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The territory of the Nenets Autonomous Okrug (NAO) has a large length from north to south and from west to east within the borders, which distinguish different biotopes that have been used for breeding reindeer for a long time. The aim of our research was the genetic and exterior assessment of reindeer micropopulations of SRO "Tabseda" (TABS) and marine brigades of the SEC "Indiga" (INDM), formed in the biotopes of the western and eastern parts of one geomorphological region of the Malozemelskaya tundra of the Nenets Autonomous Okrug. For analysis, we used the results of molecular genetic studies on nine STR markers, zootechnical examination of animals on 10 main features of the exterior and live weight, characteristics of physique, agroecological assessment of pastures (description of the relief, hydrographic network, zonal division of the vegetation cover, calculation of the INDM vegetation index in Landsat -8 and Sentinel-2A). According to the analysis of long-term values of the vegetation index NDVI, TABS pastures differ from INDM in low biological productivity, the vegetation of which is formed in vast lowlands with a highly developed hydrographic network. The micropopulation of TABS was characterized by high rates of genetic diversity: the average number of alleles (Na) per locus was 8.22, information alleles - 5.33, effective - 4.46 and private - 0.89. Heterozygous deficiency was noted in both TABS and INDM micropopulations (8.8 and 12.1%). Based on the obtained data on the exterior indicators, the INDM females had a number of advantages over TABS in chest girth (125.8 and 121.2 cm, p> 0.95), oblique body length (108.5 and 106.5 cm, p = 0, 95) and live weight (104.2 and 95.9 kg, p> 0.999), while males - by chest depth (47.5 and 44.7 cm, p> 0.99), chest width (29.9 and 27.5 cm, p> 0.99) and oblique body length (119.5 and 116.5 cm, p> 0.95), respectively. Thus, the reindeer micropopulations TABS and INDM located in the Malozemelskaya tundra have genetic and morphological differences that are associated with different environmental conditions.

In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

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.

The comparative molecular genetic study of museum and modern representatives of cattle breeds can help to elucidate the origin and maintenance of historical genetic components in modern populations. We generated the consensus genotypes for 11 microsatellite loci for 24 museum samples of Kalmyk, Kyrgyz, and Kazakh cattle, dated from the first quarter of the 20th century, and compared them with those of modern Kalmyk, Kyrgyz, and Kazakh white-headed breeds. The level of genetic diversity of the modern Kalmyk and Kyrgyz cattle (uHe = 0.771–0.778) was similar to those observed in the museum samples (uHe = 0.772–0.776), while a visible decrease in genetic variability in the modern Kazakh white-headed breed compared to museum Kazakh cattle was detected (uHe = 0.726 and 0.767, respectively). The PCA plot, FST- and Jost’s D-based networks, and STRUCTURE clustering provided strong evidence of the maintenance of the historical genetic background in modern populations of Kalmyk and Kyrgyz cattle. In spite of the allele pool of Kazakh white-headed cattle having undergone great changes compared to the museum Kazakh cattle, several animals still carry the visible aspect of the historical genetic components. Our results can be used for the selection of individuals for the creation of gene banks and may significantly improve the efficiency of conservation programs aimed at preserving genetic diversity in the national genetic resources of cattle.

Kazakh White-headed is the local beef cattle breed, which is bred in Central Asia countries. It was created in the beginning of 20 century by improving native Kazakh cattle by Hereford breed. The aim of our work was to characterize the genetic structure and to trace the presence of ancestral genetic components in the modern population of Kazakh White-headed cattle. The samples of modern representatives of Kazakh White-headed (KZWH_M, n=29) and Hereford (HRFD_M, n=25) breeds as well as historical specimens of native Kazakh breed (KZKH_H, n=2), dated by the first quarter of 20th century, were subjected to the study. All works with historical specimen were performed in dedicated facility of the L.K. Ernst research Centre for Animal Husbandry. DNA from modern samples was extracted using DNA Extran 2 kit (JSC Syntol, Russia) and from historical specimen – using COrDIS Extract Decalcine kit (GORDIZ LLC, Russia). We genotyped 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples the PCR reaction were carried out in five replicates to determine the consensus genotypes for each locus. In total, we identified 82 microsatellite alleles. Five alleles, which were found in the historical specimens, were lost in the modern population of Kazakh White-headed cattle. We observed the highest level of genetic diversity (unbiased heterozygosity, allelic richness) in historical samples. The modern population of Kazakh White-headed cattle was closer to Hereford breed as was revealed by calculation of pairwise Nei and FST genetic distances. The STRUCTURE clustering confirmed the more similarity of genetic structure of modern Kazakh White-headed cattle with Herefords, but showed the visible presence the historical genetic components. The research results will be useful for developing the programs of conservation and sustainable use of Kazakh White-headed cattle.

Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.

Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst Research Center for Animal Husbandry. The samples were genotyped using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

Domestic reindeer are bred across the Russian tundra from the Kola Peninsula to Chukotka and in the mountain-taiga zone. To understand the genetic diversity and population structure of domestic reindeer, 528 individuals were analyzed using 14 microsatellites. The sample included the Nenets breed of the Komi Republic (NEN_K, n = 42), Nenets (NEN_N, n = 148), Yamalo-Nenets (NEN_Y, n = 46), Archangelsk (NEN_A, n = 47), Murmansk (NEN_M, n = 43), Taymyr (NEN_T, n = 52) regions; the Even (EVN, n = 33), the Evenk (EVK, n = 31), the Chukotka (CHUY, n = 33) breeds of Yakutia; the Chukotka breed (CHU, n = 40) of Chukotka Region; the Tuvinian (TUV, n = 32) and Mongolian (MGL, n = 21) populations of the Tuva Republic and Mongolia. Calculations were done in R package “diveRsity,” software SplitsTree 4.14.6., Structure 2.3.4. Possibly due to permanent exchanges with animals among farms of the Nenets region and thus introduction of “foreign” alleles into the herds, a higher level of genetic diversity was found in NEN_N (HE=0.699; AR =6.086). All groups had a significant homozygote excess with the maximal value of FIS in geographically isolated populations MGL (0.326) and TUV (0.229). Neighbor-Net tree showed formation of three main clusters according to breed origin and breeding region: (1) the Nenets reindeer from different regions, (2) three breeds of Yakutia and (3) TUV and MGL populations. CHU branched individually with a distance from others. At K=11 of STRUCTURE, we observed a clear clustering of CHU, MGL, TUV, NEN_T. A middle level of admixture was detected in NEN_A, NEN_Y, NEN_M and NEN_N with NEN_K and CHUY with EVN/EVK, which formed one cluster. Here, we obtained more detailed information on genetic variability of Russian domestic reindeer, which would assist to fill current gaps in knowledge about this essential species for many indigenous peoples of the Far North. The study was funded by the RSF within Project no. 16-16-10068-P.

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726&ndash, 0.774 and 0.708&ndash, 0.739, the allelic richness values were 2.716&ndash, 2.893 and 2.661&ndash, 2.758 for the historical and modern samples, respectively. Analyses of FST and Jost&rsquo, s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.

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.

Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (Ho=0.168; Ar = 1.476). All populations showed heterozygotes deficiency (uFIS 95%, CI > 0) with higher uFIS values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068.

