Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

Abstract

Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.

Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

“…The biomaterial was picked during the corral work on the herd throughout 2018-2019. Additionally, our data set was combined with SNP genotypes of reindeer that were obtained during our previous study [4], namely, the Nenets breed from the Nenets Autonomous district (NEN_NAO, n = 33) and the Murmansk region (NEN_MUR, n = 20) and the Evenk (EVK_YAK n = 12), the Even (EVN, n = 7), and the Chukotka-Khargin breeds (CHUKH, n = 2) from the Republic of Sakha (Yakutia). All studied reindeer groups are displayed in Figure 1.…”

“…The mean number of alleles (A R ), as well as the observed (H O ) and unbiased expected U H E heterozygosity, which are commonly measured parameters to check within-breed diversity [47], were calculated for the studied reindeer set and are presented in Table 1. 4 A R , allelic richness. 5 H O , observed heterozygosity.…”

“…Despite the abundance of scientific work on the genetic biodiversity of the Cervidae family members through commercial SNP genotyping arrays [4,[29][30][31][32]-including our previous study, which attempted to determine the differences among the domestic reindeer groups within the Nenets Autonomous district, the Murmansk region, and Yakutia, as well as among wild tundra and taiga forms inhabiting Yakutia and western Taymyr-information on the genetic structure and diversity of all domestic reindeer breeds inhabiting the Russian Far North is still lacking.…”

DEVELOPMENT AND VALIDATION OF A LOW DENSITY SNP PANEL FOR ASSESSMENT OF GENETIC DIVERSITY OF THE REINDEER (Rangifer tarandus) POPULATIONS

“…(6), геном карибу включает 33177 протеин-кодирующих генов, в том числе 3820 (93,1 %) полностью реконструированных. Тем не менее, поскольку дикая и домашняя формы вида Rangifer tarandus четко дифференцируются по SNP-маркерам (8), описанная сборка генома тоже может быть не актуальной для домашних северных оленей. И, наконец, группа скандинавских исследователей (7) провела глубокое секвенирование генома домашнего оленя с использованием приборов HiSeq2500 и HiSeq 4000 («Illumina, Inc.», США).…”

“…Однако различия в паттерне распределения групп животных при К = 3 были незначительными. Эффективность применения на оленях ДНК-чипов, разработанных для крупного рогатого скота (КРС), была продемонстрирована в зарубежных (26,27) и отечественных исследованиях (8,28). Тем не менее среди всех прогенотипированных SNP только около 5 % полиморфны и непосредственно используются в анализе: 1068 для чернохвостого и белохвостого оленей (26), 1532 для представителей рода Cervus (27) и 512 для якутского домашнего оленя (28) при использовании Bovine SNP50 BeadChip; 8357 и 8145 -соответственно для домашних и диких северных оленей из 777962 SNPs на чипе BovineHD BeadChip (8).…”