Genomic Selection in the Horse

Similar to other domestic animal species, artificial selection in horses has resulted in breeds which often uniformly exhibit desirable phenotypes; in particular, phenotypes related to athletic ability, performance traits and metabolic efficiency. Our group has used an F_ST-based statistic (d_i) to identify genomic regions of selection in 800 horses from 33 breeds at over 54,000 SNP loci. Numerous potential targets of selection were identified including a ~1 Mb conserved haplotype surrounding the MSTN (myostatin) gene present in 92.8% of Quarter Horse and 50% of Thoroughbreds, but rare (<1%) in other breeds. Sequencing of MSTN identified a SINE insertion in the promoter, which, along with an intronic polymorphism, is significantly associated with altered muscle fiber type proportions. Signatures across 6 gaited breeds pointed to a conserved haplotype on ECA23 containing a novel mutation permissive for alternate gait in horses. Other regions of interest included signatures over two highly divergent haplotypes in both draft breeds and miniature horses over the same region of ECA11. We have recently used this method to identify genomic signatures of selection within Quarter Horse subpopulations, using 144 elite performers representing 6 performance disciplines. This work has indentified multiple regions within each subpopulation that are currently being investigated, including a region shared by both racing Quarter Horses and racing Thoroughbreds. Mapping signatures of selection in the modern horse is the first step in the identification of genes important in the domestication and specialization of modern horse breeds.