Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

SIMPLE SUMMARY: Throughout horse industry modernization, sport horse breeds have been genetically evolved in accordance to their abilities in sport disciplines providing an opportunity to study selection signatures in the genome level. Future selection strategies of sport horse breeds can be optimized by improving our knowledge of genomic signatures of selection. The main goals of this study are identifying and investigating the genes and their biological pathways underlying selective pressures in sport and non-sport horse breeds. Here, we detected 49 genes as selective signals using fixation index, nucleotide diversity and Tajima’s D approaches. Intriguingly, our findings in functional enrichment analysis revealed the selection footprints related to musculoskeletal system development. Detected candidate genes and biological pathways in this study may be helpful to widen our perspective in recent breeding efforts and genomic evolutionary mechanisms in sport horse breeds. ABSTRACT: Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.