Comparative genomics of Pony and Hanoverian horses versus different breeds of horses for identifying candidate genes associated with body size and athletic performance

During domestication and artificial selection, horse breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as body size, muscle composition, growth rate, reproduction and behavior. The main goal of this study was detection of signatures positive selection associated with body size and athletic performance traits in horse breeds. Herein, we used whole genome sequencing data from 86 horses. To detect genomic signatures of positive selection, we applied fixation index (FST) and cross-population composite likelihood ratio (XP-CLR) methods. For body size trait, genetic study was performed based on the small body size of Debao pony. The most significant signal of positive selection was mapped to the FGFR1 gene, which may have independently been selected for short stature in the Chinese pony population. In addition, four other loci on chromosomes 2, 3 and 4 were identified to be potentially involved in the development of body size. The screen of the potential candidate genes involved in athletic performance was carried out based on Hanoverian horse breed.  Genetic analyses showed that the ACTA1 gene is potentially involved in athletic performance in this breed, consistent with its role observed in human population. In addition, three other loci on chromosomes 1 and 20 were identified to be potentially involved in the equine physical performance. These novel candidate genes identified in this study may be useful targets for clarifying our understanding of the molecular basis of body size and athletic performance in horses. These results can provide new insight for future research into the genetic architecture of relevant traits in horse breeding program.