Genetic diversity and population structure of native and translocated Bashkir horse (Equus ferus caballus) populations based on microsatellite markers

Background and Aim: The Bashkir horse (Equus ferus caballus) is an indigenous Russian breed with a unique adaptive gene pool that is important for biodiversity conservation and sustainable breeding. However, information on the genetic differentiation between native and recently translocated populations remains limited. This study evaluated the genetic diversity, population structure, and within-breed differentiation of native Bashkir horses from the Republic of Bashkortostan and a translocated population established in the Tver Region using microsatellite markers. Materials and Methods: A total of 240 Bashkir horses were included, comprising a native population from the Republic of Bashkortostan (n = 190) and a translocated population from the Tver Region (n = 50). Genomic DNA extracted from hair follicles was genotyped at 17 International Society for Animal Genetics (ISAG)-recommended microsatellite loci using the COrDIS Horse kit. Genetic diversity indices, including the number of alleles, effective number of alleles, Shannon index, observed and expected heterozygosity, polymorphic information content (PIC), and Wright's fixation indices, were calculated. Population differentiation was evaluated using principal coordinates analysis (PCoA), pairwise fixation index among subpopulations (FST), permutational multivariate analysis of variance (PERMANOVA), and Bayesian clustering with STRUCTURE and the Evanno method. Results: Analysis of the 17 microsatellite loci identified 160 alleles in the native population and 137 alleles in the translocated population, with mean allele numbers of 9.41 and 8.06 per locus, respectively. The loci ASB17, ASB2, and HTG10 contributed most to genetic diversity in both populations. Mean effective allele numbers were 4.783 and 4.713, whereas the Shannon index averaged 1.741 and 1.676 for the native and translocated populations, respectively. High PIC values confirmed the excellent discriminatory power of the marker panel. Low mean inbreeding coefficient within subpopulations (0.012) and overall inbreeding coefficient (0.022) values indicated minimal inbreeding. PERMANOVA detected statistically significant but extremely weak population differentiation (F = 3.28, R² = 0.0136, p = 0,001, whereas bootstrapped FST (0.0072 ± 0.0012; 95% confidence interval: 0.0045–0.0093) demonstrated very low genetic divergence. Bayesian clustering identified K = 3 as the optimal model, revealing subdivision within the native Bashkir population while preserving the overall genetic integrity of the breed. Conclusion: Native and translocated Bashkir horse populations have retained high genetic diversity and exhibit only minimal genetic differentiation despite approximately two decades of geographic separation. The combined use of microsatellite markers with complementary population genetic analyses provides robust evidence supporting the conservation of the Bashkir horse gene pool while identifying subtle within-breed substructure. These findings provide a scientific foundation for genetic monitoring, conservation planning, pedigree management, and sustainable breeding programs for this valuable indigenous horse breed.