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Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (FROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation. [ABSTRACT FROM AUTHOR]

For the first time, an analysis of the genetic diversity of the Osetin sheep breed was performed using genome-wide SNP profiles in a comparison with other Russian coarse wool breeds. We established that the Osetin breed has high indicators of genetic and allelic diversity. For the first time, the recent and historical effective sizes of the population of the Osetin breed were calculated. Close genetic relationships between the Osetin and Karachaev sheep breeds were shown, which is confirmed by the low value of differentiation (Fst = 0.009) and the formation of a joint cluster on the neighbor net graph. The similarity of the population structure of the Osetin and Karachaev breeds was revealed. [ABSTRACT FROM AUTHOR]

The genetic characteristics of five Russian dairy black-pied cattle breeds, namely Black-and-white, Istoben, Kholmogor, Tagil, and Yaroslavl, are presented in this study. Analysis was performed for 112 526 single nucleotide polymorphisms (SNPs) using bovine GGP HD DNA arrays (Illumina Inc., United States). Results showed that all studied breeds had their own genetic structure, distinguishing them from the Holstein breed and from each other. The individuals that retained the highest proportion of genomic components that were inherent in the studied local breeds and did not exhibit visible introgression with Holstein were identified in all Russian breeds. This makes them suitable candidates for conservation of genetic resources program. [ABSTRACT FROM AUTHOR]

Cattle breeds used in industrial production tend to have a larger size compared to the local cattle, as the increased dairy and beef productivity is closely related to the stature. The aim of our work was to identify single nucleotide polymorphisms (SNPs), which are significantly associated with stature in diverse cattle breeds. Thirteen local and transboundary cattle breeds (n = 670) subjected to our study were divided in two groups according to the stature. The high-stature group included Angus, Ayrshire, Black-and-White, Holstein, Kholmogor, Yaroslavl, Tagil and Istoben breeds. The low-stature group comprised of Jersey, Kalmyk, Kyrgyz, Mongolian and Yakut cattle. The average height at withers was 136.3 ± 1.6 and 121.6 ± 2.8 cm in the high- and low-stature groups, respectively. The samples of 11 breeds were genotyped using high-density DNA arrays (Illumina Inc., USA). The genotypes of two remaining breeds were downloaded from the publicly available WIDDE database. Genome-wide association studies revealed four SNPs, which were strongly associated with the stature, including three SNPs at 77.3–77.8 cM on BTA4 (map53144-ss46525999, p < 7.747 × 10−101; BovineHD0400021479, p < 1.173 × 10−91; ARS-BFGL-NGS-116590, p < 7.665 × 10−105) and one SNPs at 25.2 cM on BTA14 (BovineHD1400007259, p < 1.324 × 10−109). Functional annotation showed the localization within identified regions of genes, which are responsible for growth, exterior characteristics, protein and lipid metabolism, and feed intake. Identified SNPs can be considered as useful DNA markers for marker-assistant cattle breeding aimed at increased stature. The study was funded by the Russian Ministry of Science and Higher Education No. 0445-2019-0024. [ABSTRACT FROM AUTHOR]

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management. [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]

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]

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]

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. [ABSTRACT FROM AUTHOR]

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. [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]

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