Comparative analysis of genomic diversity and genetic architecture amongst ۱۴ horse breeds using ultra high-density SNP arrays: Implications for conservation and breeding

Genetic variability is fundamental for the adaptability, health, and long-term sustainability of horse populations. This study sought to provide a comprehensive assessment of genomic diversity, population structure, and selection signatures across ۱۴ horse breeds, encompassing five indigenous Iranian breeds (Iranian Arabian-Asil, Turkmen, Caspian, Kurdish, Dareshuri) as well as nine international breeds (Thoroughbred, Quarter Horse, Belgian, Arabian, Welsh Pony, Standardbred, Icelandic, Lusitano, Morgan), based on ultra-high-density SNP array data. Following quality control and imputation, we analyzed the combined dataset of ۱.۵۷ million SNPs across ۴۳۸ individuals to assess within- and between-breed genetic diversity, population structure, and signatures of selection. Observed heterozygosity (Hₒ) ranged from ۰.۱۷۲۷ (Thoroughbred) to ۰.۲۰۶۸ (Welsh), with Iranian breeds generally demonstrating lower allelic richness and effective number of alleles. Pairwise FST and private allele analyses revealed moderate genetic differentiation, with Thoroughbred and Icelandic being the most divergent, while Iranian breeds revealed high shared ancestry. Population history assessments via Tajima’s D and Garza–Williamson M-ratio highlighted varying degrees of past bottlenecks, most evident in Dareshuri and Kurdish populations. Population structure analyses (PCA and PCoA) showed well-defined breed clusters, highlighting both geographic origin and selective breeding history. HapFLK analysis detected ۸۳ candidate genes under selection, associated with neural development, immune response, coat color and traits related to performance or reproduction. These findings emphasize the combined effects of historical selection, demographic events, and breed management on the genomic architecture of horse populations. The results provide applicable information for conservation strategies and breeding programs aimed at maintaining genetic diversity while preserving breed-specific traits, particularly in endangered Iranian and intensively selected international breeds.

کلیدواژه ها:

conservation genetics ، genomic diversity ، horse breeds ، Population structure ، selection signatures ، SNP array