Inbred individuals often show reduced fitness due to increased number of loci identical by descent as the loss of heterozygosity may lead to the unmasking of deleterious recessive alleles. Inbreeding level can be measured either based on pedigree or genetic markers. The latter can be used for heterozygosity fitness correlation (HFC) studies in populations which pedigrees are unknown. Here, we estimated individual heterozygosity level in reindeer based on ten STR and investigated heterozygosity fitness correlations. A total of 64 individuals were divided into two groups: males (M, n = 16) and females (F, n = 48). The influence of inbreeding on height at withers (HaW), chest depth (CD), chest width (CW), chest girth (CG), wrist girth (WG), body length(BL), head length (HL), body weight (BW), hip width (HW) and loin width (LW) was examined. R package “inbreedR” was used for statistical analysis. Identity disequilibrium point estimate - g2 was calculated to estimate the correlations between inbreeding, multilocus heterozygosity (MLH) and fitness. For M group the measure of g2 was 0.03390±0.02564, p (g2 >0) = 0.017, and for F group - 0.03973±0.02377, p (g2 > 0) = 0.006. Expected r2 between inbreeding level and heterozygosity was 0.49795 and 0.40812 for M and F, respectively. The highest HFCs in M group were detected for CG - 0.35, WG – 0.26, BW – 0.18 and HW – 0.14 i.e. traits that are characteristics for body composition. The highest HFCs in F group were for LW – 0.22, CW – 0.16 and HaW – 0.15 i.e. traits related to reproductivity. For all the other traits HFCs were close to zero. Our study demonstrated that STR can be used for calculations of MLH and inbreeding correlations as well as for detecting traits that are influenced by inbreeding in reindeer. The study was supported by Russian Science Foundation (Pr. no.16-16-10068).

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.

Caucasian tur (Capra caucasica) is native to Greater Caucasus Mountain Chain from Azerbaijan and Georgia in the East to Krasnodar region of Russia in the West. This species is divided into two subspecies (by some authors into species)—East-Caucasian tur and West-Caucasian tur and a subpopulation referred to as Mid-Caucasian tur. Up to date most of the genetic studies of Caucasian tur are based on mitochondrial DNA sequences and comprehensive investigation based on nuclear DNA is required for clarification of its genetic diversity and population structure. In our work, we assessed the applicability of Illumina Goat SNP50 BeadChip for genetic studies of Caucasian tur. Total of 15 specimens of Capra caucasica including East-Caucasian tur from Dagestan (E_TUR, n = 5), West-Caucasian tur from Karachay-Cherkessia (W_TUR, n = 5), and Mid-Caucasian tur from Kabardino-Balkaria (M_TUR, n = 5) were genotyped. After quality control, 5544 polymorphic loci, which were distributed all over 29 autosomes, were detected. The lowest number of SNPs was found on the 25th chromosome—68, and the highest on the 1st chromosome—348. It was shown that all the three groups of Caucasian tur clustered separately. A total of 2061 SNPs were common for all the populations, 594 were found only in W_TUR, 689 in E_TUR, and 530 in M_TUR. Individual heterozygosity ranged from 0.273 to 0.282 in W_TUR, from 0.217 to 0.253 in E_TUR, and from 0.255 to 0.283 in M_TUR. A clinal pattern of genetic variation was revealed. It was suggested to consider Caucasian tur a single species with several ecotypes. Thus, in our study we demonstrated that the Illumina Goat SNP50 BeadChip developed for domestic goats can be used as a useful tool for genetic studies of Caucasian tur.

Summary: Background. The European bison (Bison bonasus) is the only wild ox of Europe, survived to our days. Whilst numerous stu dies have been undertaken to characterize the Lowland line of European bison, it is little known about allele pool and population genetic structure of the Lowland-Caucasian line of wisent. Materials and methods. The samples were collected from twenty-six animals of Russian breeding nucleus of Lowland-Caucasian line. Ten Bos Taurus microsatellites (TGLA227, BM2113, ETH10, SPS115, TGLA122, INRA23, TGLA126, BM1818, ETH225, and BM1824) were used for analysis. Results. Eight of ten microsatellite loci (excluding TGLA227 and INRA23) were polymorphic. The number of alleles per locus is varied of one to five with average value of 2.80 0.47. The alleles, which are specific for Lowland-Caucasian line, were identified. We observed relatively high inbreeding level (FIS = 0,091) and very low effective population size (Ne = 1.8, 95% CIs, Parametric 1.1-2.9). We showed that two genetically distinct groups have taken part in formation of allele pool of studied wisent population. Conclusion. Our data indicated that the development of breeding program to decrease the inbreeding degree and to increase the level of genetic diversity is necessary.

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.

