Validation of Genetic Variants Predictive of Pacing in Standardbred Horse

A recently described mutation in DMRT3 is thought to be permissive for the ability to perform alternative gaits in the horse. However, this mutation is nearly fixed in the Standardbred breed, despite the fact that not all Standardbreds can perform the alternative pacing gait. This suggests that modifying genetic variants must exist within this breed that determine pacing ability. We previously identified seven novel SNPs that were highly predictive of gait within a discovery population of 659 Standardbred racehorses. The aim of this study was to validate this predictive model in an independent population of Standardbreds.

One hundred sixty-six Standardbred horses with race records (n = 82 trotters, n = 84 pacers) were genotyped using a custom high-throughput Sequenom assay. The genotypes at the 7 SNPs of interest were evaluated according to the conditional inference tree model developed in our discovery population. Two horses did not genotype at all 7 SNPs and could not be classified. Of the remaining 164 horses, gait (pacer/trotter) was correctly predicted for 162 (98.8%). Both misclassified horses were pacers.

While this prediction model appears highly accurate for gait in Standardbreds, it will need to be tested in other gaited breeds to determine if its predictive value is specific to Standardbreds, to breeds that pace, or if it is universally applicable. Future work will address the question of whether one or more of the predictive SNPs plays a functional role in the ability to pace, or if they are simply tagging functional variants.