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Abstract Three stable microbial consortia, each composed of Bacillus paranthracis and Staphylococcus haemolyticus strains, were isolated from milk of cows diagnosed with mastitis in three geographically remote regions of Russia. The composition of these consortia remained stable following multiple passages on culture media. Apparently, this stability is due to the structure of the microbial biofilms formed by the communities. The virulence of the consortia depended on the B. paranthracis strains. It seems plausible that the ability of the consortia to cause mastitis in cattle was affected by mutations of the cytK gene of B. paranthracis.

Abstract In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation.

This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number—only 1 SNP—for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.

Abstract The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in South‐east Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity. We found 1725 polymorphic sites (810 singletons, 853 parsimony‐informative sites and 57 indels), 701 unique haplotypes, a haplotype diversity of 0.9995 and a nucleotide diversity of 0.0015. In addition to the dominant T3 and several rare haplogroups (Q, T5, T4, T2 and T1), we have identified maternal line in Austrian Murbodner cattle that possess surviving aurochs’ mitochondria haplotype P1 that diverged prior to the Neolithization process. This is convincing evidence for rare female‐mediated adaptive introgression of wild aurochs into domesticated cattle in Europe. We revalidated the existing haplogroup classification and provided Bayesian phylogenetic inference with a more precise estimated divergence time than previously available. Occasionally, classification based on partial mitogenomes was not reliable; for example, some individuals with haplogroups P and T5 were not recognized based on D‐loop information. Bayesian skyline plot estimates (median) show that the earliest population growth began before domestication in cattle with haplogroup T2, followed by Q (~10.0–9.5 kyBP), whereas cattle with T3 (~7.5 kyBP) and T1 (~3.0–2.5 kyBP) expanded later. Overall, our results support the existence of interactions between aurochs and cattle during domestication and dispersal of cattle in the past, contribute to the conservation of maternal cattle diversity and enable functional analyses of the surviving aurochs P1 mitogenome.

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs—for group of traits withers height, rump height, body length, 2 SNPs—for withers height and rump height, 1 SNP—for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

Argali (Ovis ammon), the largest species among all wild sheep, is native to mountainous regions of Central and East Asia, spreading mainly throughout such countries as Tajikistan, Kyrgyzstan, Kazakhstan, Afghanistan, Mongolia, Russia and China. Intraspecific taxonomy of argali remains unclear, and currently, most researchers recognize up to nine subspecies. The aim of our work was to investigate the phylogenetic relationship between populations of O. ammon based on genome-wide SNP analysis. Five subspecies, Altai (O. a. ammon) (n = 6), Gobi (O. a. darwini) (n = 5), Pamir (O. a. polii) (n = 12), Tian Shan (O.a. karelini) (n = 15) and Kyzylkum (O. a. severtzovi) (n = 4), were genotyped using Illumina OvineHD BeadChip. In addition, complete mitogenome sequences from 30 of those samples were obtained. After quality control procedures, 65,158 SNPs were selected for the subsequent analyses. Neighbor-Net dendrogram and principal component analysis (PCA) revealed that the five subspecies could be grouped into four clusters. It was shown that a population from Altai formed a cluster with Gobi subspecies. The highest pairwise FST genetic distance was between O. a. ammon and O. a. severtzovi (0.421) and the lowest were between O. a. polii and O.a. karelini (0.083) and between O. a. ammon and O. a. darwini (0.040) subspecies. Genetic diversity was higher in Central Asian argali as compared to East Asian populations. O. a. severtzovi had an admixed origin and consisted of two genetic components—73.5 ± 0.2% of O. a. polli and 26.5 ± 0.2% of urial (O. vignei). TreeMix analysis revealed a migration event from urial to O. a. severtzovi argali. The analysis of complete mitogenomes supported the results based on whole-genome genotyping. Considering that all the mtDNA sequences of O. a severtzovi belonged to O. ammon and not to O. vignei, we concluded that gene flow in this group was associated with urial males. As this is only the first work on intraspecific taxonomy and genetic diversity of argali based on genome-wide SNP genotyping and the analysis of complete mitogenomes, we suggest that more genetic studies are needed to clarify the status of Gobi and Tian Shan argali.

This paper shows a straightforward, but surprisingly effective approach to detect genomic regions of importance, illustrated on two Simmental cattle populations. Medium density genomic data of 42 German/Austrian (denoted as “Western“) and 38 Russian Simmental cattle were used to identify the most frequent haplotypes within the two populations. The haplotypes were defined as non-overlapping segments of ten single nucleotide ploymorphisms (SNP). The phasing was done with the SHAPEIT software, with a follow up analysis of haplotypes using the GHap package. Despite the low sample size a number of high frequency haplotypes could be identified across the whole genome. The identified genes residing directly in these high frequency haplotypes were extremely relevant for the dual purpose Simmental cattle. A large part of these genes influenced growth rate and carcass traits, others were relevant for the milk production. A smaller proportion was connected to the reproduction, immune system and cellular processes, with indirect influence on production traits.

