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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.

Prolificacy is a very important trait in sheep. Romanov sheep, the well-known Russian sheep breed, are characterized by very high prolificacy; however, the genetic basis of this unique property of Romanov sheep is still unknown. It was reported that Ovine BMPR1B gene, located on the OAR6, is associated with prolificacy in several sheep breeds. The aim of our study was to identify candidate SNPs within BMPR1B gene, related to prolificacy. To achieve this goal, using NGS technology, we sequenced ovine BMPR1B gene in Romanov sheep (n = 6), which are characterized by high prolificacy (about 270 lambs per 100 ewes). The sequences of BMPR1B gene of Noire du Velay, Tan, Southdown and Australian Horned Merino sheep breeds as well as Asiatic mouflon (n = 1), which are characterized by significantly lower prolificacy (from 110 to 180 lambs per 100 ewes) were derived from publicly available sources and used for comparison. FST analysis performed in PLINK 1.9 program revealed 10 SNPs with values higher than 0.8. The majority of candidate SNPs under putative selection were localized in the region from 29,382,098 to 29,430,387 on OAR6 of Ovine reference genome (Oar_v3.1 (Ensembl release 98). Thus, we can suggest, that this region of the BMPR1B gene can be considered as the putative region, associated with high prolificacy of Romanov sheep. Additional studies will be needed to confirm the effect of identified candidate SNPs on prolificacy traits. The research results will be useful for artificial selection of sheep with higher prolific capacity, including the introduction of desired alleles in sheep populations using genome editing technologies. This work was supported by the Russian Ministry of Science and Higher Education No. 0445-2019-0024 and RFBR No. 20-516-56002.

Maintaining high levels of genetic diversity is a key factor of successful breeding of resilient, resistant to diseases and productive sheep. Prevention of inbreeding is of special importance in the mountainous hard-to-get habitats where gene flow is limited or absent. An assessment of inbreeding coefficients based only on pedigree information is not always correct. In addition, pedigree information is often missing for flocks of native sheep. In this regard, we performed a genomic assessment of inbreeding in 15 local sheep breeds inhabiting severe environments of Russia and neighboring Asian countries based on estimations of standardized multilocus heterozygosity (sMLH) and runs of homozygosity [F(ROH)]. For this study, we used SNP genotypes of twelve Russian local breeds (n = 316) and three Kyrgyz local breeds (n = 68), which were generated using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). The sMLH values were calculated using R package inbreedR and visualized in R package ggplot2. The F(ROH) values were calculated using the R package detectRUNS by applying the consecutive runs method. Mean sMLH values were varied from 0.962 ± 0.006 in the Andean breed to 1.031 ± 0.002 in the Buryat breed and averaged to 1.001± 0.004. The least mean F(ROH) value was detected in the Mongolian breed (0.0043 ± 0.0009) while the greatest ones were observed in the Alai and Andean breeds (0.0364 ± 0.0049 and 0.0357 ± 0.0061, respectively). The strong negative correlations between sMLH and F(ROH) were detected for all of studied breeds (r2 = –0.8496, CI = –0.8752… –0.8192). The obtained data is relevant for control of inbreeding level in the populations and for future sustainable management of native fat-tailed sheep breeds. The study was funded by RSF No. 19-16-00070.

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.

A rapid spreading of cosmopolite breeds leads to decrease of population sizes of Russian local sheep that consequently might result in their 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 distribution of the ROH and to estimate genome inbreeding in Russian local sheep breeds based on SNP-genotyping. Medium-density SNP-genotypes of twenty-three local sheep breeds (n = 332) were obtained in our previous study. We used a consecutive runs method implemented in the R package “detectRUNS” to calculate ROH which were estimated for each animal and then categorized in the ROH length classes (1–2 Mb, 2–4 Mb, 4–8 Mb, 8–16 Mb, >16 Mb). The frequency of short ROH segments (≤2 Mb) were the highest in all studied breeds (63.15–93.10%). The longest segments (>16 Mb) were the least frequent and were missing in four breeds. The genomic coefficients based on ROH estimation varied from medium (0.114) to low (0.035). Thus, we found that Russian local sheep breeds are characterized by a low level of genomic inbreeding.

