Mapping Athletic Performance Related Genes in the Equine Genome and a Genome Scan for Superior Athletic Performance in the Thoroughbred

The primary goal of the Thoroughbred industry is to breed and train superior equine athletes capable of excelling on the racetrack. To date, research into the genetic underpinnings of athletic ability has been limited in the horse. Advances in equine genomics and the genetics of athletic performance in humans have opened up the possibility of investigating this important trait in the Thoroughbred. Initially, 46 candidate genes associated with human athletic performance were mapped in the equine genome by radiation hybrid (RH) and fluorescent in situ hybridization (FISH) mapping. RH data and later the draft equine genomic sequence allowed us to identify microsatellites adjacent to these and other candidate genes (95 in total). Additional microsatellites were added to increase genome coverage, producing a final panel of 186 markers. All the potential markers were initially screened on a pool of DNA for 16 Thoroughbreds to ensure they were polymorphic. The panel was genotyped on 162 Thoroughbreds in total; Centimorgans (cM) between microsatellites were determined with CRI-MAP. The animal?s athletic ability was estimated using career winnings loge transformed to create a linear trait; unraced animals were treated as missing data. Linkage analysis was carried out using the MERLIN program, and association analysis was carried out using the QTDT program. Appropriate thresholds for statistical significance were determined by carrying out 1000 simulated genome scans based on the structure of the original data. LOD scores above 1.54 met the criteria of statistical significance (with a 5% chance of type I error). In the actual genome scan, the marker L12.2 had the highest observed LOD score of 1.16 and p-value of 0.01 and consequently was not significant; the association analysis also did not detect significant association with performance on the track. Given the complexity of the phenotype under investigation and the modest sample size, the lack of linkage/association was not unexpected. Nevertheless, this study has contributed to the RH and FISH maps of the equine genome. Additionally, the development of the genome scanning panel for this study has provided useful information on the most informative microsatellites for linkage or association studies in the Thoroughbred.