Signatures of selection in four indigenous horse breeds of Iran

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 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 a
de-correlated composite of multiple selection signals
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
QTL 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 provide a genome-wide map of selection signatures in the studied
breeds, which represent valuable information for formulating genetic
conservation and improved breeding strategies for the breeds.