Arabian horses were selected for metabolic efficiency, beauty, efficiency and endurance. Therefore, Bedouins have for centuries traced their prized horses’ ancestries. With the establishment of the World Arabian Horse Organization (WAHO), registration of Arabian horses became centralized and countries worldwide registered them in its database. Most existing Arabian horses in Oman today were imported after the 1970s and are predominantly flat-racing Arabians. This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a diverse genetic background. To that end, we genotyped 63 randomly sampled Arabian horses from Oman using the Illumina Equine SNP70. For comparison, SNP genotypes of 12 Saudi Arabian horses, 27 French, 77 Egyptian, 11 Polish and 36 US Arabians were included in the study. We additionally included 17 Thoroughbred horses and 21 horses representing large and small breeds as an outgroup. Our MDS analysis and phylogenetic analysis showed that the Arabian horses in Oman cluster primarily with French Arabian horses, with a few horses clustering within the Polish/US Arabians. The French Arabian horse cluster was the closest to the Thoroughbred horses. Amongst the Arabian horses, plink average genomic inbreeding levels were highest in the Egyptian Arabian (0.169) followed by the Saudi Arabian horses (0.137) and lowest in the Omani and French Arabian horses, −0.041 and −0.079 respectively. To our knowledge, this is the first report on the genetic background and diversity of Arabian horses in Oman. Our results demonstrated a definite subpopulation structure among Arabian horses and this information should advise future decision-making on Arabian horse breeding.
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