Genetic Diversity of Kazakhstani Equus caballus (Linnaeus, 1758) Horse Breeds Inferred from Microsatellite Markers

SIMPLE SUMMARY: Traditional horse breeding has long developed several kinds and lineages of horse breeds in Kazakhstan. Among them, Kushum and Mugalzhar are the breeds most prolific and resistant to harsh climatic conditions. Microsatellite analysis is employed to examine present genetic variability and population structure. The subpopulation structure shows three regional groups indicating (I) purebred Kushum populations from western Kazakhstan, (II) the Kozhamberdy type of Mugalzhar interbreed in populations from central Kazakhstan, and (III) admixed Kushum–Mugalzhar populations from western and southwestern Kazakhstan. The majority of microsatellite markers utilized are informative, with seven of them being extremely variable. A high level of genetic admixture among Kazakhstani Equus caballus breeds is found, as well as a shallow level of genetic differentiation between the examined populations. ABSTRACT: Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are 136 alleles, with the mean number of alleles per locus ranging from 9 to 19. VHL20 is the most variable locus across groups, while loci HTG4, AHT4, AHT5, HTG7, and HMS3 are variable in most populations. The locus AHT5 in the Emba population shows the highest frequency of rare alleles, while the lowest frequency, 0.005, is observed in the Kulandy population. All loci were highly informative for the Kazakhstani populations of E. caballus, with PIC values higher than 0.5. Pairwise variations in Wright’s F(ST) distances show that the examined varieties have little genetic differentiation (0.05%), indicating a high degree of admixture and a continuing lineage sorting process. Phylogenetic and population structure analyses reveal three major clusters of Kazakh horses, representing (I) the Uralsk population of the Kushum breed and the monophyly of two groups: (II) the Kozhamberdy population of the Mugalzhar breed, and (III) the Mugalzhar–Kushum breed populations. Kazakhstani horse populations, while being regionally isolated, were recently in contact with each other.