Long-term studies, devoted to investigation of beta-casein (CSN2) and kappa-casein (CSN3) in cattle, indicate the effect of polymorphism in these genes on milk properties. The nomenclature describing 11 allelic variants for β-casein and 13 allelic variants for kappa-casein is the most popular. Most authors are focused only on markers defining the A1 and A2 alleles for beta-casein and A and B alleles for kappa-casein. At the same time, several studies report associations between less popular allelic variants (for example, the B, F, and I alleles of beta-casein and E allele of kappa-casein) and technological properties of milk and quality of dairy products. Thus, an association of the beta-casein B allele with a decrease in curdling time was noted, while the kappa-casein E and G alleles are characterized by unfavorable effect on milk coagulation. Thus, the aim of the present study was to develop a targeted next-generation sequencing (NGS) panel for cattle genotyping for expanded list of CSN2 and CSN3 markers. During the study, the primers and operating conditions for the test system were selected, and the protocols were optimized. A total of 332 individuals from ten cattle populations of dairy, beef, and dairy–beef directions were genotyped. Verification of the results obtained was conducted using Sanger sequencing (n = 7). The allelic variants typical for Grey Ukrainian, crossbred Altai cattle and a number of factory breeds were described. The created test system can be used for genetic and breeding work, including for the formation of a herd of cows with A2 milk, as well as selection of individuals with high milk suitability for cheese production. The obtained test system can be also used to search for new genotype–phenotype associations.

The aim of this study was to assess the genetic diversity and population structure of eight indigenous sheep (Ovis aries) breeds from Altai, Tuva, and Mongolia. DNA samples from 327 individuals were used as material. Their genetic diversity was evaluated using 12 microsatellite markers. A total of 187 alleles were identified in the sample. The number of alleles per locus ranged from 7 to 22, confirming a high level of polymorphism. Analysis of Molecular Variance (AMOVA) revealed that the majority of genetic diversity (>90

The modern challenges faced by global animal husbandry necessitate a shift from classical breeding approaches, which rely solely on genotype, toward more integrative models that account for gene–environment interactions. Epigenetics—the study of heritable changes in gene expression that do not involve alterations in the DNA sequence—provides a powerful framework for understanding these interactions. This review systematizes current knowledge on the roles of major epigenetic mechanisms, including DNA methylation, histone modifications, and regulation by noncoding RNAs, in shaping economically important traits in farm animals. The impact of epigenetic regulation on meat and milk productivity, product quality, reproductive performance, and fertility is examined in detail. Particular attention is devoted to the epigenetic foundations of adaptation to such stress factors as housing conditions, temperature regimes, nutrition, and extreme environments, including high-altitude hypoxia. The phenomenon of transgenerational epigenetic inheritance—whereby environmentally induced epigenetic marks can be transmitted to subsequent generations—is analyzed as a promising avenue for the long-term improvement of livestock breeds. Moreover, modern technological approaches to epigenomic research, from whole-genome bisulfite sequencing (WGBS) to single-cell chromatin accessibility assays (scATAC-seq), and their applications in animal science are discussed. Finally, the review highlights prospects and opportunities for the implementation of epigenomic selection and epigenome-editing technologies (CRISPR/dCas9) as next-generation tools for targeted enhancement of productivity, health, and resilience in farm animals.

On the basis of whole-genome sequencing of mitochondrial DNA and comparative analysis of sequences from domesticated and wild reindeer, the highest level of nucleotide diversity was detected in wild populations. In total, 1551 polymorphic sites were identified, of which 405 were informative. The most conserved regions included the 12S and 16S rRNA genes (π < 0.002) as well as the segment between ND2 and COI containing tRNA genes (π < 0.001). The most variable regions were ND1 (π = 0.001–0.003), ND2 (π = 0.001–0.003), and ND5 (π > 0.003 except in wild reindeer from Amur oblast), which correlate with adaptation to cold environments. Differences in genetic diversity levels between domesticated and wild reindeer populations reflect both demographic processes and possible selective pressure acting on specific regions of the mitochondrial genome. Reconstruction of demographic history revealed distinct effective population size dynamics among reindeer breeds. The Nenets breed exhibited a pronounced population expansion about 3000 years ago. No comparable effective size increase was observed in the Chukotka and Evenk breeds. Fu and Li’s D test showed contrasting patterns between domesticated and wild samples: domesticated reindeer displayed localized signals of deviation, consistent with artificial selection and restricted herd sizes, whereas wild populations demonstrated more extended and pronounced patterns indicative of demographic processes and natural selection. Modern reindeer mitogenomes retain ancient haplotypes, and several regions appear to have undergone selection, particularly ND5, Cytb, and ATP6. The Nenets, Evenk, and Chukotka breeds do not form distinct clades, contrary to expectations, considering their geographically distant ranges; instead, they comprise extensive mixed branches sharing similar or closely related haplotypes.

