The study of horse genetic diversity is imperative for informing conservation strategies, safeguarding ancestral lineages, and enhancing breed adaptability to environmental and disease pressures. This study employed 13 microsatellite markers with fluorescent-labeled capillary electrophoresis to analyze the genetic diversity of the Kyrgyz horse (n = 30) and Barkol horse (n = 30) for the first time, comparing them with three other indigenous horse breeds (n = 30 per breed) from Xinjiang, China. A total of 208 alleles were detected. The Polymorphic Information Content (PIC) results from GenAlEx 6.5115 show that all loci, except for the HTG06 locus in the Yanqi horse races, were highly polymorphic (PIC > 0.5), indicating a high level of genetic diversity across the five races. Among the five races, the Kyrgyz horse exhibited the lowest mean values for the effective number of alleles (Ne), observed heterozygosity (Ho), and expected heterozygosity (He), which were 6.025, 0.737, and 0.810, respectively. In contrast, the Barkol horse showed the highest mean number of alleles (Na), Ne, and He values, at 11.308, 6.330, and 0.816, respectively. Principal Coordinate Analysis (PCoA), performed using GenAlEx 6.5115, revealed the smallest genetic distance between the Kyrgyz and Yanqi horse breeds. Combined with phylogenetic tree and clustering analysis results, this supports the hypothesis that the two breeds share a common origin. This study offers valuable scientific insights for conserving and utilizing the genetic resources of indigenous Xinjiang horse breeds, specifically the Kyrgyz and Barkol horses.
Hou et al. (Sun,) studied this question.