Study of the allele pool and the degree of genetic introgression of semi-domesticated and wild populations of reindeer (Rangifer tarandus L., 1758) using microsatellites

The coexistance of domestic and wild reindeer populations ( Rangifer tarandus L., 1758) - is an important feature of this species. Both forms inhabit in conditions, which remain substantially unchanged for a long time. Due to gene flow between domestic and wild populations we observe a relatively high amount of admixture in the gene pool. Biodiversity characteristics of two most numerous reindeer populations (semi-domesticated Nenets breed and wild population of reindeer inhabiting territories of Nenets Autonomous Okrug (NAO) and Taimyr Autonomous Okrug (TAO) based on the analysis of microsatellites are given and the degree of introgression in these populations is determined. Samples of Nenets breed of domestic rein deer were collected in several farms in NAO and TAO ( n = 115, four subpopulations). Samples of wild Taimyr population were collected in the course of field research in different geographic regions of TAO ( n = 63, five subpopulations). Genomic DNA was isolated using Nexttec columns («Nexttec Biotechnologie GmbH», Germany). Polymorphism of 9 STR-loci (NVHRT21, NVHRT24, NVHRT76, RT1, RT6, RT7, RT9, RT27, RT30) was determined according to the previously developed technique for DNA analyzer ABI3130xl («Applied Biosystems», US). To estimate the allele pool of each population average number of alleles (Na), the effective number of alleles (Ne) based on the locus, rarified allelic richness (Ar), private allelic richness (PrAr), observed (Ho) and expected (He) heterozygosity and inbreeding coefficient (FIS) were calculated. The degree of genetic differentiation of populations was assessed using pairwise FST values and Nei's genetic distances. We calculated the degree of migration of genes between populations based on microsatellite allele frequencies. Distribution of genetic variation between and within populations was studied by analysis of molecular variance (AMOVA). It was found that the wild population of reindeer is characterized by a higher level of genetic diversity: the average number of alleles per locus was 10.00±0.78 vs. 8.44±0.80, the observed heterozygosity - 0.633±0.060 vs. 0.589±0.049. STRUCTURE analysis revealed the formation of two independent clusters corresponding to the wild and domestic populations with high values of the membership coefficient in own clusters: QWLD = 0.940±0.013 and QDOM = 0.938±0.010. However, a few individuals (4.4-4.8 %) carrying a mixed genetic origin were found. The degree of introgression between the populations was around 6 %. Cluster analysis of genetic structure performed separately for wild and domestic populations at the level of subpopulations for the number of cluster k ranged from 2 to 5 did not reveal a clear clustering between subpopulation. It's confirmed the homogeneity of genetic structure within populations. Examination of overall genetic diversity with AMOVA procedure indicated that most of the variation was observed within populations (95.4 %, p < 0.001). Principal component analysis (PCA) revealed clear differentiation of the studied domestic and wild populations along the axis 1 with their slight overlapping; herewith the principal component 1 was responsible for 5.15 % of variability. Evaluation of differentiation degree between subpopulations of rein deer, performed by calculation of the pairwise values of FST and Nei's genetic distances (DN) showed relatively higher degree of genetic differentiation between subpopulations within wild population comparing to domestic population (maximal FST and DN values were 0.046 vs 0.023 and 0.353 vs 0.151, respectively). The obtained results of genetic diversity and population structure of reindeer will be used to develop the breeding program with Nenets breed of domestic rein deer and to organize the measures for protection and sustainable use of wild reindeer bioresources.