The gene pools of two local horse breeds from the Altai Republic were studied. Specimens from Altai breed and the developed on its basis Novoaltai breed were collected during expeditions from 2011 to 2024. The population structure of these breeds was analyzed in comparison with Russian and European local horse breeds. Close relationships between Altai horses and the breeds of Mongolian origin were revealed. Phylogenetic analysis was conducted, and the frequencies of different coat colors in the Altai horse population were calculated. In addition to the basic chestnut, black, and bay coat colors, a large number of diluted and pinto colors were identified. It was demonstrated that the Altai horse had similar origin with Tuvinian and Mongolian horses, as supported by dendrogram data and Bayesian analysis in the STRUCTURE software program.

Domestication profoundly shapes the evolutionary trajectories of both humans and animals. Despite significant scientific interest, the genetic underpinnings of domestication, particularly those related to behavior, remain elusive. This paradox may be reconciled by considering that behavior-associated genes have already been identified but categorized exclusively to other functional groups. Our investigation into this hypothesis utilized goat genome and human brain transcriptome data, focusing on the pigmentation gene KITLG due to its frequent association with domestication. Through analysis of interpopulation covariation between KITLG and candidate genes in the domestic goat genome (Capra hircus), we identified eight genes evolutionarily linked with KITLG. These genes were divided into three functional categories: (i) regulation of the glucocorticoid (GC) signal, (ii) initiation, and (iii) control of structural neuroplasticity. In the human brain, the regional expression patterns of the corresponding transcripts were complementary and most pronounced in areas associated with social interaction. We propose that a mutation in KITLG may decrease the activation threshold for GC-mediated neuroplasticity in these regions, enhancing the processing of social stimuli. The association of this allele with spotted coat patterns likely facilitated its selection, with the uniqueness of the pattern promoting selective social contacts. Consequently, the genomes of domesticated animals is probably more profoundly influenced by behavioral functions than previously believed. Further research could unveil novel functional attributes of the nervous systems in both animals and humans.

This study investigates the relationships between hair cortisol levels, behavioral traits, and morphological characteristics in domestic goats (Capra hircus). Statistically significant correlations were found between hair cortisol concentration and coat color parameters, including pigmentation. A link between hair cortisol levels and stress resilience was confirmed using quantitative behavior assessment (QBA). The results of this study may be used in the development of noninvasive methods for assessing stress resilience in goats for livestock management purposes.

Using 14 microsatellite markers (BM1824, BM2113, CSRM60, CSSM66, ETH3, ETH10, ETH225, ILSTS006, INRA023, SPS115, TGLA53, TGLA122, TGLA126, TGLA227), samples of Ukrainian Grey cattle herds of the Ivanov Institute Askania-Nova (Kherson oblast) (n = 101) and experimental farm of Cherga (Altai Republic) (n = 41). When considering Wright’s F-statistics for the studied loci, the value FIS = –0.0285 indicates an excess of heterozygous genotypes in the population of Ukrainian Grey cattle, with a low probability of encountering alleles of the common ancestor FIT = 0.1161, and the level FST = 0.1394 indicates an average divergence of subpopulations, the largest contribution to which is contributed by the Eth3 locus. At the same time, the number of detected polymorphic loci of 95.64

Biobanks play an important role in population genetic studies of animals as a valuable resource for ex situ conservation of genetic diversity and research in evolution, zoology, ecology, and genetics. One of the main objectives of biobanks is to preserve samples of genetic material from different animal species, thus preserving information on genetic diversity and conserving in situ populations. This is particularly important for rare and endangered species, animal breeds, and plant varieties, where genetic diversity may be declining because of population loss. Biobanks enable the exchange of specimens and data, which plays an important role in the study of the evolution and origins of different species, helping scientists to investigate the processes of divergence and adaptation. They also serve as a source for work in the study of genetic diseases, behavioral traits, and interaction of species in ecosystems. Biobanks provide the basis for various types of genetic research, such as genome sequencing, phylogeny, DNA variability analysis, and functional genomics, which in turn provide the opportunity to develop new methods for detection of genetic diseases, genomic selection, and conservation and restoration of animal populations. Biobanking thus plays an important role in population genetic research of animals, providing scientists with access to a wide range of genetic information that is essential for understanding and conserving our planet’s biodiversity. The issue of environmentally sound and efficient storage of biomaterial is more relevant than ever. In this review, we consider different approaches to the organization of a bank of biomaterials and DNA in the field of population genetic studies of animals and features of their collection, transport, processing, and storage.

