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

Thoroughbred horse racing is a global sport with major hubs in Europe, North America, Australasia and Japan. Regional preferences for certain traits have resulted in phenotypic variation that may result from adaptation to the local racing ecosystem. Here, we test the hypothesis that genes selected for regional phenotypic variation may be identified by analysis of selection signatures in pan-genomic SNP genotype data. Comparing Australian to non-Australian Thoroughbred horses (n = 99), the most highly differentiated loci in a composite selection signals (CSS) analysis were on ECA6 (34.75-34.85 Mb), ECA14 (33.2-33.52 Mb and 35.52-36.94 Mb) and ECA16 (24.28-26.52 Mb) in regions containing candidate genes for exercise adaptations including cardiac function (ARHGAP26, HBEGF, SRA1), synapse development and locomotion (APBB3, ATXN7, CLSTN3), stress response (NR3C1) and the skeletal muscle response to exercise (ARHGAP26, NDUFA2). In a genome-wide association study for field-measured speed in two-year-olds (n = 179) SNPs contained within the single association peak (33.2-35.6 Mb) overlapped with the ECA14 CSS signals and spanned a protocadherin gene cluster. Association tests using higher density SNP genotypes across the ECA14 locus identified a SNP within the PCDHGC5 gene associated with elite racing performance (n = 922). These results indicate that there may be differential selection for racing performance under racing and management conditions that are specific to certain geographic racing regions. In Australia breeders have principally selected horses for favourable genetic variants at loci containing genes that modulate behaviour, locomotion and skeletal muscle physiology that together appear to be contributing to early two-year-old speed.

Déclaration de conflit d'intérêts

I have read the journal's policy and the authors of this manuscript have the following competing interests: EWH and DEM and shareholders, EWH, HH and BAM are paid employees and LMK is a paid consultant of Plusvital Ltd. EWH is a Director of the company. EWH, DEM and LMK are coinventors on multiple patents relating to the MSTN g.66493737 SNP, which is not relevant to the current manuscript. Plusvital Ltd has not applied for protection of IP arising from the results in the current manuscript and at time of manuscript submission has no commercial offering relating to the results. Due to the confidential nature of the privately owned horses, data are available on request from the UCD Technology Transfer Office and Plusvital Ltd. for researchers who meet the criteria for access to confidential data. This does not alter our adherence to PLOS ONE policies on sharing data and materials.