Intense selection for athletic phenotypes in the Thoroughbred horse (Equus caballus) during the past 300 years has resulted in structural and functional system-wide adaptations that have significantly enhanced the physiological characteristics that enable elite athletic performance (Constantinopol et al. 1989; Jones et al. 1989; Evans et al. 1993). The athleticism of the Thoroughbred is attributed to a range of extreme physiological characteristics including a large muscle mass to body weight ratio, high skeletal muscle mitochondrial density and oxidative enzyme activity and considerable intramuscular stores of energy substrates (Hinchcliff et al. 2008).
While the phenotypic adaptations to elite athleticism in Thoroughbred horses are well described, the understanding of the molecular contributions to such exquisitely adapted exercise-related phenotypes is still in its infancy (Harrison & Turrion-Gomez 2006; Eivers et al. 2009; Gu et al. 2009; McGivney et al. 2009; Hill et al. 2010). Genetic contributions to athletic performance phenotypes in humans are well documented and more than 220 genes have been described (Bray et al. 2009). Although it is likely that Thoroughbred racing performance is also influenced by a large number of genes, only one performance-associated sequence variant in an exercise-relevant gene has previously been reported for the horse (Hill et al. 2010). The recent and strong selection for exercise-related traits has left signatures in the genome of the Thoroughbred. In a population genetics-based genome scan, positively selected loci have been identified in the extreme tail-ends of the distributions for statistics (FST and Ewens–Watterson test) that identify departures from patterns of genetic variation expected under neutral genetic drift (Gu et al. 2009). Such outlier approaches have led to an understanding of the selective forces that have shaped the recent evolution of human populations (Akey 2009; Oleksyk et al. 2010; Pritchard et al. 2010). Within the positively selected genomic regions, enrichments for genes involved in insulin signalling, fat substrate utilization and muscle strength have been identified. Genes in these functional categories likely play key roles in contributing to the lean, muscular, athletic phenotype that is typical for Thoroughbreds.
Genomic regions that have been targets for selection represent the most likely regions to contain structural genetic variation contributing to functional and phenotypic variance in exercise-relevant traits. Therefore, to identify genes that represent the most likely targets for selection, we investigated whether genes within these regions may contain sequence variants that contribute to the genetic variation in racetrack performance in the Thoroughbred population (Gaffney & Cunningham 1988).
We interrogated the EquCab2.0 SNP database for Thoroughbred SNPs located within the genomic sequence of 20 putative exercise-relevant genes located within the top-ranked outlier genomic regions previously described (Gu et al. 2009). A panel of 68 SNPs in 17 genes was selected for genotyping. To investigate associations between the sequence variants and racing phenotypes, we genotyped a group of Thoroughbred horses (n = 148) and performed a series of population-based case–control genetic association investigations by separating the samples on the basis of retrospective racecourse performance. In addition, we performed quantitative trait association tests using best race distance and handicap rating (Racing Post Rating, RPR) as phenotypes.