The European roe deer (Capreolus capreolus) is the most numerous species (over 6 million individuals) of the deer family (Сervidae) and is found throughout the European continent. In addition, the European roe deer is one of the most common species in the European part of the Russian Federation. Despite the fact that the range of the European roe deer covers an area of 7.2 million km2, it is quite fragmented. At the same time, the decisive role in the formation of the gene pool of the European roe deer was played by glaciers, which contributed to the geographical isolation of populations, postglacial recolonization, and in recent times it was anthropogenic impact. Thus, in the late 19th and early 20th centuries, as a result of hunting and human activity, there was a signifi cant reduction in the number of roe deer, but later there was an artificial resettlement of the European roe deer to its former habitats with a partial reintroduction of a closely related species as the Siberian roe deer (Capreolus pygargus). In the presented work microsatellite analysis was used and we attempted to provide a population-genetic characteristic of three subpopulations of the European roe deer: the Kaliningrad and Bryansk regions of the Russian Federation, and the Minsk region of the Republic of Belarus, and to determine their relationships. It was established according to the results of a comparative analysis of the genetic diversity of natural populations of roe deer from the Kaliningrad, Bryansk regions of Russia, and the Minsk region of the Republic of Belarus that the considered subpopulations of the European roe deer are characterized by close genetic similarity, an insignificant level of allelic and genetic diversity, a slight deficit of heterozygotes and a decrease in the level of genetic variability in the direction from East to West relative to their geographic localization.

This study gains insight into the population–genetic structure of Askanian Karakul sheep of the Askania-Nova Ivanov Research Institute of Livestock Husbandry and Plant Growing of Steppe Regions using 12 STR-markers (McM042, INRA006, McM527, ETH152, CSRD247, OarFCB20, INRA172, INRA063, MAF065, MAF214, INRA005, and INRA023). A total of 66 animals have been genotyped. According to the results of microsatellite analysis of Askanian Karakul sheep, it has been established that the considered population is characterized by the absence of inbreeding FIS = –0.006, polymorphism indices P = 76.26

Using 12 STR- markers (MCM042, INRA006, MCM527, ETH152, CSRD247, OARFCB20, INRA172, INRA063, MAF065, MAF214, INRA005, INRA023), the population genetic structure of Askania Karakul sheep of the Ivanov research institute of livestock husbandry and plant growing of steppe regions "Askania- Nova", was studied. A total of 66 animals were genotyped. According to the results of microsatellite analysis of Askania Karakul sheep, it was established that the population under consideration is characterized by the absence of inbreeding F = − 0.006 , polymorphism indices P = 76.26% and a sufficiently high level of genetic diversity H = 0.726 . The revealed intrapopulation genetic heterogeneity of Askania Karakul sheep, expressed in segmentation on embryonic clusters, is the progress of the conducted interline crossings. The obtained results can be used in the development of selection and breeding programs for breeding Askania Karakul sheep.

A comparative analysis of the genetic structure of domesticated reindeer populations of the Chukotka and Koryak highlands (northeastern edge of the species range) was performed using a panel of 16 microsatellite loci. The data of statistical analysis show a high level of consolidation of the studied Chukotka reindeer breed and a high degree of differentiation with the breeds of the western and central parts of the range. One of the important objectives of the study was to monitor the genetic structure of the populations of the Chukotka and Evenki reindeer breeds, on the basis of a comparative analysis of samples from populations of the mid-20th century and modern populations. The results of research indicate a high level of stability of the main indicators of the genetic structure of the species.

Goats were the first animals to undergo domestication. Despite the fact that they are bred across much of the world, they have not yet been widely used as a research model. However, goats have remarkable cognitive abilities and complex and varied social behavior, and owing to their size and low maintenance requirements, they may serve as a promising model for studying neurological conditions, especially neurodegenerative diseases. This review focuses on current research into the central nervous system of goats, as well as their behavior and cognitive abilities.

Domestic goats remain important as farm animals, whose health influences the quality and yield of livestock products. Animal health depends on housing conditions and nutrition, including effective digestion, which is significantly influenced by microorganisms inhabiting the gastrointestinal tract. Ruminants, such as goats, host a unique community of bacteria that varies depending on age and region of residence. A major challenge is identifying the normal members of the goat gut microbiome and distinguishing these from members that may vary in goats without causing disease. This study synthesizes available published data to address this issue.

Comparative genotyping of a population of zeboid cattle (Bos taurus × Bos indicus) and eight populations of B. taurus breeds, including six domestic (Нolmogorskaya, Yaroslavskaya, Red Gorbatovskaya, Kostromskaya, Tagil’skaya, Gray Ukrainian) and two transboundary European breeds (Holstein and Brown Swiss). A total of 562 individuals were examined. Based on the results of the STR analysis, it was found that all population samples of B. taurus were characterized by an average allelic diversity AR = 4.87–6.7 and a fairly high level of genetic variability HE = 0.68–0.76 with a slight predominance of random matings FIS = –0.1... 0.0. In zeboid cattle, the corresponding indicators were AR = 5.96, HE = 0.72 and FIS = –0.0278. At the same time, differences in the genetic structure of the B. taurus breeds under consideration were largely determined by population-demographic fluctuations, and the genetic and phenotypic heterogeneity detected in the population of zeboid cattle was determined by a decrease in the effect of artificial selection.

