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How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667–248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Domestic reindeer in Russia are a valuable resource of vital importance to the physical and cultural survival of the Northern indigenous minority. During the last decades, the mitochondrial (mt) genetic markers have been widely used as a molecular tool to investigate genetic structure and diversity of livestock species. Here we aimed at the assessing the mtDNA diversity of the domestic reindeer inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east. A complete cytochrome b (cytb) sequences (1,140 bp) from representatives of six populations, including Nenets (NEN, n = 16), Evenk (EVK, n = 12), Even (EVN, n = 6), Chukotka (CHU, n = 6), Chukotka-Khargin (CHUKH, n = 6) and Tuva (TUVA, n = 6) were obtained. Sequences’ alignment was conducted using MUSCLE algorithm in R package msa. In total, 34 haplotypes were identified. Median-joining network, constructed in PopART 1.7, revealed three major groups of haplotypes: the first one joined the samples of all the populations, the second one included NEN, EVN and CHUKH, and the third group was presented by the one sample of CHU. AMOVA, calculated in Arlequin 3.5.2.2, showed that only 9.58% of molecular variance could be explained by the differences between populations and 90.42% - within populations. Genetic diversity parameters calculated in DnaSP 6.12.03, demonstrated that average number of nucleotide differences (K) was highest in CHUKH (28.333) and EVN (27.409) and lowest in TUVA (4.533) and EVK (5.400). Nucleotide diversity (Pi) was 0.01238±0.00559, 0.00474±0.00091, 0.02404±0.00453, 0.01281±0.00464, 0.02485±0.00744, and 0.00398±0.00110 for NEN, EVK, EVN, CHU, CHUKH and TUVA, respectively. Our study demonstrated the lack of clear genetic structure of the studied reindeer populations in relation to cytb sequence. The level of genetic diversity was associated with census size and was lowest in the smallest Tuva population. This study was supported by RSF-21-16-00071 and Russian Ministry of Science and Higher Education-0445-2019-0024.

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

Native coarse wool fat-tailed sheep breeds are the main producers of mutton in mountainous, steppe and semi-desert regions of Southern Russia. An assessment of homozygosity is required to prevent loss of genetic diversity and inbreeding depression onset. The aim of our work is estimation of genomic inbreeding and distribution of the runs of homozygosity (ROH) segments in Russian sheep breeds. Sample collection included Andean (n = 20), Buryat (n = 18), Buubei (n = 11), Edilbai (n = 20), Karachaev (n = 20), Kalmyk (n = 22), Karakul (n = 20), and Lezgin (n = 15) breeds. All sheep were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, USA). Quality control and raw data processing were performed in PLINK 1.9. A consecutive runs method implemented in the R package “detectRUNS” was used for estimation of ROH segments. We detected the ROH in all breeds with mean length ranging from 0.35 in Lezgin to 11.18 Mb in Karachaev. Andean had the greatest number of the ROH segments (total of 8496), while 3094 ROH segments were found in Buubei. Short ROH segments (< 2 Mb) were predominant in all breeds and varied from 96.83% in Andean to 99.87% in Buubei. The frequencies of the ROH segments of 8–16 Mb ranged from 0.03% in Karakul to 0.18% in Andean. ROH segments of 8–16 Mb did not occur in the Buubei and Lezgin breeds. The ROH segments were found on all autosomes. The largest genome coverage in the ROH was identified on OAR1, OAR 12 and OAR 20 and the lowest was accounted for OAR 17, OAR 18 and OAR 19. The values FROH ranged from 0.042 in Buubei to 0.084 in Andean. Except of Andean, no traces of long-term inbreeding were detected in local breeds. The obtained data are relevant for future sustainable management of native fat-tailed sheep breeds in Russia. The study was funded by RSF No. 19-16-00070.

