Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Authors

Jessica Lynn Petersen, University of Nebraska-LincolnFollow
James R. Mickelson, University of Minnesota - Twin Cities
Aaron K. Rendahl, University of Minnesota - Twin Cities
Stephanie K. Valberg, University of Minnesota - Twin Cities
Lisa S. Andersson, Swedish University of Agricultural Sciences
Ernie Bailey, University of Kentucky
Danika L. Bannasch, University of California - Davis
Matthew M. Binns, Equine Analysis
Alexandre S. Borges, University Estadual Paulista
Pieter Brama, University College Dublin
Artur da Câmara Machado, University of the Azores
Stefano Capomaccio, University of Perugia
Katia Cappelli, University of Perugia
E. Gus Cothran, Texas A & M University - College Station
Ottmar Distl, University of Veterinary Medicine Hannover
Laura Fox-Clipsham, Animal Health Trust
Kathryn T. Graves, University of Kentucky
Gérard Guérin, French national Institute for Agricultural Research
Bianca Haase, University of SydneyFollow
Telhia Hasegawa, Nihon Bioresource College
Karin Hemmann, University of Helsinki
Emmeline W. Hill, University College Dublin
Tosso Leeb, University of Bern
Gabriella Lindgren, Swedish University of Agricultural Sciences
Hannes Lohi, University of Helsinki
Maria Susana Lopes, University of the Azores
Beatrice A. McGivney, University College Dublin
Sofia Mikko, Swedish University of Agricultural Sciences
Nicholas Orr, Breakthrough Breast Cancer Research Centre
M. Cecilia T. Penedo, University of California - Davis
Richard J. Piercy, Royal Veterinary College, London
Marja Raekallio, University of Helsinki
Stefan Rieder, Agroscope Liebefeld-Posieux Research Station
Knut H. Røed, Norwegian School of Veterinary Science
June Swinburne, Animal Health Trust
Teruaki Tozaki, Laboratory of Racing Chemistry
Mark Vaudin, Animal Health Trust
Claire M. Wade, University of Sydney
Molly E. McCue, University of Minnesota - Twin CitiesFollow

Date of this Version

1-2013

Citation

PLoS Genetics (January 2013) 9(1): e1003211. DOI: 10.1371/journal.pgen.1003211.

Comments

Copyright 2013, the authors. Used by permission.

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.