The Search for Genetic Determinants Influencing Standardbred Performance

Racehorse performance can be influenced by many factors including: training, the driver/jockey, nutrition, track condition and genetics. In humans, more than 200 variants have been associated with performance. The objective of this study is to use genome-wide association (GWAS) to identify regions of interest and variants that influence performance in Standardbred racehorses. Variants identified could influence the musculoskeletal, cardiovascular, respiratory, and nervous systems. Preliminary data was obtained using 293 Standardbred horses genotyped on the Illumina Equine SNP70 bead chip in a genome-wide association study (GWAS) for the fastest time over a mile. The Standardbreds were divided by gait; 165 were pacers and 127 were trotters. Each horse was genotyped for 73,716 single nucleotide polymorphisms (SNPs) and after quality control conducted in PLINK, 50,585 SNPs remained. A GWAS was performed using PLINK and qqman in R version 3.3.1 was used to visualize the manhattan plot. In the pacers, SNPs on 3 chromosomes reached genome-wide significance (p=9.88x10^-07) and in the trotters, SNPs on one chromosome reached genome-wide significance for association with the fastest time over a mile. A second genome wide association study will be performed using 661 Standardbreds genotyped on either the 74K SNP array (329 horses) or the 670K SNP array (332 horses) and imputed to 1,924,259 SNP markers using BEAGLE4. Of the 661 Standardbreds genotyped, 384 are pacers and 277 are trotters. Any SNPs reaching genome-wide significance will be used to identify regions of interest that likely harbor performance related alleles.