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.

Breeding fast-growing sheep with good carcass traits is beneficial for lamb producers. However, genomic selection for relevant traits is still lagging in Russian sheep industry. In this regard, detection of the QTLs and candidate genes specific for local sheep is of great scientific and practical interest in Russia. In our research, we aimed to perform GWAS for growth and carcass traits in the QTL-mapping sheep population obtained from crossing slow- and fast-growing breeds. Backcrosses from (Katahdin× Romanov) × Romanov mapping population were genotyped with Ovine Infinium HD SNP BeadChip (Illumina, USA). Quality control in PLINK v.1.9 resulted in 459,868 SNPs which were used for GWAS. Threshold p-value for Bonferroni genome-wide significance was estimated as p = 1.09х10–7. The Manhattan plots were visualized in R package qqman. The measurements included body weight (BW), chest depth (CD), chest width (CW), and width at the iliac tubercle (WT) were recorded at the age of 6, 42 and 180 days. Significant SNPs including oar3_OAR7_44462236 (p = 8.40E-07), oar3_OAR7_44496608 (p = 8.40E-07) and oar3_OAR7_44975375 (p = 8.60E-07) were associated with WT at age of 180 days (13.31±0.23 cm). In addition, genomic regions located on chromosome 7 (44462236 – 44975375) and chromosome 2 (148067154 – 148077728) contained SNPs associated with CD at age of 180 days (21.42±0.39 cm) as well as with WT at age of 180 days. One SNPs (oar3_OAR4_4568047) on chromosome 4 and four SNPs on chromosome 7 (oar3_OAR7_44462236, oar3_OAR7_44496608, oar3_OAR7_44975375, and oar3_OAR7_45012432) were associated with BW at age of 180 days (22.61± 0.89 cm). The genes identified by GWAS were annotated. There were candidates responsible for bone metabolism, prenatal growth, skeletal muscle growth, related to meat quality and involved in carbohydrate and lipid metabolism. The reported study was funded by RFBR, project No. 17-29-08015.

National livestock genetic resources are the valuable source of genetic variability, which are necessary to ensure the sustainability of the local animal production systems. The aim of our work was to characterize the genomic architecture and to detect signatures of selection in two oldest Russian native cattle breeds, using high-density DNA arrays. Fifty-six animals of Yaroslavl (n = 31) and Kholmogor (n = 25) were selected for the study. The Illumina Bovine HD BeadChip (777,962 SNPs) was used for genotyping. High-density SNP genotypes for Holsteins (n = 25) were used as the reference. Three methods (Fst, hapFLK, and ROH) were implemented to detect the genomic regions to be under putative selection. The results of the PCA-plot, Neighbor-Net analysis and Admixture clustering showed clear genetic differences between Yaroslavl and Kholmogor breeds as well as between them and Holsteins. Comparison of the results produced by different methods showed presence of twelve regions in genome of Yaroslavl breed and nine regions in genome of Kholmogor breeds, which were identified at least by two methods. We have confirmed nine regions under putative selection in genome of Yaroslavl cattle and six regions in genome of Kholmogor cattle, which were described previously based on medium-density SNP genotypes, herewith the flanking positions of the most of these regions were expanded. Additionally, we detected three new putative genomic regions affected by selection in each studied breed, which were localized on chromosomes 4, 15 and 17 in Yaroslavl breed and on chromosomes 12, 15 and 18 in Kholmogor breed. The functional annotation of genes localized within identified regions was carried out. Our research results can be useful for genetic improvement of the studied cattle breeds and for developing the programs for their conservation. The study was supported by RSF within project No. 19-76-20012.

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.

