A genomic prediction model for racecourse starts in the Thoroughbred horse

Abstract

Durability traits in Thoroughbred horses are heritable, economically valuable and may affect horse welfare. The aims of this study were to test the hypotheses that (i) durability traits are heritable and (ii) genetic data may be used to predict a horse's potential to have a racecourse start. Heritability for the phenotype 'number of 2-and 3-year-old starts' was estimated to be h 2 m = 0.11 AE 0.02 (n = 4499). A genome-wide association study identified SNP contributions to the trait. The neurotrimin (NTM), opioid-binding protein/cell adhesion molecule like (OPCML) and prolylcarboxypeptidase (PRCP) genes were identified as candidate genes associated with the trait. NTM functions in brain development and has been shown to have been selected during the domestication of the horse. PRCP is an established expression quantitative trait locus involved in the interaction between voluntary exercise and body composition in mice. We hypothesise that variation at these loci contributes to the motivation of the horse to exercise, which may influence its response to the demands of the training and racing environment. A random forest with mixed effects (RFME) model identified a set of SNPs that contributed to 24.7% of the heritable variation in the trait. In an independent validation set (n = 528 horses), the cohort with high genetic potential for a racecourse start had significantly fewer unraced horses (16% unraced) than did low (27% unraced) potential horses and had more favourable race outcomes among those that raced. Therefore, the information from SNPs included in the model may be used to predict horses with a greater chance of a racecourse start.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

“…For example, in the skeletal muscle transcriptome response to exercise training, neurological processes were the most significantly over-represented gene ontology (GO) terms, with the top three ranked GO terms being Neurological system process (P = 4.85 × 10 −27 ), Cognition (P = 1.92 × 10 −22 ) and Sensory perception (P = 4.21 × 10 −21 ) 40 . Furthermore, in genome-wide association (GWA) studies genes involved in behavioural plasticity are the most strongly associated with economically important traits in racing Thoroughbreds: precocity (early adaptation to racing) 41 and the likelihood of racing 19 . For Thoroughbred horses, behavioural plasticity enables adaptation to the rigours of an intense exercise training programme in an unnatural environment, with considerable variation in the abilities of horses raised in the same environment to adapt to stress.…”

“…Surprisingly, according to a recent study 18 , Thoroughbreds appear to have a lower than expected mutational load, suggested to be due to effective purging through negative selection on phenotypes. This may be facilitated in the Thoroughbred in practice by the unusually large census population size relative to the effective population size, with a high proportion of horses that do not ever race 19 . However, the results from that study are likely not representative of the genetics of the current breeding population in the major bloodstock regions of the world; the sample cohort of Thoroughbreds examined was small (n = 19) and all the horses were registered Thoroughbreds in Korea.…”

Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed

“…For example, in the skeletal muscle transcriptome response to exercise training, neurological processes were the most significantly over-represented gene ontology (GO) terms, with the top three ranked GO terms being Neurological system process (P = 4.85 × 10 −27 ), Cognition (P = 1.92 × 10 −22 ) and Sensory perception (P = 4.21 × 10 −21 ) [34]. Furthermore, in GWA studies we have demonstrated that genes (HTR7, NTM and PCRP) involved in behavioural plasticity are the most strongly associated with economically important traits in racing Thoroughbreds: precocity (early adaptation to racing) [45] and the likelihood of never racing [59]. For horses entering exercise training, behavioural plasticity enables the adaptation to an unnatural environment by reducing stress, with considerable variation in the abilities of horses raised in the same environment to adapt to stress.…”

Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

“…Surprisingly, Thoroughbreds appear to have a lower than expected mutational load, suggested to be due to effective purging through negative selection on phenotypes. This may be facilitated in the Thoroughbred in practice by the unusually large census population size relative to the effective population size, with a high proportion of horses that do not ever race [19]. However, the results from that study are likely not representative of the genetics of the current breeding population in the major bloodstock regions of the world; the sample cohort of Thoroughbreds examined was small ( n = 19) and all the horses were registered Thoroughbreds in Korea.…”

“…For example, in the skeletal muscle transcriptome response to exercise training, neurological processes were the most significantly over-represented gene ontology (GO) terms, with the top three ranked GO terms being Neurological system process ( P = 4.85 × 10 −27 ), Cognition ( P = 1.92 × 10 −22 ) and Sensory perception ( P = 4.21 × 10 −21 ) [66]. Furthermore, in genome-wide association (GWA) studies genes involved in behavioural plasticity are the most strongly associated with economically important traits in racing Thoroughbreds: precocity (early adaptation to racing) [67] and the likelihood of racing [19]. For Thoroughbred horses, behavioural plasticity enables adaptation to the rigours of an intense exercise training programme in an unnatural environment, with considerable variation in the abilities of horses raised in the same environment to adapt to stress.…”