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.
Digital Object Identifier (DOI)
Petersen, Jessica L.; 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.; and McCue, Molly E., "Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds" (2013). Veterinary Science Faculty Publications. 22.
Output of di calculations for all breeds. The y axis denotes di values while the 31 autosomes are on the x axis designated by alternating colors. Each dot represents one, 500 kb window. The dashed horizontal line represents the 99th percentile of the empirical distribution of di for each breed.
Table_S1.pdf (38 kB)
Genomic coordinate (chr:bp position) of the center of the thirty-three, 500 kb windows for each breed that fell into the 99th percentile of the empirical distribution and were therefore designated putative signatures of selection.
Table_S2.pdf (16 kB)
Annotated genes (or other features) within high-frequency, extended haplotypes of interest.
Table_S3.pdf (18 kB)
Variants (position and type) identified in sequencing MSTN in 6 Thoroughbred and 8 Quarter Horse individuals. The Intron 1 SNP and promoter SINE insertion used in further analyses are noted in bold. A dot (·) indicates missing data while “N” indicates no SINE insertion and “S” indicates the presence of the insertion.
Table_S4.pdf (27 kB)
Primers used for sequencing of MSTN.