Development and validation of a low density SNP panel for assessment of genetic diversity of the reindeer (Rangifer tarandus) populations

Reindeer ( Rangifer tarandus ) is a valuable member of the Arctic ecosystems and the main livestock species of the Russian North, which require the analysis of the genetic structure and the possibility of addressing the differences between wild and domestic forms, breeds and populations using modern molecular genetic approaches. The use of DNA chips based on parallel genotyping of hundreds of thousands of SNP markers is an effective approach to study the reindeer genome, but at the same time due to a high price, it is not beneficial for wide practical application. In this regard, the aim of our work is to select the optimal number of SNP markers that allow conducting population and genetic studies of reindeer without loss of bio-informatics content. The sample collection included wild deer (WLD, n = 83) inhabiting the Taimyr Peninsula and the Republic of Sakha (Yakutia), and domestic deer of the Nenets breed from the Nenets Autonomous Okrug (NEN, n = 100) and the Murmansk Region (MUR, n = 19), as well as from Even and Evenki breeds from the Republic of Sakha (Yakutia) (YAK, n = 19). All deer were genotyped using a high-density DNA chip BovineHD BeadChip (777,962 SNPs). After quality control and filtering, 4456 polymorphic SNP markers remained in the analysis. In the TRES program, using the Delta method, 368 of the most informative SNP markers were selected. Data processing was performed in the Admixture 1.3, PLINK 1.9 programs and R packages (ggplot2, adegenet 1.3-1, pophelper, diveRsity). It was shown that 70 % from 368 selected SNPs had a high minor allele frequency (MAF ≥ 0.3), while about 50 % from set including 4456 markers had MAF ≤ 0.1. Comparing the results of principal component analysis (PCA), discriminant principal component analysis (DAPC), and cluster analysis, no loss of information value was found for 368 SNPs compared to using the set of 4456 markers. Comparing pairwise FST values between the studied groups of reindeer, the similarity of the interpopulation linkages was demonstrated, based on 4456 and 368 SNP markers, respectively. Thus, the selected panel of SNP markers is an informative, universal for both wild and domestic deer and a cheap approach for creating a custom DNA chip for reindeer.