Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

伊朗本土马品种在进化上受到不同系统发育支系中自然和人工选择的影响，从而以几种独特的方式塑造了它们的基因组。本研究的目的是评估四种伊朗本土马品种的遗传多样性和全基因组选择特征。我们 使用全基因组基因分型数据评估了来自里海 ( n  = 21)、土库曼 ( n  = 29)、库尔德 ( n  = 67) 和波斯阿拉伯 ( n = 52) 群体的 169 匹马。土库曼、里海、波斯阿拉伯和库尔德品种的当代有效种群规模分别为 59、98、102 和 113。通过对种群遗传结构的分析，我们将北方品种（里海和土库曼）和西方/西南品种（波斯阿拉伯和库尔德）分为两个反映其地理起源的系统发育支系。使用基于成对比较的多重选择信号统计的去相关组合，我们在六个成对比较中检测到了不同数量的显着 SNP，从 13 到 28 个（FDR < 0.05）。在推定选择下鉴定出的 SNP 与先前与形态、适应和适应性特征的已知 QTL 相关的基因一致。我们的结果表明，HMGA2和LLPH是小型里海马与其他研究的中等体型马之间身高变异的强候选基因。利用从 GWAS 目录中检索到的人类身高研究结果，我们建议选择 38 个新的假定候选基因。这些结果提供了所研究品种的选择特征的全基因组图谱，这代表了制定遗传保护和改进品种育种策略的宝贵信息。