Tuva breed is the oldest native sheep breed in Russia with more than 2000 year-history and comes in third place by population size among coarse wool sheep. Tuva sheep produce high-quality meat as well as coarse wool to make traditional clothing in the Republic of Tyva. In present study, we aimed to evaluate genetic diversity and to establish genetic links of the Tuva breed with the other Russian coarse wool sheep to understand the origin and current status of this valuable livestock species. Twenty samples of Tuva were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). SNP-data were processed in PLINKv1.9, R package ‘diveRsity’ and SneP software. High-density SNP-genotypes of 10 coarse wool sheep breeds were used as comparison groups. Observed heterozygosity (Ho) and allelic richness (Ar) in Tuva breed were 0.336 and 1.884, respectively, and were practically equal to mean values estimated across all analyzed sheep breeds (Ho=0.335, Ar=1.884). All coarse wool breeds showed moderate heterozygote excess which was the highest in Tuva breed (1.6%). Effective population sizes estimated for three and five generations ago for Tuva breed (Ne3 =118 and Ne5 =179) were less than those in other breeds (Ne3 = 314 and Ne5 = 441 for Edilbai or Ne3 = 300 and Ne5 = 450 for Kalmyk) but not the lowest (Ne3 = 49 and Ne5 = 72 for Buubei). Values of historical effective population size estimated for 60 generations ago for Tuva breed was 1457 that was compatible with those obtained for other breeds (Ne60 from 586 for Buubei to 2634 for Kalmyk). Despite the obvious decrease in effective population size, levels of genetic diversity are not critical that would allow to develop programs to ensure preservation and sustainable development of Tuva breed. The study was funded by RSF No. 19-16-00070.

Simple Summary Russia has diverse specifically selected and multipurpose goat resources. However, the origin of the local goats is still enigmatic. In this study, we sequenced and analyzed mitochondrial DNA (mtDNA) fragments of seven Russian local goat populations to provide the first insight into their maternal lineage. Abstract The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.

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.

Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar‐Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor‐Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population—TIK, and maximum values were observed in the most southern population—SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.

Genetic characteristics of the allele pool of four groups of the Yakut snow sheep subspecies (Ovis nivicola lydekkeri) inhabiting various parts of the Verkhoyansk Mountain Range such as Kharaulakh Ridge, Orulgan Ridge, ridges of the Central Verkhoyansk, and Suntar-Khayata Ridge is presented. Fragment analysis using 17 microsatellite loci was carried out using the ABI 3131xl genetic analyzer. Significant heterozygote deficiency was detected in all investigated snow sheep populations. Differentiation of the studied groups in accordance to their geographical origin was revealed.

The Romanov breed is the most interesting local Russian sheep breed with unique biological traits (out-ofseason breeding ability, prolificacy). Conservation of genetic resources of the breed requires constant careful monitoring using DNA markers. In this regard, the aim of our work was to compare the parameters of the allele pool and genetic diversity, as well as to assess genetic similarity of regional populations of the Romanov breed in comparison with archetypal animals. Tissue samples were selected in different regions of Russia (Yaroslavl, Ryazan and Tula regions, Republics of Khakassia and Komi). Polymorphism of 11 microsatellites was studied with the genetic analyzer АВІЗ 130x1. We estimated an average number of alleles (Na), effective number of alleles (Ne), number of informative alleles (Na>5%), observed (Ho) and expected heterozygosity (He), fixation index (FIS), constructed Neighbour-Net and carried out PCoA and cluster analyzes. The Khakass population was characterized by the greatest allelic diversity: Na = 11.30; Ne = 5.99 and Na>5% = 5.50 alleles, while minimal Ne (3.95) and Na>5% (4.30) were detected for the first and second Yaroslavl populations, respectively. Deficiency of heterozygotes from 6 to 19.5% was observed in all groups, except for the Tula population. Based on the results of Neighbour-Net, PCoA and cluster analysis, genetic isolation of three Yaroslavl populations was found. Also, a certain genetic detachment of the Ryazan population (Fst from 0.038 to 0.059) was revealed. Thus, we demonstrated that the parameters of allele pool and the indices of genetic diversity can vary greatly within the breed. In addition, it has been established that the Yaroslavl populations of the Romanov breed still represent a separate group.