Genomic assessment of local sheep breeds is relevant to the reconstruction of post-domestication migrations and to filling in gaps in the developmental history and contemporary phylogeographic-differentiation patterns in Eurasia. In this study, we aimed to reveal possible genetic relationships between local sheep breeds in Russia and the Persian Highlands (Iran) based on high-density SNP genotypes. All samples (n = 395) from 11 Iranian and 10 Russian sheep breeds were genotyped by using the Ovine Infinium HD BeadChip (Illumina, San Diego, CA, USA). Principal Component Analysis, maximum-likelihood assessment, and Neighbor-Net graph analysis demonstrated a clear differentiation between Russian sheep breeds of European ancestry from the Iranian local cluster and Russian breeds of Asian origin. Admixture analysis revealed a shared ancestral background, which was detected in several Iranian-local and Russian-local fat-tailed coarse-wool sheep breeds. Our findings contribute to a better understanding of the pattern of historic admixture, which is present in the genomes of many Eurasian sheep breeds.

Cheap pasture fodder and a long grazing season are favorable for cattle breeding in the Dagestan Republic of Russia. However, specific natural and geographical conditions, including mountain terrain, hypoxia, and high humidity slow down the intensification of cattle breeding in this region. Thus, the maintenance of genetic diversity of local cattle breeds, which fits well into specific environments, is of special importance for mountain ethnic communities. Dagestan Mountain cattle have valuable biological traits, including strong hooves, stamina, and adaptability to extreme mountain conditions. This sample included 32 individuals of Dagestan Mountain cattle collected from private owners in the mountain villages of Dagestan during a scientific expedition. We observed a high level of genetic diversity in Dagestan Mountain cattle, as revealed by calculations of the mean number of alleles per locus (6.82 compared to 4.79–5.82 in other breeds) and observed heterozygosity indices (Ho = 0.73, which was higher compared to the other breeds (Ho = 0.69) excluding Simmentals and Brown Swiss (Ho = 0.74). Based on STRUCTURE results, the individuals with a low level of admixture with other breeds were found within Dagestan Mountain cattle, which can be considered as candidates for using conservation programs in germplasms.

Staphylococcus aureus is a causative agent of different infectious processes, food poisoning, and autoimmune disorders. The horizontal transfer of pathogenic strains can occur from animal to human under both house and farm conditions, and the spread of strains with antibiotic resistance is an existing problem. In addition to the spread of antibiotic-resistant strains in clinics, this problem also exists in veterinary medicine. It is especially important to monitor antibiotic resistance on farms where antibiotics are the standard treatment of animals, which may trigger the spread of antibiotic-resistant strains among animals and to the human population, and these strains can also be distributed in milk products produced by these farms (milk, cheese, and butter). In this work, we investigated 21 S. aureus isolates using whole-genome sequence analysis and tried to establish a relationship between these isolates with the development of bovine mastitis in seven regions of Western Russia. An S. aureus virulence profile was identified. We identified two groups of S. aureus associated with subclinical mastitis, namely, the enterotoxin-positive and enterotoxin-negative groups. The most prevalent factor associated with bovine mastitis in Russia was cytotoxins, including hemolysins and leukocidins. Multidrug resistance strains were investigated, and antibiotic resistance genes were identified. We identified S. aureus ST 97 type as the most common type in the regions in Western Russia. To the best of our knowledge, this is the first in-depth study of a range S. aureus isolates originating from cattle infections in Russia.

Primary immunodeficiency diseases (PID) area heterogeneous group of disorders caused by genetic defects of the immune system, which manifest clinically as recurrent infections, autoimmune diseases or malignancies. Early detection of PID remains a challenge, particularly in older children with milder and less specific symptoms. This study aimed to assess TREC and KREC diagnostic ability in PID. Data from children assessed by clinical immunologists at Speransky Children's Hospital, Moscow, Russia with suspected immunodeficiencies were analyzed between May 2013 and August 2016. Peripheral blood samples were sent for TREC/KREC, flow cytometry (CD3, CD4, CD8 and CD19), IgA and IgG analysis. A total of 434 children [189 healthy, 97 with group I and II PID (combined T and B cell immunodeficiencies & well-defined syndromes with immunodeficiency) and 148 group III PID (predominantly antibody deficiencies)] were included. Area under the curve (AUC) for TREC in PID groups I and II diagnosis reached 0.82 (CI = 0.75–0.90), with best model providing sensitivity of 65% and specificity of 92%. Neither TREC, nor KREC had added value in PID group III diagnosis. In this study, the predictive value of TREC and KREC in PID diagnosis was examined. We found that the TREC had some diagnostic utility for groups I and II PID. Possibly, addition of TREC measurements to existing clinical diagnostic algorithms may improve their predictive value. Further investigations on a larger cohort are needed to evaluate TREC/KREC abilities to be used as diagnostic tools on a wider scale.