Reindeer herding is traditional in Tuva, Russia. This region is located in the southern part of the country, on the border with Mongolia and isolated from the other reindeer herding areas of Russia. During the last three decades, the census population size of Tuva reindeer has decreased drastically, from 15,000 to 1,500 heads. The aim of our study was to assess genetic characteristics of Tuva population of reindeer. Samples of Tuva reindeer (n = 12) were genotyped using Illumina BovineHD BeadChip. To perform the comparison with other ecotypes of domestic reindeer we added samples of all the breeds, which are officially recognized in Russia: the Chukotka (n = 12), the Nenets (n = 31), the Even (n = 12) and the Evenk from Yakutia (n = 12) and Krasnoyarsk region (n = 19). Reindeer from Mongolia (n = 11) as well as the wild reindeer from Yakutian and Taimyr tundra (n = 20), and Baikal and Amur taiga (n = 9) were added to our dataset. After quality control, 7,202 SNPs were selected for subsequent analyses. On PCA plot Tuva reindeer were clustered together with Mongolian reindeer. The FST genetic distance was lowest between these two groups – 0.039 comparing to FST values between Tuva and other groups of domestic reindeer, which ranged from 0.092 (the Evenk from Yakutia) to 0.137 (the Chukotka) and were highest between Tuva and wild reindeer populations (0.146). Allelic richness was lowest in Mongolia (1.288±0.004) and Tuva reindeer (1.301±0.004). In other breeds this parameter ranged from 1.323±0.004 (the Chukotka) to 1.356±0.004 (the Evenk from Yakutia). In our study, it was shown that reindeer from Tuva do not belong to any official breed of Russia and genetically are very close to Mongolian ecotype. Our results should be considered at developing programs for restoration of Tuva reindeer. This work was supported by Russian Science Foundation grant 16-16-10068-P

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

We analyzed 110 wild boars of European (EU) and Asian (AS) parts of Russia, which inhabited 14 different regions, with respect to patterns of genetic differentiation and diversity. Our study was based on the sequences of the 590 bp fragment of the D-loop of mtDNA and on the genotypes at ten nuclear microsatellite loci. The D-loop sequences showed, that all 14 haplotypes, which were identified in the European wild boars, belong to the major European clade E and all 35 haplotypes, which were identified in the Asian wild boars, belong to the major Asian clade A. Haplotype and nucleotide diversity was Hd=0.961 and π=0.025, respectively. The higher level of mitochondrial genetic diversity was observed in EU population of wild boar comparing to AS population. Analysis of the UPGMA tree showed that the EU boars has clearly separated from the AS boars and the presence of two clusters specific to Asian wild boars. Microsatellite-based analysis showed the similar level of heterozygosity (0.597 and 0.598 for the EU and AS, respectively). The FIS values were 0.079 and 0.188 for EU and AS, respectively. Microsatellite analysis and mitochondrial sequencing revealed a high degree of genetic differentiation of EU population of wild boar, which indicates the uniqueness of their allele pool. Analysis of molecular variance for both marker systems and Bayesian structure analysis of our microsatellite data revealed a clear break between European and Asian populations. The clear distinction between EU and AS populations may be due to phylogeography origin of the Sus scrofa l. The presented results can be used to study as a genetic information for the preservation of S. scrofa in Russia. Our data are consistent with that backcross events have increased the diversity of nuclear DNA in wild boar, resulting in a different genetic pattern between male and female lineages.

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.