Poaching is one of the major types of wildlife crime in Russia. Remnants of goats (presumably the wild endemic species, the Caucasian tur) were found in an area of the Caucasian mountains. The case study involves a suspected poacher whose vehicle was found to have two duffel bags containing pieces of a carcass, which he claimed was that of a goat from his flock. The aim of the forensic genetic analysis for this case was to (i) establish individual identity and (ii) perform species identification. DNA typing based on fourteen microsatellites revealed that STR-genotypes generated from pieces of evidence found at crime scene fully matched those obtained from the evidence seized from the suspect. The results of genome-wide SNP-genotyping, using Illumina Goat SNP50 BeadChip, provided evidence that the poached animal was a wild Caucasian tur (Capra caucasica). Thus, based on comprehensive molecular genetic analysis, evidence of poaching was obtained and sent to local authorities. To our knowledge, this case study is the first to attempt to use DNA chips in wildlife forensics of ungulates.

Azerbaijani sheep breeds are of particular interest since this region is in close proximity to the Fertile Crescent – the proposed place of domestication. Molecular genetic studies of local breeds will help shed light on the history of sheep breeding. Our work was aimed to identify genetic characteristics of three sheep breeds from Azerbaijan: Bozakh (n = 19), Karabakh (n = 16) and Mazekh (n = 19). For genotyping, we used Illumina OvineHD BeadChip (AgResearch) containing around 600 thousand SNPs. PLINK 1.9 was used to perform quality control. Genetic diversity parameters and pairwise FST distances were calculated in R package diveRsity. After all quality control procedures, including LD pruning, 286663 SNPs were selected for subsequent analyses. PCA revealed that, while all the breeds formed their own clusters, only 1.62% of genetic variability was explained by the first component (PC1). Cluster analysis conducted in Admixture 1.3 showed that Bozakh was derived from Karabakh and Mazekh breeds. However, based on CV error, the number of clusters (K) judged to be one. Pairwise FST distances were quite low, with highest value of 0.017 between Karabakh and Mazekh and lowest (0.006) between Mazekh and Bozakh breeds. The global fixation index (FST) was 0.01, which indicated that 99% of genetic variability was due to within breeds differences. Expected heterozygosity was similar in Bozah and Mazeh (0.363±0.000 and 0.360±0.000, respectively) and a slight lower in Karabakh breed (0.353±0.000). We observed neither heterozygotes excess nor deficiency in all of the studied breeds. The inbreeding coefficient (Fis), ranged from 0.001 in Karabakh to 0.011 in Mazekh sheep. Our results demonstrate that the studied Azerbaijani sheep breeds are genetically close, but carry specific genomic components that allows consider them as valuable genetic resources. The study was funded by the RSF 21-66-00007 (genotyping) and the Russian Ministry of Science and Higher Education 0445-2019-0024 (expedition studies).

Karachaev sheep is a fat-tailed breed from North-Caucasus, Russia. It has good adaptability to local environments and excellent meat quality. The aim of our study was to investigate genetic characteristics of Karachaev sheep and its relationship with other fat-tailed breeds. Samples of Karachaev (n = 22), Lezgin (n = 21), Edilbai (n = 21), Karakul (n = 21), Alai (n = 20), and Gissar (n = 20) breeds were genotyped using Ovine HD BeadChip. For phylogenetic analyses, we additionally included 50K genotypes of Afshari, Awassi, Barki, Chios, Cyprus Fat-Tailed, and Red Maasai breeds. PLINK 1.9 was used for quality control and performing PCA. Genetic diversity parameters were calculated in R package diveRsity. Historical effective population size (Ne) was estimated using SNeP 1.1. Cluster analysis was conducted in Admixture 1.3. TreeMix tree was constructed in TreeMix 1.13. Genetic diversity indices (observed and expected heterozygosity, allelic richness) were highest in Karachaev and Lezgin breeds. Karachaev sheep was phylogenetically closer to Lezgin and Edilbai breeds. Trends in historical Ne were very similar for these breeds. We observed the increased decline in Ne around 20–25 generations ago (which corresponds to 1940s) that can be associated with deportation of Karachaev people to Kazakhstan and Kyrgyzstan in 1943, which resulted in lost almost all of its livestock. TreeMix analysis allowing one migration event revealed gene flow from Karakul to Karachaev/Lezgin nod. Admixture analysis showed the presence in Karachaev sheep of Edilbai and Karakul specific genomic components (~80 and ~20%, respectively). Our study allow suggest that Karachaev breed was extinct during World War II and then was restored in 1960s after Karachaev people returned to their land. It originated from the sheep they brought from Central Asia (Edilbai), and was improved by Karakul breed and local sheep. This work was supported by RSF No. 21-46-00001 (genotyping) and the Russian Ministry of Science and Higher Education No. 0445-2019-0024 (expedition studies).

