TITLE: Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1958): a novel approach using BovineHD BeadChip
AUTHORS: Veronika Ruslanovna Kharzinova, Arsen Vladimirovich Dotsev, Tatiana Evgenievna Deniskova, Anastasiya Dmitrievna Solovieva, Valeriy Ivanovich Fedorov, Kasim Anverovich Layshev, Tatiana Michailovna Romanenko, Innokentiy Michailovich Okhlopkov, Klaus Wimmers, Henry Reyer, Gottfried Brem, Natalia Anatolievna Zinovieva

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Reindeer (</span><span style = "font-style:italic;">Rangifer tarandus</span><span> 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. </span></div></div>

[STEPS]
?. [Sample collection and preparation of genomic DNA]
Genomic DNA was extracted from muscle and tissue samples using Nexttec columns (Nexttec Biotechnology GmbH, Germany) following the manufacturer's instructions. The quality of the extracted DNA was examined by electrophoresis using 1 % agarose gels viewed under ultraviolet light. The concentration of DNA solutions was quantified using a Qubit 3.0 fluorimeter (Thermo Fisher Scientific (formerly Life Technologies), Wilmington, DE, USA). The OD260/OD280 ratio of DNA solutions was determined by NanoDrop-2000 (Thermo Fisher Scientific, Wilmington, DE, USA).
?. [SNP genotyping and quality control]
All reindeer individuals were genotyped with Illumina BovineHD Genotyping BeadChip, which contains 777,962 SNPs. Genotypes were called and processed using Genome Studio (Illumina, Inc. San Diego. USA). Samples with a call rate below 90 % were excluded from the data set. Additional criteria to filter SNPs were applied: SNPs with more than 10 % missing genotypes across all the samples; SNPs with minor allele frequency less than 5 % (--maf 0.05); SNPs located on sex chromosomes of the UMD 3.1 assembly;SNPs with unknown map positions; SNPs with the value of linkage disequilibrium (LD) between a pair of single nucleotide polymorphisms equal to r2>0.05 (we used a sliding window of 50 SNPs, sliding along in 5 SNP increments);SNPs not corresponding to the χ2 criterion for Hardy-Weinberg equilibrium in a population (p≤1×10-6). Additionally, to assess the quality of SNP genotyping, we used GC Score (quality of reading SNP) and GT Score (level of clustering SNP) of at least 0.5 (50 %). These quality control steps were carried out using PLINK v1.07 [37]. The final data set comprised 8357 SNPs for 135 reindeer individuals and 8145 SNPs for 61 wild reindeer from the BovineHD BeadChip (Illumina, Inc. San Diego. USA).
?. [Genetic diversity and differentiation analysis]
To assess genetic diversity of the studied reindeer populations, the values of observed (Ho) and unbiased expected (He) heterozygosity, inbreeding coefficient (FIS), and rarified allelic richness (Ar) were calculated in R package diveRsity. Pairwise fixation index (FST) values were estimated through the R-package StAMMP The neighbor-joining algorithm was applied to generate the Neighbor-Net Tree from a distance matrix of pairwise FST values and implemented in Splitstree 4.14.5.Multidimensional scaling (MDS), based on pairwise identity-by-state distance matrix, was carried out with PLINK 1.07 (--cluster, --mds-plot 4) and visualized in R package ggplot2.
?. [Genetic structure analysis ]
The genetic structure analysis was performed with the software package STRUCTURE 2.3.4
?. [TreeMix]
For inferring the patterns of population splits and gene flow between reindeer populations, we used the software TreeMix1.13 Standard errors (-se) and p-values were calculated with jackknife blocks of 10 SNPs (-k 10). Since significant effects were revealed when two migration events were allowed (pThe tree graph and residuals were visualized using R