Background: Iran is home to genetically distinct horse breeds shaped by geography and history. Breeds like the Kurdish, Caspian pony, and Turkmen reflect deep-rooted diversity and unique adaptive traits. Aims/Objectives: This study aimed to identify genomic regions exhibiting signatures of selection and to detect candidate genes and biological pathways related to body size that may influence performance in various Iranian and exotic horse breeds. Methods: Samples were collected from three Iranian native breeds (Caspian pony, Turkmen, and Kurdish) and three exotic breeds (Fell pony, Arabian, and Akhal-Teke) originating from England, the Middle East, and Turkmenistan, respectively. Genotyping data included 50 K SNPs for the exotic breeds and 70 K SNPs for the Iranian breeds. To explore population structure and genetic differentiation, Discriminant Analysis of Principal Components (DAPC) was conducted. Results: Population structure analysis showed clear separation between pony and light horse breeds, with AkhalTeke and Turkmen clustering together and Fell ponies forming a distinct group. Using FLK and hapFLK tests, we identified 124 and 127 candidate genes under selection, respectively. Several genes were linked to body size traits, including those involved in bone mineralization, osteoblast differentiation, growth factor signaling, and tissue development. Notably, we identified novel genes including SAMD7, SPARC1, IBSP, MEPE, DEUP12, PLAAT1, and SPP1 that not previously reported in horse studies, offering new insights into equine morphology. Conclusion: Results revealed selection signatures linked to genes influencing body size and development, including several novel candidates. These findings deepen our understanding of equine morphology and warrant further investigation using larger sample sizes.
