Evaluating of population diversity and detecting of genomic footprints of selection in four main Iranian horse breeds

Natural and artificial selections change the allele frequencies among populations and consequently leave detectable patterns on the genome during domestication. A little information about the differences of genetic structures of Iranian native breeds that result in these selective pressures are available. Therefore, in this study, we examined genetic diversity using four native horse breeds including Turkmen (29 samples), Caspian (21 samples), Kurdish (67 samples) and Persian Arabian (52 samples).

For this purpose, three methods including Principal Component Analysis (PCA), neighbor joining (NJ) and admixture were investigated. In addition, with the integrating of three different selection of signature methods, including TajimaD, nucleotide divergency (pi) and integrated haplotype homozygosity score could identify the selection traces in these breeds. To integrate the different results of these three methods, De-correlated composite of multiple signals framework was used.

All the methods used to examine the genetic structure well separated these four breeds and showed a pattern related to geographical origin for their genetic diversity. By combining different methods of identifying the selection signatures, many genes affected by the selection pressure were identified in all four breeds. These genes were associated with specific GO terms and QTL, in which 16 shared candidate genes among all four breeds were identified as suggested candidates for selection. Additionally, 11 different QTL types was identified in all four studied breeds, which was divided into the category of traits related to adaptation, fitness through genetic disorders or morphological and behavioral traits.

Overall, the results of this study can help better understand the process of natural and artificial selections in Iranian horses. In addition, this research has helped to improve our understanding about the genetic differences between studied Iranian horse breeds, which can help in finding the best solution to preserve and improve genetic diversity.