danika Bannasch, Matthew M Binns, Alexandre S Borges, Pieter Brama, Artur da Câmara Machado, Stefano Capomaccio, Katia Cappelli, E Gus Cothran, Ottmar Distl, Laura Fox-Clipsham, Kathryn T Graves, Gérard Guérin, Bianca HaaseTelhisa Hasegawa, Karin Hemmann, Emmeline W Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A McGivney, Sofia Mikko, Nicholas Orr, M Cecilia T Penedo, Richard J Piercy, Marja Raekallio, Stefan Rieder, Knut H Røed, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M Wade, Molly E McCue

Research output: Contribution to journalArticlepeer-review

204 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)e1003211
JournalPLoS Genetics
Issue number1
Publication statusPublished - 2013


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


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