Shahid Bahonar University of Kerman and Iranian Society of Animal Science Journal of Livestock Science and Technologies 2322-3553 15 1 2027 07 01 Comparative analysis of genomic diversity and genetic architecture amongst 14 horse breeds using ultra high-density SNP arrays: Implications for conservation and breeding 25 36 5323 10.22103/jlst.2026.26366.1702 EN Moslem Moghbeli Damane Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran Department of Animal Science, Faculty of Agriculture, university of Jiroft, Jiroft, Iran Ahmad Ayatollahi Mehrgardi Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran Ali Esmailizadeh Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran Journal Article 2025 11 22 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 14 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 1.57 million SNPs across 438 individuals to assess within- and between-breed genetic diversity, population structure, and signatures of selection. Observed heterozygosity (Hₒ) ranged from 0.1727 (Thoroughbred) to 0.2068 (Welsh), with Iranian breeds generally demonstrating lower allelic richness and effective number of alleles. Pairwise F_ST 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 83 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. https://lst.uk.ac.ir/article_5323_dac5f6cbc86da444d0ad7ed975ec06fb.pdf