Genome-Wide SNP Analysis Reveals the Genetic Diversity and Population Structure of the Domestic Reindeer Population (<i>Rangifer tarandus</i>) Inhabiting the Indigenous Tofalar Lands of Southern Siberia

Operating under the assumption that decline in population size increases the threat of loss of genetic diversity, herein, our first aim was to monitor and document the genetic diversity and population structure of the endemic Tuva–Tofalar reindeer, the number of which has seen a dramatic decrease. Second, we were interested in understanding of Tuva reindeer genetic relationship with four officially recognized reindeer breeds, whose wild populations inhabit the Far North of Russia, as well as with the domestic reindeer making up the Mongolian population. Our results, based on the genome-wide SNP genotypes generated by the BovineHD BeadChip, revealed a low level of genetic variability of Tuva population in terms of the values of both allelic and genetic diversity. The ADMIXTURE analysis, the PCA plot, and the Neighbor Net network results, showed that Tuva population shared genetic background with reindeer inhabiting Mongolia, an implication of their common origin. Moreover, all statistic approaches used in our study showed a distinctive shared genetic structure revealed in independent clusters found in the composition of: an admixed cluster of Tuvan and Mongolian populations, a cluster of domestic reindeer breeds, and a cluster of the wild populations—all of which indirectly points to the possibility of the independent origins (with regard to the domestication) of the reindeer groups studied herein. We believe that our findings will contribute to the formation of a rational basis for solving problems related to the conservation of domestic Tuva-Tofalar reindeer in order to increase the number of this substantial reindeer population which will contribute to the sustainable functioning of ecosystems and the lives and culture of indigenous peoples inhabiting the southern sections of Eastern Siberia

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis.

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses-calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals-were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4-25.1 Mbp and on BTA 16 at 42.5-43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74-5.36 Mbp, BTA 15 at 17.80-18.77 Mbp, and BTA 17 at 45.59-45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40-81.69 Mbp, BTA 15 at 16.04-16.62 Mbp, and BTA 18 at 0.19-1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds

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

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

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds

Background: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. Conclusions: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes