Signatures of Selection Associated With Athletic Performance in Quarter Horse Subpopulations

Selective breeding for athletic performance in various disciplines has resulted in population stratification within the Quarter Horse (QH). The goals of this study were to utilize high density genotype data to: 1) identify genomic regions undergoing positive selection within or among QH subpopulations; 2) investigate haplotype structure within each QH subpopulation; and 3) identify candidate genes within genomic regions of interest (ROI) that might account for increased ability in each performance group.

65K SNP genotyping data on 144 individuals from 6 QH subpopulations (racing, working cow, cutting, reining, western pleasure and halter) were imputed to 2M SNPs (imputation accuracy estimated as 99.6%) using Beagle. Signatures of selection were identified using two F_ST-based statistics - di and hapFLK, accompanied by hapQTL, which identifies local haplotype structure and sharing within subpopulations. Data from racehorse breeds (Thoroughbred and Standardbred) were also used to investigate haplotype sharing with racing QHs.

Genomic regions (152 total) undergoing positive selection in the study cohort were identified on all 31 autosomes; on 5 chromosomes (ECA1, 10, 18, 20 and 28), at least one ROI was shared among all subpopulations. Transcripts within each ROI were retrieved using the BioMart software, and functional and pathway analyses were conducted using DAVID and PANTHER, respectively, to identify genes that might contribute to performance. Examples include genes associated with heart and lung function within the ‘racing ROI’ on ECA1, shared among all racehorse breeds, as well as ROI associated with learning, cognition and memory on ECA13 in the working cow subpopulation.