Assessment of Genetic Diversity and Structure of Russian and Mongolian Autochthonous Horse Breeds Using Nuclear and Mitochondrial DNA Markers

In the present study, on the basis of the analysis of 17 microsatellite loci, 866 horses from nine breeds, including Altai, Tuvan, Kushum, Pechora, Mezen, Transbaikal, Buryat, Russian Riding, and Mongolian breeds, were examined. The studied breeds were characterized by the high level of observed heterozygosity (from 0.699 to 0.798), which did not cause concern. A total of 183 alleles were identified, including 15 private ones. In Mongolian horses of the Tes breed, rare allele D of the AHT4 locus and a previously undescribed allele were identified. Phylogenetic relationships, structure, and interaction of the gene pools of Mongolian and Russian horses were demonstrated. The polymorphism analysis of the mtDNA control region (D-loop) in 142 horses provided identification of 16 haplotypes, of which four, found in the Mongolian, Buryat, Transbaikal, and Tuvan breeds, were previously found only in ancient horse samples from Europe and Asia. Haplotypes X2 and D3 turned out to be the most common among the studied breeds. The hypothesis that the majority of mtDNA haplotypes were not associated with the particular breed or geographic region was confirmed. Horse populations were different only in the haplotype sets and frequencies. High polymorphism of horse mtDNA is thought to be associated with multiple domestication events, as well as active horse movements across the world and their breeding history.