A genome-wide signatures of selection study of Welsh ponies and draft horses revealed five genes associated with horse type variation

The modern horse populations with diverse types have been shaped through evolutionary forces, domestication, and recent breeding programs. Horse breeds are grouped into pony, light, and draft, mainly based on their body morphology. Identifying the selection pressure patterns on the genome level can improve our knowledge of evolution of horse types. The genome-wide single nucleotide polymorphisms of 42 Welsh ponies and 38 draft horses were used to detect selection signals by employing Z-transformed of fixation index (Z(F-st)) and extended haplotype homozygosity (xp-EHH). Our findings revealed a total number of 549 genes as signatures of selection out of which five were observed in both methods. These genes are known as candidate genes for osteolysis (SRCIN), growth (LAP3), and morphological traits including body size (LCORL and ZFAT), hock circumference and body length (FAM184B). A gene enrichment analysis based on these identified genes revealed two significant biological processes: macromolecule metabolic process (GO:0043170) and nitrogen compound metabolic process (GO:0006807), which might be related to regulation of skeletal muscle growth, and bone formation in horses. These results can help us to better understand the genetic background of evolving type and body morphology of draft horses, and ponies. Additionally, our findings in this study might be helpful to develop the SNP panels for future genomic selection programs in horses.