Sheep are a main livestock species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of large-scale livestock improvements, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n = 31), Gissar (n = 30), Kyrgyz coarse wool (n = 13), Aykol (n = 31), and Tien-Shan (n = 24) breeds were genotyped with the OvineSNP50 BeadChip or the Ovine Infinium HD BeadChip (Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (FROH = 0.034), while the maximum was found in the Alai breed (FROH = 0.071). Short ROH segments (ROH ≤ 4 Mb) were predominant in all breeds. Long ROH segments (ROH > 16 Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (Ne5 = 660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (Ne5 = 176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol, and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.

Abstract Background It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-kb interval on bovine chromosome 3 and, subsequently, assigned to a 336-kb haplotype block based on an animal set that included, Brown Swiss, Dutch Belted (Lakenvelder) and Belted Galloway individuals. A possible candidate gene in this region i.e. HES6 was investigated but the causal mutation remains unknown. Thus, to elucidate the causal mutation of this prominent coat color phenotype, we decided to remap the belted phenotype in an independent animal set of several European bovine breeds, i.e. Gurtenvieh (belted Brown Swiss), Dutch Belted and Belted Galloway and to systematically scan the candidate region. We also checked the presence of the detected causal mutation in the genome of belted individuals from a Siberian cattle breed. Results A combined linkage disequilibrium and linkage analysis based on 110 belted and non-belted animals identified a candidate interval of 2.5 Mb. Manual inspection of the haplotypes in this region identified four candidate haplotypes that consisted of five to eight consecutive SNPs. One of these haplotypes overlapped with the initial 922-kb interval, whereas two were positioned proximal and one was positioned distal to this region. Next-generation sequencing of one heterozygous and two homozygous belted animals identified only one private belted candidate allele, i.e. a multiplication event that is located between 118,608,000 and 118,614,000 bp. Targeted locus amplification and quantitative real-time PCR confirmed an increase in copy number of this region in the genomes of both European (Belted Galloway, Dutch Belted and Gurtenvieh) and Siberian (Yakutian cattle) breeds. Finally, using nanopore sequencing, the exact breakpoints were determined at 118,608,362 and 118,614,132 bp. The closest gene to the candidate causal mutation (16 kb distal) is TWIST2. Conclusions Based on our findings and those of a previously published study that identified the same multiplication event, a quadruplication on bovine chromosome 3 between positions 118,608,362 and 118,614,132 bp is the most likely candidate causal mutation for the belted phenotype in cattle.

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.

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

Abstract Background Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3–V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

Replacement pigs’ genomic prediction for reproduction (total number and born alive piglets in the first parity), meat, fatness and growth traits (muscle depth, days to 100 kg and backfat thickness over 6–7 rib) was tested using single-step genomic best linear unbiased prediction ssGBLUP methodology. These traits were selected as the most economically significant and different in terms of heritability. The heritability for meat, fatness and growth traits varied from 0.17 to 0.39 and for reproduction traits from 0.12 to 0.14. We confirm from our data that ssGBLUP is the most appropriate method of genomic evaluation. The validation of genomic predictions was performed by calculating the correlation between preliminary GEBV (based on pedigree and genomic data only) with high reliable conventional estimates (EBV) (based on pedigree, own phenotype and offspring records) of validating animals. Validation datasets include 151 and 110 individuals for reproduction, meat and fattening traits, respectively. The level of correlation (r) between EBV and GEBV scores varied from +0.44 to +0.55 for meat and fatness traits, and from +0.75 to +0.77 for reproduction traits. Average breeding value (EBV) of group selected on genomic evaluation basis exceeded the group selected on parental average estimates by 22, 24 and 66% for muscle depth, days to 100 kg and backfat thickness over 6–7 rib, respectively. Prediction based on SNP markers data and parental estimates showed a significant increase in the reliability of low heritable reproduction traits (about 40%), which is equivalent to including information about 10 additional descendants for sows and 20 additional descendants for boars in the evaluation dataset.

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

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–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.

An amendment to this paper has been published and can be accessed via the original article.