Analysis of the Genetic Structures of 29 Horse Breeds of Russian Selection by STR Markers

Abstract—The current stage of genetic certification of horses of cultural and local breeds based on microsatellite analysis makes it possible to quite effectively carry out identification and genetic examination of the origin of breeding animals, as well as solve the problem of assessing and preserving genetic resources. With a reduction in the number of breeding stock to 200–300 mares observed in a number of breeds, the threat of a decrease in the genetic diversity of populations and the accumulation of genetic load increases, which necessitates the need to study and monitor the genetic structure of horse breeds. In this regard, our comparative genetic analysis of polymorphism of 17 microsatellite loci in 20 541 horses of 29 cultural and local breeds allows us to certify the basic part of the genetic resources of the horse breeding of the Russian Federation. including riding, trotter, draft, and local breeds. During the genetic population analysis of the studied breeds, basic parameters were assessed: the total number of allele variants (N_a), the effective number of alleles (A_e), the average number of alleles per locus (MNA), the level of observed (H_o) and expected heterozygosity (H_e), as well as the coefficient of intrapopulation inbreeding F_is. Phylogenetic relationships of breeds were assessed using the R and R Studio software packages. Among horse breeds of different specializations, the highest values of all indicators of genetic diversity (A_e, H_o, H_e, and N_a) were determined in aboriginal populations. In the allele pool of local horse breeds, there were rare alleles ASB2T, HMS7S, HMS6J, HMS6H, HMS2T, HMS1O, HTG7L, HTG6L, HTG6H, VHL20S, ASB17Z, ASB17X, ASB17U, LEX3S, LEX3R, and CA425E, which were absent in horses of stud breeds. Among the riding horse breeds created in Russia, the Budennovskaya, Donskaya, and Kabardian horse breeds stood out due to the presence of rare alleles. Alleles ASB2G, ASB2F, HMS2F, HTG7Q, and ASB23O were found in trotter horses, which were not identified in the genetic structure of other breeds. The phylogenetic analysis showed the division of horse breeds into two clear subclusters, the first of which included only stud breeds. The second cluster united all the native breeds, as well as the Orlov Trotter and a group of draft breeds, which were used for many years as improvers of the local horse population. The analysis of the genetic structure of domestic horse breeds revealed a fairly high reserve of diversity even in small populations, which is an indispensable condition for successful selection in horse breeding.