The research was carried out for the purpose of a comparative assessment of the allele pool of the Novoaltayskaya horse breed and the breeds that participated in its creation. The experimental sample included 5736 horses, including: Novoaltayskaya breed – 363, Altai – 39, Lithuanian Heavy Draft – 159, Russian Heavy Draft – 617, Soviet d Heavy Draft – 288, Orlov trotter – 4,177, Budenny – 93. Population genetic analysis was performed using generally accepted methods. The following indicators were determined: the total number of alleles at 17 loci, the average number of alleles per locus, the level of polymorphism, observed and expected heterozygosity, coefficients of intrapopulation inbreeding, genetic similarity and genetic distances. It was established that horses of the Novo-Altai breed had the highest level of genetic diversity (154 alleles) and polymorphism (Ae = 4,909). Analysis of genetic differentiation showed the absence of intrapopulation inbreeding in the groups of Altai, Lithuanian Heavy Draft and Budenny breeds. Groups of horses of the Novoaltayskaya, Orlov trotter, Russian Heavy Draft and Soviet Heavy Draft breeds were distinguished by a slight deficiency of heterozygotes. It has been established that horses of the Novoaltayskaya and Heavy Draft breeds are characterized by a high frequency of occurrence of the HTG6 O allele, and the Altai breed is characterized by a high frequency of occurrence of the HTG4 M allele. A number of loci of alleles identical in spectrum to those of the Altai, Russian Heavy Draft and Soviet Heavy Draft breeds were identified in the Novoaltayskaya horse. Cluster analysis demonstrated a high level of genetic similarity of horses of the Novoaltayskaya breed with the Russian Heavy Draft (0,903) and Altai (0,899) breeds. As part of the study, using molecular genetic markers, new data was obtained on horses of seven breeds, with the help of which it is possible to improve breeding programs in horse breeding, allowing to control the biodiversity and genetic similarity of populations, preserving the originality and heterogeneity of the allele pool of horses of different breeds.
