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Summary: Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed‐specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds. [ABSTRACT FROM AUTHOR]

Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (Capra caucasica): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection. The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats. [ABSTRACT FROM AUTHOR]

Abstract: 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Among the variety of cattle breeds in Russia, the Russian red dual-purpose cattle breeds have great importance because of their ability to produce high milk yields as well as to provide excellent milk quality. The low census size of the Russian red cattle breeds requires development of programs for conservation of their biodiversity. Our study aimed to investigate selection footprints in Russian red cattle breeds, using high values of linkage disequilibrium (LD) in SNP haplotype blocks as indicators. For finding such LD blocks, we used the genotypes (?35K SNPs) of Red Gorbatov (RGB, n = 26), Bestuzhev (BST,n = 27), and Suksun (SKS,n = 17) breeds, as well as Red Holstein (RH,n = 16) as an outgroup. Quality control and LD calculations for different distances were performed in Plink 1.90. Top 0.01% SNP pairs by LD value (0.9=r2< 1.0) were selected for further analysis. The effective population size derived from LD patterns was estimated using SNeP tool. Comparison of LD values for 70 kb interval between breeds and chromosomes by MANOVA pairwise testing significantly distinguished RH/RGB and BST/SKS breeds (P < 0.05-0.001). LD values among chromosomes were 0.195-0.287 for RH, 0.194-0.272 for RGB, 0.172-0.237 for BST, and 0.157-0.217 for SKS. The SKS and BST breeds had higher Ne values (84 and 113, respectively) compared to RH (63) and RGB (79). Selection footprints by LD blocks in Russian red cattle genome covered several relevant genes on BTA1 (EPHA6,DGKG), BTA2 (LRP1B,THSD7B,STAT1), BTA5 (CPM,BAIAP2L2), BTA9 (TRDN,UTRN), BTA10 (KCNN2,CAPN3), BTA11 (SH3RF3,RABGAP1,RALGPS1), BTA14 (ZNF16,ARHGAP39,TOX,DGAT1), and BTA19 (MYH10), BTA22 (FHIT). Detected genes were found to be responsible for milk fat and protein contents, fatty acid composition, somatic cells score, fertility, feet and legs, and udder conformation traits. Our results can be useful for developing the breeding and conservation programs of the Russian red cattle genetic resources. The study was funded by RFBR within project No. 20-516-00020. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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). [ABSTRACT FROM AUTHOR]

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 fattailed 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). [ABSTRACT FROM AUTHOR]

Russia is reach by local cattle genetic resources, which are well adapted to the different environment. However, the modern cattle husbandry tends to the replacing the local cattle breeds by highly productive commercial breeds, which can lead to the decline of genetic diversity. The aim of our work was to estimate the genetic identity of five Russian local cattle breeds, including Yaroslavl (n = 52), Kholmogor (n = 26), Istoben (n = 21), Tagil (n = 26), and Black-and-White (n = 44). The Holstein breed (n = 49), which is actively used for improvement of above breeds was included in the study for comparison. The genotyping was performed using GGP Bovine 150K Array (Illumina, San Diego, CA, USA) and more than 112000 autosomal SNPs passed through the quality control and were selected for the analysis. We observed the significant excess of heterozygotes in four studied breeds (the values of unbiased inbreeding coefficient were varied from -0.009 to -0.022), except for Black-and-White breed. The effective population size (Ne) for Istoben, Tagil and Kholmogor breeds was declined until present, while Holstein and Black-and-White breeds showed the increase of Ne values starting at 5 generations ago. The Black-and-White breed was the closest to the Holsteins (Fst=0.014), while the Yaroslavl breed was the most distant (Fst=0.115). The highest ratio of Holstein specific genomic components was shown for Tagil (18.79%) and Black-and-White (59.73%) breeds. Our results indicated replacing the part of aboriginal genomic components in several Russian local cattle breeds by Holstein specific components. The comprehensive strategies for conservation of the Russian local cattle breeds are needed to avoid the further decline of genetic diversity of these valuable national animal genetic resources. The study was funded by the Ministry of Science and Higher Education of the Russian Federation within theme 0445-2019-0024. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 turanomongolian 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. [ABSTRACT FROM AUTHOR]

Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 < mo >±">±± 0.003 for Kholmogor, 0.048 < mo >±">±± 0.006 for Istoben, 0.129 < mo >±">±± 0.007 for Holstein, and 0.102 < mo >±">±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle). [ABSTRACT FROM AUTHOR]

The world-famous Romanov breed of sheep fits easily into different production systems including private households, smallholders, and large farms. Such a resilience and extraordinary reproduction traits combining with good meat qualities have made the Romanov breed as a choice to produce mutton in the Central Russia regions. However, little is known on genetic mechanisms underlying the complex of specific traits of this breed. In this regard, we performed a scan of signatures of selection by identification of runs of homozygosity (ROH) islands in the Romanov sheep population. Forty-eight samples of the Romanov sheep from the Yaroslavl and Kaluga regions of Russia were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). ROHs were estimated in the R package "detectRUNS" using window-free method for consecutive. The ROH shared in more than 50% of sheep were considered as ROH islands. The genes overlapped with the ROH islands were annotated using Ensembl genome browser 103. Enrichment for functional categories of the identified genes was performed using DAVID Functional Annotation Bioinformatics Microarray Analysis tool. More than 88 SNPs were found in ROH islands located on OAR1, OAR10, OAR11, OAR13, OAR14, OAR15, OAR16, OAR17 and OAR18. We detected a major group of genes related to reproduction traits. The identified candidates included UBE2Q1 (embryo implantation, fertilization, prolactin secretion), RNF17 (spermiogenesis), HSD11B2 (pregnancy, follicle function), FANCA (gonad development), and CUBN (embryonic development). In addition, several identified genes were involved in fatty acid metabolism (ACOX1, HAO2, and EIF6), lipid transport (OSBPL11), and biosynthesis of lipid-binding serum glycoproteins (BPIFB4) as well as in osteoblast differentiation (ADAR). The studies will be continued on a larger sample with further validation of the most promising candidate genes. Genotyping of twenty-four samples was performed within RFBR project No. 20-516-56002. Other twenty-four SNP-genotypes were generated within the theme No. 0445-2019-0024. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Romanov breed stands out from the global variety of sheep breeds. Romanovs originated from local sheep at the end of 17th century in the Volga Valley. Since the 1970s, the breed has become popular in France, Canada, and the United States. Some unique traits are of permanent interest to this Russian breed. Primarily, Romanovs have outstanding reproduction qualities: early sexual maturity, out-of-season breeding ability, and extraordinary prolificacy. Using Romanov ewes in crossbreeding programs is a profitable, practical method to increase the number of highly viable hybrids. In addition, the Romanov breed has unique wool properties, which are very suitable for manufacturing felt products, rugs, and mats. However, detailed genetic information on the breed is lacking. Therefore, we performed the whole-genome SNP analysis of the original Romanov sheep to study its genetic diversity and genetic relationships with other Russian breeds. We genotyped 42 samples of Romanovs using the OvineSNP50K BeadChip and pooled the data with the set from 24 Russian breeds. Quality filtering was performed in PLINK version 1.07. Calculations were done in PLINK version 1.07, GENETIX version 4.05, and HP-Rare 1.1. We found a lower level of genetic diversity in Romanovs (Ho = 0.350 and Ar = 1.862) in comparison with other coarse wool breeds (Ho = 0.377 and Ar = 1.899). At the same time, Romanovs, compared with the 24 breeds, were characterized by the most insignificant deviation from Hardy-Weinberg equilibrium (Fis = -0.005). In other breeds, Fis values varied from -0.028 to -0.082. Pairwise Fst values ranged from 0.084 to 0.124 between Romanovs and Kuibyshev and Kuchugur, respectively. The MDS analysis revealed the genetic uniqueness of Romanov sheep. Principal component (PC) 1 divided all breeds into 2 groups according the wool type (fine wool + semifine wool and coarse wool) with 4.7% of total genetic variance. By PC1 the Romanov formed an incorporated bunch and logically clustered with coarse-wool breeds. However, the Romanov was clearly separated from the others by PC2, which explained 3.8% of additional genetic variability. Most likely, a high level of consolidation and genetic differentiation of the Romanov breed from other Russian sheep are explained by its "pure gene" origin and was not improved by any breed. Our study is the first attempt to reveal the outstanding genetic nature of original Romanov sheep on whole-genome level. We will extend our study by genotyping more samples with medium-density DNA chip and using NGS technology. The research was performed under financial support of Russian Scientific Foundation (number 14-36-00039). [ABSTRACT FROM AUTHOR]

