Analysis of the Genetic Diversity and Population Structure of the Nenets Native Breed of Reindeer Based on Microsatellite Markers

Northern reindeer breeding is the basis of the cultural and economic complex of the indigenous peoples and ethnic groups of the north of Russia. The study of breeds and intrabreed types of domestic reindeer and their genetic structure to a large extent helps to solve the problem of supporting the traditional way of life of this part of the population of our country. To study the genetic differentiation and phylogeny of populations of the Nenets breed of reindeer (Rangifer tarandus L.), we used a test system based on multiplex PCR analysis of 16 highly polymorphic STR markers: Rt6, BMS1788, Rt30, Rt1, Rt9, FCB193, Rt7, BMS745, C143, Rt24, OheQ, C217, C32, NVHRT16, T40, and C276. Using the developed test system based on the Laboratory of Comparative Animal Genetics of the Institute of General Genetics, 228 animals from four samples of the same breed from different farms of the Russian Federation were examined. For 16 microsatellite loci, 132 alleles were identified, ranging from 2 alleles (locus C217) to 16 alleles (locus OheQ). The average number of alleles per locus for all samples was 8.25. No significant deviations from the Hardy–Weinberg equilibrium (p-value < 7.8 × 10–⁴ with Bonferroni correction) were observed for the “sample–locus” combinations. For four populations of the Nenets breed of reindeer, 85 alleles for microsatellite loci are common. In total, 16 unique alleles were found: KhMAO–Yugra, Beloyarsk district, village of Nunto (Nen.HMAO)—7; YaNAO, Salekhard and Priuralsky district (Nen.YamSHOS)—4; YaNAO, the upper reaches of the Hanmei River (Nen.YaNAO)—3; NAO, the western part of the Bolshezemelnaya Tundra (Nen.NAO)—2. The analysis of microsatellite variability revealed the levels of multilocus heterozygosity and allelic diversity, as well as the degree of inbreeding. According to the indicator of allelic diversity (Aᵣ), deer from the Yamal experimental station stand out with a value of 6.25, while in animals from the SPK ERV, the value was 5.85. In general, despite the presence of inbred animals in the samples, we can talk about a low level of inbreeding depression in the studied populations of Nenets reindeer.