For the first time nuclear DNA polymorphisms were studied in Kodar snow sheep (Ovis nivicola kodarensis, KOD). KOD is a representative of a small isolated population of Asian snow sheep (Ovis nivicola Eschscholtz, 1829) inhabiting the Kodar Ridge (Irkutsk oblast, Transbaikal krai). We compared KOD with the geographically closest Yakut subspecies (Ovis nivicola lydekkeri). Genome-wide study of single-nucleotide polymorphisms (SNPs) was performed using the Illumina OvineSNP50 BeadChip (Illumina, United States). The final set of markers for analysis included 1030 SNPs. We found that Kodar snow sheep had almost 10 times lower level of genetic diversity evaluated by multilocus heterozygosity—MLH (0.027 for KOD vs 0.215–0.270 for individuals of Yakut subspecies) and standardized MLH—stMLH (0.116 against 0.910–1.147). The results of multidimensional scaling (MDS), Nei distances calculations (DN) and STRUCTURE analysis showed a clear genetic differentiation of Kodar snow sheep from Yakut subspecies. Our data is the first step to understanding the demographic history of the original Kodar population of snow sheep.

A territory of northern Russia covering more than 4,194 square kilometers is the world’s largest dwelling and breeding area of wild and domestic reindeer. Unlocking its complete genome sequences should have promoted design and development of species-specific genotyping arrays, but this process is still in progress. However, evaluation of state of gene pool of reindeer populations cannot be paused to prevent dramatic losses in genetic diversity. Thus, we aimed to select SNPs to create low-density panel to perform genetic assessments without losing biological content. Our study was based on SNP genotypes of wild reindeer (n = 83), and domestic reindeer from the Nenets District (Nenets breed, n = 100), Murmansk Region (Nenets breed, n = 19), Republic of Sakha (Yakutia) (Evenk breed, n = 19) obtained using Illumina BovineHD BeadChip. The data processing performed in PLINK 1.9 revealed 4456 polymorphic SNPs. Using Delta method implemented in the TRES software, 368 informative SNPs were selected from the whole set of polymorphic SNPs for further analysis. To compare the resolution power of low-density SNP panel with a whole set of polymorphic SNPs, we estimated minor allele frequencies (MAF) and performed PCA analysis and Admixture clustering. In case of low-density panel, we observed obvious bias to higher MAF (≥ 0.30), and 4% of SNPs had MAF around 0,1. Among the whole set of polymorphic SNPs, 70% SNPs had MAF ≤ 0.2. PCA obtained with low-density panel and the whole SNP set provided similar pattern of genetic differentiation between studied groups. Wild animals were clearly separated by PC1 from their domestic relatives. Besides Evenk reindeer was distant from two Nenets groups. The Admixture clustering demonstrated the identical patterns for both SNPs sets. The next step of our study will be developing custom DNA array based on 368 selected informative SNPs. The research was funded by RSF № 16-16-10068-P.

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.