Conservation of native cattle populations' biodiversity is a crucial element in breeding selection programs. Reduction of local and improved livestock gene pool leads to the loss of valuable alleles for adaptation to specific environments. In our work, we investigated the genetic structure of the most essential native cattle breeds in Russia. Using Illumina Bovine 50K BeadChip, we genotyped nine breeds: Bestuzhev (BEST, n = 26), Black and White (BLWT, n = 21), Kalmyk (KALM, n = 14), Kholmogor (KHLM, n = 25), Kostroma (KSTR, n = 20), Red Gorbatov (RGBT, n = 23), Suksun (SKSN, n = 20), Yakut (YAKT, n = 25), and Yaroslavl (YRSL, n = 21). Statistical analysis was performed with PLINK 1.07, Admixture 1.3 software, and R packages "diveRsity" and "adegenet." Multi-dimensional scaling (MDS) analysis showed that all of the breeds formed their own clusters. The YAKT cluster was completely separated on the first component (C1) and was most distant from all other populations. KALM also separated on C1 but was much closer to the other clusters. Both of these breeds are of Asian origin. The other seven breeds, which are of European origin, separated from one another mostly on the second component (C2). Admixture analysis showed that the most probable number of populations (K) was 8. At K = 2, YAKT was separated from the other populations. Considerable admixture of YAKT was only found in the KALM cluster (from K = 2 to K = 8). At K = 8, all of the breeds but KALM formed their own clusters. KALM was combined from the seven other breed fragments (all but SKSN). Pairwise genetic distances (FST) values were higher for YAKT (from 0.126 with KALM to 0.187 with RGBT). Fst values between the other breeds ranged from 0.036 (BLWT and SKSN) to 0.103 (KSTR and RGBT). The lowest rarified allelic richness value was observed for YAKT (1.781 ± 0.002). For all of the other breeds, it ranged from 1.919 ± 0.001 for KSTR to 1.958 ± 0.001 for KALM. Expected heterozygosity was the lowest in YAKT (0.273 ± 0.001) while in all of the other breeds it ranged from 0.329 ± 0.001 in KSTR and RGBT to 0.352 ± 0.001 in BEST. Inbreeding coefficient (FIS) values in all of the breeds were close to zero (from -0.05 to 0.01). Our study revealed that all of the evaluated Russian breeds were structured, and only KALM had a more complex admixture. The most diverged, indigenous YAKT breed had a lower genetic diversity than all of the other breeds. The study was supported by the Russian Science Foundation within Project no.14-36-00039. [ABSTRACT FROM AUTHOR]

