Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Abstract 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 principal aims of this study were to evaluate genetic diversity and genome-wide 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 genome-wide genotyping data. The contemporary effective population sizes were 59, 98, 102 and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish, respectively. Analysis of population genetic structure classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using de-correlated composite of multiple selection signals (DCMS) statistics based on six pairwise comparisons, we detected different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05), respectively. 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 with a small size and the other studied breeds with a medium size. Using results of studies for human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results suggest that the identified sweeps might have been enriched as an adaptation to environmental conditions or a response to human-mediated artificial selection.