Specific environmental conditions and local livestock management systems resulted in creation of valuable native breeds. The timely monitoring of genetic diversity within native breeds based on using high-throughput DNA arrays will prevent their irreparable loss. In this regard, we aimed to assess genome-wide diversity and to study demographic history of Russian native goat breeds (Altai Mountain, Orenburg, Soviet Mohair, Dagestan Milk, Dagestan Local, Dagestan Fluff and Karachaev) based on SNP-data. A total of 200 goats were genotyped using Goat 50K SNP BeadChip (Illumina, USA). Quality control and SNP-filtering were performed in PLINKv1.9. R package ‘diveRsity’ was used to calculate observed heterozygosity (Ho), expected heterozygosity (He), and inbreeding coefficient (Fis). Effective population sizes (Ne) were estimated in SneP software. Observed heterozygosity was high and exceeded 0.402 in five out of seven breeds. Orenburg, Soviet Mohair, Dagestan Milk, and Karachaev breeds showed slight excess of heterozygotes varied from 0.6% (Fis= -0.015) in Orenburg to 1.7% (Fis= -0.04) in Karachaev breed. The traces of insignificant inbreeding were found in Dagestan Local (Fis=0.005) and Dagestan Fluff (Fis= 0.01) breeds. The recent effective population sizes estimated for four generations ago varied from 140 in Karachaev to 472 in Orenburg breed. Analysis of historical trends in effective population sizes estimated for sixty generations ago revealed obvious decrease ranging from 10.25% in Dagestan Local to 34.65% in Orenburg breed. However, recent effective sizes in Russian native goats are higher than critical threshold (Ne= 100) that is essential to breed maintenance in the future. Our research findings provide an evidence that Russian native goat breeds are not in endangered status, but development of the effective utilization programs is highly recommended. The genotyping of 96 goats was funded by RSF No. 19-76-20006. The reported study was funded by RFBR according to the research project № 18-316-20006.

Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A.

Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.

Due to mountain relief, sheep breeding has always been a traditional husbandry branch in the Kyrgyz Republic. The geographical location of this country in Central Asia, where the Silk Road crossed Eurasia, resulted in genetic interchange between the Kyrgyz native breeds and sheep flocks, which had been accompanying the human migrations. In this regard, genetic studies of the Kyrgyz local breeds could provide valuable information on ancestry and relations of Eurasian sheep breeds. Wide implementation of the multiple SNPs array created the possibility of assessments at the genome level. Thus, the aim of the research was to provide a pattern of whole-genome diversity and population structure of Kyrgyz local sheep breeds using OvineSNP50K BeadChip. We genotyped Kyrgyz mountain merino (KYMM, n=6), Kyrgyz local sheep (KYLO, n=8), Kyrgyz coarsewooled (KYCW, n=6), Alai coarse-wool sheep (ALAI, n=8), Gissar (GISR, n=6), Tien-Shan (TNSH, n=11). The level of genetic diversity of Kyrgyz breeds was quite high. Observed heterozygosity varied from 0.363 in ALAI to 0.388 in TNSH, while allelic richness ranged from 1.884 in KYCW to 1.927 in KYLO. Analyzing the MDS plot, we found that ALAI, GISR and KYCW clustered together and were clearly separated from TNSH and KYMM by the PC1. Such a differentiation was in accordance with the Neighbor Net graph and was confirmed by the pairwise Fst values: Fst from 0.057 between ALAI and TNSH to Fst = 0.70 between TNSH and KYCW. Fst values with the KYLO were lower (from 0.023 with ALAI to 0.037 with KYCW). The PC2 divided ALAI+GISR+ KYCW and TNSH from KYMM and KYLO. Our study is the first SNP genotyping of Kyrgyz sheep breeds. Next stage is pooling our SNP set with the data on other Eurasian sheep breeds to contribute new insights on their origin. The RSF № 14-36-00039 funded the research. Key Words

Reindeer (Rangifer tarandus L., 1758) represents one of the most economically and culturally important species of Russian Northeast area, providing a significant source of nutrition for the entire human population. The wild form consists of two populations: Yakut and Taimyr whereas the domestic form is presented by four breeds and the Nenets is the largest one. Single nucleotide polymorphisms have gained wide use for estimation genetic diversity in model species and are becoming the marker of choice for applications in non-model such as reindeer. Here, we conducted the whole genome analysis with the BovineHD BeadChip to study the genetic structure and differentiation of the Nenets breed (NEN, n = 33) and wild reindeer populations inhabiting territories of the Taimyr Peninsula (TMR, n=27) and Yakutia (YAK, n=20).For data processing we used PLINK 1.07, Admixture 1.3 software and R packages diversity with subsequent visualization in the R packages pophelper and ggplot2. After quality control, 9623 SNPs were taken for the further analyses. Most likely, due to active migration, wild form surpassed the domestic one by all parameters of genetic diversity. MDS and ADMIXTURE analysis clearly showed the differentiation of the domestic and wild forms from each other, while majority of wild deer were not distributed according to the population affiliation and formed several mixed groups. Despite the fact that the reindeer genome is not yet sequenced, the genomic screening using the HD SNP array, developed for cattle, is the most modern highly informative method for studying the reindeer genome. Our results allowed to assess the level of genetic diversity and showed the possibilities of differentiation among domestic and wild reindeer populations that might be used to create effective programs for breeding and for conservation of unique populations. This work was funded by the Russian Science Foundation no.16-16-10068.

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.