The genetic potential of ungulates of the Arctic zone of the Russian Federation is rich and diverse, but requires modern research. The use of genetic systems makes it possible to study the genome of animals, determine the state of the genetic diversity of the species, suggest reasonable ways to maintain the level of heterozygosity in domesticated animals, purposefully obtain individuals that are necessary for humans. The analysis of the above-described gene pools of their structure is interesting both for modern breeding and environmental genetics, and may be in demand in the future when planning the development of animal husbandry in the Arctic zone for decades to come. The unique adaptive capabilities of animals to the harsh conditions of the Far North open up wide opportunities for their rational use. Reindeer, musk ox and snow sheep are the most important components of high-latitude ecosystems, in which other ungulate species can practically not live, so they are of great scientific and practical value in preserving agro-diversity in the Arctic zone of the Russian Federation.

The problem of preserving the genetic resources of farm animals and breed diversity is one of the priorities in the global livestock industry. As of September 1, 2023, the State Breeding Register of the Russian Federation registered 83 gene pool farms for breeding 63 breeds of 16 species of farm animals, of which 42 are domestic breeds bred in 23 of the 89 constituents of the Russian Federation. As a consequence, it requires the creation of a national system for preserving the gene pool of farm animals based on legislative, economic and biological principles for them. The main centers of breeds formation and the current state of the local breeds in the Russian Federation have been examined in detail in the article. Ways to improve the legislative framework in the fi eld of preserving breed diversity and economic stimulation of gene pool farms were proposed. At the same time, the optimal approach for the selection of small in number local breeds is the use of traditional evaluation of their breeding value together with genotyping for a number of specific genetic markers. The authors have developed appropriate proposals for the conservation of the gene pool of national breeds of farm animals such as: 1) the adoption of the Federal Law on the Conservation of Agrobiodiversity and the creation of an Advisory Council under the Ministry of Agriculture of the Russian Federation and the Russian Academy of Sciences for the conservation of gene pool breeds of animals; 2) the formation of a network of gene pool farms for the main types of farm animals, with their inventory at the genetic level, the creation of information bases and the Federal Bank for the cryopreservation of semen, embryos and DNA of animals of gene pool breeds with budgetary fi nancing of gene pool livestock.

Human cytochrome P450 2F1, as well as its ortholog 2F3 in domestic goat, is considered to be a rather unusual enzyme. The only type of reaction it catalyzes has been described: the conversion of skatole, a product of anaerobic tryptophan metabolism, into a pulmonary toxin. Endogenous substrates of CYP2F are unknown, and although more than 30 years have passed since the discovery of the enzyme, its biological role remains unclear. We hypothesized that the physiological functions of CYP2F can be specifically implemented in the brain, remaining previously unnoticed owing to the high compartmentalization of the organ. Using open data, we studied the covariation of the expression of CYP2F1 and genes for behavioral traits: in the human brain, as well as the polymorphism of their orthologs and CYP2F3 in 180 populations of domestic goats (Capra hircus). Two SNPs were found in the CYP2F3 gene, one of which had pronounced traces of selection, and the frequency of homozygotes increased with geographic distance from the center of domestication. Expression of CYP2F1 mRNA in the human brain also had regional specificity. In both species, factor analysis revealed the relationship between CYP2F1/3 and a number of genes regulating behavior: the serotonin transporter SLC6A4 and its receptor HTR2A3, the ABCB1 transporter, the purine receptor P2RX7, the GABA receptor GABRA4, the circadian rhythm regulator PER3, and T-cadherin CDH13. Thus, analysis of the genomic data of the domestic goat and human transcriptomic data revealed the evolutionary and functional relationships of CYP2F cytochromes and neurochemical systems for regulating behavior. This evidence of the cerebral function of the enzyme is indirect, since it is based on correlation analysis, but indicates the promise of further search in this direction.

Marker-assisted selection for improving reindeer meat production is at the early stages of development, which requires analysis of variation within the candidate genes for meat production. The calpastatin and androgen receptor genes were chosen as such genes to study their variability in reindeer. In different domesticated animal species, polymorphisms and indels in the androgen receptor gene were associated with growth and weight characteristics. Based on the results from many studies, sequence variation in the calpastatin CAST gene region was associated with meat quality and meat production of livestock. Principal component analysis of CAST variability grouped wild and domestic deer from Yakutia, as well as wild and domestic deer from Amur oblast, which implies gene flow between local breeds of domesticated deer and wild populations. At the same time, in the case of three microsatellite loci found in the present study in the intron of the androgen receptor gene, principal component analysis separated wild and domestic deer.