Genetic diversity of the Nenets reindeer breed based on microsatellite markers

Abstract

Research objective To conduct a comparative analysis of the genetic diversity of the Nenets reindeer breed (Rangifer tarandus tarandus) in Russia using a new microsatellite panel. Material and methods used In total, 228 individuals from four populations of the Nenets (47 samples), Yamalo-Nenets (151), and Khant-Mansi (30) regions of the Russian Federation were studied. The new panel consists of 16 microsatellite loci: 10 dinucleotide loci - Rt6, BMS1788, Rt30, Rt1, Rt9, Rt7, Rt24, FCB193, BMS745, NVHRT16 and 6 tetranucleotide STR markers - OheQ, C217, C32, T40, C276, C143. GeneMapper ID-X 1.4 software (Applied Biosystems) used to analyze the obtained data. The statistical analysis was performed in the R package, 3.6.1 version (R Core Team, 2019). Research results For 16 microsatellite loci 132 alleles were found, from 2 alleles (locus C217) to 16 alleles (locus OheQ). The average number of alleles per locus for all samples was 8.25. The smallest number of alleles per sample was observed in the samples of reindeer from the Nen.NAO and Nen.KhMAO, 103 alleles, and the largest from the Nen.YaNAO, 119. Allelic richness (Ar) ranged from 5.85 to 6.25. For each sample, the distribution of individual inbreeding coefficients f was constructed. We can talk about the presence of inbreeding in all samples, since the high values of f indicate a decrease in the heterozygosity of individual genomes in the samples due to inbreeding. The Polymorphism Information Content (PIC) values were calculated for each pair of “locus-sample” which were estimated based on the number and frequency of alleles at the locus. The average PIC value turned out not to be very high: 0.613 ± 0.049. The highest levels of polymorphism were obtained for 3 loci: Rt9 (PIC = 0.906), OheQ (PIC = 0.913), and Rt1 (PIC = 0.920). It is proposed to investigate the polymorphism of microsatellite loci of all four Russian reindeer breeds. The following will be determined for each breed: genetic structure, its effective number, inbreeding coefficient; the degree of differentiation between the breeds has been established. As a result of a detailed analysis we will build a model for the demographic history of the reindeer.