Study of the genetic diversity of domestic and wild reindeer (Rangifer tarandus L., 1758) populations using nuclear and mitochondrial genomic markers

The reindeer ( Rangifer tarandus L., 1758) is an important biological species that plays a key role in the supporting livelihood of the peoples of the Far North of Russia. Due to climate change and anthropological impacts, this species may be endangered, therefore, in the modern world, the study and conservation of the genetic diversity of the reindeer is relevant. In this work, for the first time, the genetic variability responsible for the differentiation of domestic and wild forms of the reindeer was studied using an integrated molecular genetic approach, which consisted in the analysis of nuclear and mitochondrial genomes. Our aim was to evaluate the genetic diversity, genetic structure, and phylogenetic relationships of domestic and wild populations of reindeer bred in the Russian Federation based on complete mitochondrial DNA CytB gene sequences and microsatellite loci polymorphism. The research was carried out in 2022. Cuts from reindeer antlers served as material. The sample included wild reindeer from the tundra population (WLD), as well as domestic reindeer from Nenets (NEN), Chukchi (CHU), Even (EVN) and Evenk breeds comprising the Krasnoyarsk (EVK_KRA) and Yakut (EVK_YAK) populations. For the study of mtDNA, 123 unrelated individuals were selected. Microsatellite analysis was performed in 213 individuals of domestic breeds and 119 representatives of the wild population. The complete sequences of the CytB gene were determined using next generation sequencing (NGS) on a miSeq sequencer (Illumina, Inc., USA). Polymorphism of nine STR loci (NVHRT21, NVHRT24, NVHRT76, RT1, RT6, RT7, RT9, RT27, RT30) was investigated by fragment analysis using an ABI3130xl genetic analyzer (Applied Biosystems, USA). To assess the genetic diversity of each group of reindeer, indicators of mitochondrial variability (number of polymorphic sites S, average number of nucleotide differences K, number of haplotypes H, haplotype diversity HD, nucleotide diversity π) and microsatellite variability (rarefied allelic richness AR, observed heterozygosity HO, unbiased expected heterozygosity uHE, unbiased inbreeding coefficient FIS) were calculated. The degree of genetic differentiation between groups was assessed based on pairwise FST and JostD values. Statistical processing of the raw data was performed using the programs MEGA 7.0.26, PopART 1.7, PartitionFinder 2, Arlequin 3.5.2.2, MrBayes 3.2.7, FigTree 1.4.3, DnaSP 6.12.01, SplitsTree 4.14.5, STRUCTURE 2.3.4 and R packages diveRsity, pophelper, adegenet and ggplot2. Analysis of mtDNA CytB gene sequences showed that all studied populations were characterized by high haplotype diversity, HD = 0.519 (CHU)-0.997 (WLD), and nucleotide diversity, p = 0.00238 (CHU)-0.00626 (WLD). Based on the mtDNA analysis no clear genetic structure was revealed in the studied reindeer populations. Analysis of microsatellite variability showed that values of allelic richness ranged from 6.188 in CHU to 8.76 in WLD. In all six populations, observed heterozygosity ranged from 0.566 (CHU) to 0.687 (EVK_YAK) and 0.693 (WLD). All studied reindeer groups were characterized by a deficit of heterozygotes, as indicated by positive values of the fixation index, FIS = 0.11 (EVK_YAK)-0.262 (EVK_KRA). Network analysis showed the differentiation of the Chukotka breed from the rest groups, as evidenced by the highest FST and JostD values, which varied from 0.203 and 0.488 for EVK_KRA to 0.212 and 0.564 for EVN, respectively. Based on both nuclear and mitochondrial markers, wild reindeer populations showed higher genetic diversity compared to domestic populations. It may be assumed that selection work with domestic reindeer breeds led to the creation of unique populations that differ from the original wild relatives. However, both domestic and wild reindeer populations, which were studied in this work, were characterized by high genetic