Genetic diversity and signatures of selection in Anglo-Arabian racehorses based on medium-density genotype data

The Anglo-Arabian horse breed (AA) is the result of crossing between Thoroughbred and Arabian horses renowned for versatility in show-jumping and racing. Southwest France and Sardinia in Italy are considered the historical nucleus of European AA breeding. Since little is known on genetic variability in the AA breed, especially those bred in the Sardinia region, this study investigates: i) inbreeding levels via pedigree and SNP genotyping; ii) runs of homozygosity (ROH) and selection signatures; iii) effective population size; and iv) distinctiveness of AA compared to Arabian and Thoroughbred horses. The ROH revealed an excessive amount of homozygosity, with a high kurtosis value observed in several chromosomes and an average inbreeding based on ROH of 21.1%. This latter value is higher compared to what was found based on pedigree data, highlighting the importance of complete pedigree records when estimating inbreeding based on genealogical data. The genomic inbreeding in AA horses was higher compared to other Italian horse breeds but lower than what was found in pure Thoroughbred and Arabian horses. This result suggests that the selection process for AA horses, may have prioritised racing ability over breed preservation which is the main goal in most local Italian breeds. The reduction in effective population size found in the latest 20 generations corroborates the potential presence of genetic diversity reduction due to selection in the AA breed. Remarkably, a large ROH island was identified on ECA17, which overlapped with two QTLs associated with racing performance.