Genomic Signatures of Selection in the American Quarter Horse

The American Quarter Horse (QH) is the most popular breed in the US, corresponding to one third of the equine population. Known for its versatility, the QH has been increasingly bred for performance in various disciplines, leading to population stratification within the breed. The goal of this study was to identify genomic signatures of selection within or among QH subpopulations, and to identify putative functional alleles within regions of interest (ROIs) that account for the divergence among performance groups.  

144 individuals from 6 QH subpopulations (racing, working cow, cutting, reining, western pleasure and halter) were genotyped for ~65,000 SNP markers and an F_ST-based statistic, di, was calculated for 500kb windows across the genome. Haplotype structure and frequency within each significant di window, and haplotype sharing among the QH subpopulations, were used to identify genomic regions most likely harboring alleles under selection. Data from Thoroughbred (TBs) and Standardbred racehorses were used to investigate haplotype sharing with racing QHs.

25 ROIs in 14 different chromosomes were identified. Of those, 22 were shared between at least 2 performance groups (5 were shared between the racing QH subpopulation and the TB), and 3 were unique to a subpopulation. These ROIs were further refined using data from an additional 2 million SNPs genotyped in 7 to 13 QHs within each subpopulation. Whole genome sequencing data for 4 racing and 4 halter QHs were used for the discovery and annotation of biologically relevant variants that might account for the divergence among these two performance groups.