Snow sheep (Ovis nivicola) is endemic of North-East Siberia, Russia. To date, the taxonomy of this species, based primarily on morphological characteristics, is controversial. In order to clarify the taxonomy of snow sheep, modern molecular genetic approaches can be used. Here we applied Illumina Ovine 50K BeadChip to examine genetic characteristics and differentiation of four subspecies, which currently are considered as valid: Putorana (O.n.borealis) (PUT, n=7), Yakut (O.n.lydekkeri) (YAK, n=23), Koryak (O.n.koriakorum) (KOR, n=20) and Kamchatka (O.n.nivicola) (KAM, n=10). As long as Yakut snow sheep areal covers vast territories, this subspecies was represented by two groups from Verkhoyansk Range (YAK-1, n=15) and Momsky ridge (YAK-2, n=8). Statistical analysis was performed with PLINK 1.9, Structure 2.3.4, Genetix 4.05 software and R package “diveRsity”. After quality control, 1190 polymorphic SNP markers were selected for further investigations. Bayesian structure analysis revealed that at K=2 KAM and KOR were assigned to one distinct cluster and at K=3 PUT separated from the other groups. At K=4, which was determined as the most probable number of populations, all the subspecies were assigned to their clusters. However, four KAM individuals demonstrated an admixture pattern with KOR. Nei’s genetic distances (Nei, 1978) ranged from 0.037 between YAK-1 and YAK-2 to 0.206 between KAM and PUT. The distances between KAM and KOR, KOR and YAK-1, YAK-1 and PUT were 0.057, 0.060 and 0.149, respectively. Allelic richness (Ar) was lower in the isolated population PUT - 0.021 ± 0.003. In YAK-1, YAK-2, KOR these values were respectively: 1.642 ± 0.0012, 1.607 ± 0.014, and 1.620 ± 0.012, and significantly higher than in KAM – 1.501 ± 0.014. Our results demonstrated that the studied groups of snow sheep were genetically differentiated and confirmed their taxonomic status as subspecies. The samples were provided partly by the Mountain Hunters Club, Russia. The study was supported by the Russian Science Foundation (Project no.14–36–00039).

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.

A comparative study of the informativeness of SNP and STR markers for interspecific and intraspecific differentiation of the two species of the genus Ovis, snow sheep (O. nivicola) and domestic sheep (O. aries), was conducted. Eleven STR loci combined into two multiplex panels were examined. SNP analysis was performed with the DNA microarray OvineSNP50K BeadChip featuring 54241 SNPs. The possibility of clear differentiation of the studied Ovis species with both types of genetic markers was demonstrated. The advantages of SNP markers for intraspecific differentiation of the O. aries breeds and O. nivicola geographical groups were revealed. The areas of application of the studied types of DNA markers are discussed.

Background The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references. Results The observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource. Conclusions Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies. Electronic supplementary material The online version of this article (10.1186/s12711-018-0408-8) contains supplementary material, which is available to authorized users.

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.

Background Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data. Results We recorded similar observed heterozygosity (0.354–0.395) and allelic richness (1.890–1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their wool type (fine wool, semi-fine wool and coarse wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The coarse-wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran). Conclusions In this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations. Electronic supplementary material The online version of this article (10.1186/s12711-018-0399-5) contains supplementary material, which is available to authorized users.

In this study, we present the first complete mitochondrial genomes of two species of the genus Ovis – snow sheep (Ovis nivicola) and thinhorn sheep (Ovis dalli). The mitochondrial genomes h...

Scrapie is the transmissible spongiform encephalopathy or prion disease that causes fatal degenerative damages in the central nervous system of affected sheep. To-date two forms of scrapie are known: classical, and atypical, or Nor98. Genetic susceptibility to classical scrapie is determined by allele polymorphisms in codons 136, 154 and 171 of the PRNP gene. Thus, A136R154R171 allele is associated with resistance while V136R154Q171 is linked with susceptibility. The F allele in 141 PRNP codon is responsible for susceptibility to Nor98. In this regard, the aim of our research was to analyze PRNP polymorphisms in 136,141, 154 and 171 codons in five Russian locally derived sheep breeds including Altai Mountain (n=16), Kuibyshev (n=16), North Caucasian (n=19), Russian Longhaired (n=14) and Tsigai (n=21). Identification of the alleles in the codons 136 (A/T/V), 141 (L/F), 154 (R/H) and 171 (Q/R/H/K) of PRNP was performed by pyrosequencing on the PSQ96MA (Qiagen, USA). We found eight different PRNP genotypes in five Russian breeds. The most frequent genotypes were ARR/ARQ (G2, genetically resistant) in the Kuibyshev (50.0%), North Caucasian (47.4%), Russian Longhaired (42.9%) and ARQ/ARQ (G3, little genetic resistance) in Altai Mountain (43.8%) and in Tsigai (42.9%). Sheep of the most genetically resistant class G1 were detected in all studied breeds with frequency varying from 4.8% in Tsigai to 35.7% in Russian Longhaired. The allele VRQ was found in all breeds (from 3.6 to 7.1%) except for North Caucasian. The F141 allele presented in two animals belonging to North Caucasian breed and with satisfactory genotypes for classical scrapie as ARQ/ARR and ARQ/ARQ. Thus, we demonstrated the necessity to test genetic susceptibility for both scrapie forms in sheep herds. The research was performed within the framework of the Federal Agency of Scientific Organizations No. 0600-2018-0014. Key Words