Spermatogonia cells are considered as a valuable genetic material to produce individuals with desired traits in the framework of preservation of animal and poultry gene pool (cryobanks) and genetic modification of their genome (transgenesis). This technology is based on the introduction of donor spermatogonia into the testes of male recipients and the following obtaining the exogenous sperm to produce progeny with desired characteristics. A key step of this technology is the removal of own spermatogenic cells (spermatogenesis inhibition) in the male recipient. We have optimized the method to inhibit the spermatogenesis in chicken testes using alkylating agent busulfan. The multiple injections of busulfan at the concentration from 40 to 100 mg per 1 kg of body weight was performed directly into the parenchyma of testes of six month old chicken males (n = 16). In order to detect the presence of spermatogenic cells in seminiferous tubules, we carried out the histological studies of testes in one month after injection. We observed the decrease in diameters and the number of spermatogenic cells at the cross sectional area of the seminiferous tubules in the experimental group as compared to the control. When using busulfan at concentration of 40 mg/kg the number of cells averaged 35±3 cells per seminiferous tubule, which was 32.8 times less as compared to the control (1149±95). At higher concentrations of busulfan the number of cells decreased and averaged 20±2, 12±0.5 and 9±0.4 cells at concentration of 60, 80 and 100 mg/kg, repectively. Analysis of cell types of the seminiferous tubules revealed that mainly the Sertoli cells and spermatogonia represented the cell population. Moreover, with increasing concentrations of busulfan the ratio of spermatogonia was significantly reduced. The ratio of Sertoli and spermatogonia cells after introduction of busulfan into the testes at a concentration of 40, 60, 80 and 100 mg/kg was 57 and 43%, 75 and 25%, 95 and 5 % and 96 and 4%, respectively. However, the application of busulfan at a concentration 100 mg/kg led to high mortality of chicken. Thus, we demonstrated that the optimal concentration of busulfan to kill the spermatogonial cells was 80 mg/kg. The complete inhibition of spermatogenesis was observed in 9-10 months after introduction of busulfan at this concentration. The study was supported by the Russian Science Foundation within Project no.16-16-10059. [ABSTRACT FROM AUTHOR]

Reindeer herding is the historical branch of animal husbandry in the northern regions of the Russian Federation. There are four reindeer breeds, the most numerous of which is Nenets (with over 800,000 reindeer). For further development of the reindeer herding, in addition to traditional breeding methods, it is necessary to apply modern technologies, such as genetic analysis. The aim of the current work was to identify the possible association between microsatellites loci and phenotypic traits of the Nenets reindeer breed. DNA was extracted from tissue samples of 43 female individuals using Nextech column (Agrobiogen Biotechnologie GmbH, Munich, Germany) according to the manufacturer's recommendations. Fourteen microsatellite loci (NVHRT21, NVHRT24, NVHRT76, RT1, RT6, RT7, RT9, RT27, RT30, RT25, RT13, NVHRT03, RT5, and NVHRT73) were selected to examine the associations between marker genotypes and eight phenotypic traits: height at the withers (HaW), chest depth (CD), chest width (CW), chest girth (CG), wrist girth (WG), body length (BL), head length (HL), and body weight (BW). Associations between the genotypes and the traits were evaluated using the one-way ANOVA model. Results were considered statistically significant if the P-value was less than 0.05. All of the microsatellites loci were polymorphic, and the number of alleles ranged from three (NVHRT03) to six (RT25 and NVHRT73). The RT6 marker was associated with four traits: BW (P < 0.001), CG (P < 0.05) BL (P < 0.01), HL (P < 0.01), whereas the RT27 marker was linked to three traits: HaW (P < 0.05), BW (P < 0.05), and HL (P < 0.01). The variability of the HL trait was also associated with two loci: RT25 (P < 0.05) and NV 24 (P < 0.001). The RT30 marker was only significantly associated with height at the withers (P < 0.05). Thus, our study revealed that five microsatellite loci were significantly associated with five phenotypically important traits (HaW, HL, BW, CG, and BL), and these markers could be potentially used for the improvement of the reindeer herding breeding program. This research was funded by Russian scientific foundation project No. 16-16-10068. [ABSTRACT FROM AUTHOR]