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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.

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.

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).

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.

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