This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations.

Creating panels for parentage assignment based on the most informative SNPs (minor allele frequency, MAF≥ 0.3) is an important problem of the modern sheep breeding. International Society of Animal Genetics (ISAG) recommends the parentage panel consisting of 88 autosomal SNPs, developed by the International Sheep Genomics Consortium. However, selection of SNPs, which were included into the panel, was performed on the base of DNA profiles of North American, Australian and New Zealand sheep. There were no Russian breeds in these researches, and the possibility of applying ISAG panel to parentage testing of these sheep must be studied. We have performed the whole genome SNP study in four local Russian sheep breeds — Romanov (ROM, n = 22), Baikal’s fine-fleeced (ZBL, n = 7), Buryat sheep Buubey (BUB, n = 15), and Tuvan short fat tailed (TUV, n = 16) using Ovine SNP50k BeadChip. Data were processed for the total number of markers (54241 SNPs) and for 88 autosomal SNPs, recommended by ISAG. We estimated percentage of markers with MAF  0.3, mean MAF value, probability of identity (PI) and probabilities exclusion (P1, P2, P3) to evaluate the power of parentage panel for each of single breed and for entire sample. The universality of the panel was evaluated by comparing the degree of genetic differentiation of breeds based on the study of the entire number of SNPs and panel ISAG. For this purpose, we took in account such criteria as pairwise values of Fst (AMOVA) and results of principal component analysis (PCA-plot). We did summary statistics in Plink 1.09 and GenAlEx 6.5. After the quality control of the entire sample, we selected 47385 SNPs with mean MAF of 0.292±0.131 for the further analysis. The mean MAF for 88 parentage SNPs was 0.380±0.091. Analysis of the SNPs’ distribution depending on theirs MAF showed that most of the SNPs (81.8 %) were informative (MAF≥ 0.3). Proportion of informative SNPs differed between breeds and was 56.8 % in ROM, 63.4 % in ZBL, 71.6 % in BUB and 72.7 % in TUV. Twenty-one SNPs (23.9 %) were highly informative in all four breeds, while 37 SNPs (42.0 %), 17 SNPs (19.3 %) and 10 SNPs (11.4 %) were informative, respectively, in three, two or only one breed. Marker DU196132_525.1 was monomorphic in TUV (MAF = 0). Three SNPs with MAF < 0.3 (DU232924_365.1, DU501115_497.1 and DU372582_268.1) were not informative for all four breeds. Lower pairwise values of Fst based on 88 SNPs with the same character of genetic relations compared with those using whole genome SNP profiles shown high flexibility of ISAG panel. PCA confirmed the low breed’s dependence of SNP panel by creating purely consolidated overlapping areas corresponding to different breeds. The probability of identity for 88 SNPs ranged from 4.32½10-33 in TUV to 7.48½10-33 in BUB. Probability of exclusion was P1≥99.99 % for all four breeds. The value of P2 was the highest in TUV (P2≥99.99 %) with P2≥99.98 % for others. The value of P3 was 99.9 % for all breeds. Instead of some breeddependent character of DNA profiles of 88 autosomal SNPs, our results confirmed the possibility of applying of ISAG panel for parentage testing in four local Russian sheep breeds.