ROH as hint of selection in the genome of a modern sport horse breed

The horse breeding sector has to meet the growing demand of horses for high level competitions, while guaranteeing good health standards. Knowledge of the genetic background of sport-related traits could benefit the selection process. Recent advances in genome mapping are paving the way to further explore effects of selection. Strong selective pressure reduces genetic diversity which results in increased homozygosity at genome level. In this project, Runs of Homozygosity (ROH) were studied to find genomic regions under selective pressure of an equestrian sport horse breed. To identify differences in selective pressure between sport horses and a pony breed with low selective pressure on sport performance, data from 380 Swedish Warmblood horses (SWB), genotyped with a high density SNP array (670K) were analysed and compared to Exmoor pony genotypes. ROH were detected using a sliding windows approach in PLINK v1.90: short ROH reflect population history, whereas long ROH are indicators of recent selection. Length and location of ROH differed between the two breeds in agreement with the known breed history, with ROH more evenly distributed in the genome of the inbred Exmoor ponies. Long ROH were the rarest, although in both breeds they covered the largest proportion of the genome. Specific patterns in the location of long shared ROH (85% of the population) were found in SWB horses but not in Exmoor ponies. In SWB horses, enrichment analyses of the 65 shared ROH pointed out genomic regions in ECA4, ECA6 and ECA7, harbouring genes involved in muscle function, excitatory synaptic transmission, and development of central nervous system. Altogether, this indicates that movements, cognitive functions and personality related traits represent important targets of selection in the SWB breed, which has become a breed shaped for sport purposes.