Three semi-domesticated reindeer breeds inhabiting the Republic of Sakha – Yakutia have been characterized using nine microsatellite markers. Genomic DNA was isolated from tissue samples of 123 individuals of the Chukotka (Khargin) (CHU, n=47), the Evenk (EVK, n=32) and the Even (EVN, n=44) breeds, collected from different regions of Yakutia. Fragment analysis and sizing were run on ABI 3131xl genetic analyzer. Allele frequencies were calculated and used for the characterization of reindeer breeds and the evaluation of their genetic biodiversity. Nei’s standard genetic distance was calculated and used for the construction of a neighbor-joining tree. Statistical analysis was conducted with GenAIEx 6.5.1, PAST2.15 and STRUCTURE2.3.4 software. The highest number of alleles, such as informative (with a frequency more than 5%), effective (Ne) and private (Pr), was detected in the CHU breed: Na ≥5% =5.333±0.441, Ne=4.517±0393 and Pr =1.111±0.389, while the EVN breed had the lowest number: 4.778±0.324, 4.315±0.488 and 0.444±0.242, respectively. The EVN breed occupied an intermediate position (5.000±0.373, 4.408±0.315 and 0.889±0.261). Among reindeer breeds, observed heterozygosity ranged from 0.729 ± 0.026 to 0.608±0.050 with the lowest value found in CHU reindeer and the highest in EVK reindeer. A heterozygotes’ deficiency was observed in all reindeer breeds. At K=3, STRUCTURE analysis matches with the data of Nei's genetic distance dimension results, indicating the presence of a common consistent pattern. CHU and EVK reindeer breeds are characterized by a closer genetic relationship in comparison with the EVN breed, which formed a separate cluster.

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka&ndash, Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.

For the first time, comprehensive studies of the phenogenetic features of the Ural ecotype of domestic reindeer of the Nenets breed were performed. It was found out that the Ural reindeer relative to other ecotypes of the Nenets breed have smaller linear dimensions and live body weight. The studied group of reindeer was characterized by the minimum values of the majority of population genetic indicators, including the effective number of alleles (Ne = 4.422 ± 0.614), the Shannon information index (I = 1.663 ± 0.102), and the level of both the observed and expected heterozygosity (Ho = 0.561 ± 0.064 and He = 0.740 ± 0.035, respectively). It exceeded two other samples from neighboring breeding regions (Nenets Autonomous district and the Komi Republic) in the average number of alleles per locus: (Na = 9.667 ± 0.577 versus Na = 9.555 ± 0.669 and Na = 9.557 ± 0.709, respectively). Animals of the Ural population (YAM) have a closer genetic structure with reindeer individuals of the neighboring Nenets Autonomous district (NAO). The studied sample of the Nenets breed was characterized by a shift in genetic diversity towards a lack of heterozygotes, as evidenced by the positive Fis values. The introduction of genetic methods in the reindeer herding will allow improving the breeding work in the industry, revealing intraspecific genetic variation in inbreeding herds and identifying intrabreed groups of animals.

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.

Russia is the place of origination more than twenty local pig breeds since 19(th) century. Although originally developed from imported breeds, pigs in Russia were adapted to the local harsh climate and low feeding conditions, forming unique characteristics. The processes of drift and leaching of genes in local species cause interest in the problem of preserving their biodiversity. The development of genomic technologies allows us to accelerate the process of studying these issues. Here the porcine 60K BeadChip (Illumina Inc., USA) was used for analysis and describing of biodiversity and population structure of local pigs and wild boars from European part of Russia for comparison (BR – Breitov (n=18), LIV – Livni (n=16), MUR – Murom (n=12), URZ – Urzhum (n=9), RUEU – Russian wild boar (n=69)). For data processing Plink 1.9., Tassel and Archaeopteryx plugin, Treemix 1.1, SNEP and Vienny 2.1 were used. After QC (geno=0.1, maf=0.05) 35600 SNPs were remained. On MDS plot and NJ-tree, local pigs form a common cluster while RUEU are equally remote from most representatives of local pigs subgroup on PC1. We can observe that URZ locates separately from remained animals. However, all local pigs illustrated close parallel divergence across all generations (13–750). We detect strong migration of RUEU (0.45) to MUR and URZ to LIV (0.3). This may be due to free conditions of detention outside the closed premises several generations ago, which caused to crossing with a wild boar. In total, both populations had 80.9% of common SNPs, and only BR and MUR had unique SNPs (825 and 1193 respectively). The research was performed within the framework of the Federal Agency of Scientific Organizations No. АААА-А18-118021590138-1.

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

Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.

Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.