Population-Genetic Structure of Local Sheep (Ovis aries) Breeds from Altai, Tuva, and Mongolia Based on Microsatellite Markers G. R. Svishcheva, A. P. Todoshev, S. A. Beketov, M. T. Semina, Yu. A. Stolpovsky Russian Journal of Genetics, 2026 Abstract 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%) is concentrated within breeds, which is typical for local indigenous populations. Analysis of genetic distances (FST) and Discriminant Analysis of Principal Components (DAPC) demonstrated significant differentiation between the breeds studied, allowing for the identification of genetic clusters corresponding to their geographic origin. The results highlight substantial within-population genetic diversity and the unique genetic status of each of the breeds studied, underscoring their value as objects for the conservation of genetic resources and for further breeding.
Mitochondrial Genome Variability and Demographic History of Domesticated and Wild Reindeer (Rangifer tarandus) M. T. Semina, E. A. Konorov, K. A. Layshev, V. N. Voronkova, Yu. A. Stolpovsky Russian Journal of Genetics, 2026 Abstract 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.
Monitoring the Genetic Structure of Domesticated Reindeer (Rangifer tarandus L.): Mainland and Island Populations of the Northeast of Russia S. N. Kashtanov, E. S. Zakharov, M. T. Semina, A. A. Onokhov, V. V. Baranyk, P. A. Filimonov, J. Wei, V. V. Dodokhov, V. E. Kolodeznikov, N. V. Vinokurov, O. I. Zakharova, G. V. Tymnenkav, K. A. Layshev, Yu. A. Stolpovsky Russian Journal of Genetics, 2025 Abstract 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.
DQA1 Gene Variability in Wild and Domestic Reindeer (Rangifer tarandus) of the Asian Part of Russia E. A. Konorov, K. A. Kurbakov, M. T. Semina, V. N. Voronkova, A. A. Onokhov, K. A. Layshev Russian Journal of Genetics, 2025 Abstract Modern tendencies to intensification of breeding of domestic farm animals, including reindeer, necessitate a detailed study of genetic variability in candidate genes associated with meat productivity. At present, the primary task is to search for molecular genetic markers for identification and selection of individuals with desired characteristics. One such potential candidate gene is the DQA1 gene. It is hypothesized that individual genes of the immune system may influence the growth performance of animals. Variability in the DQA1 gene region has been associated with cattle size and beef production in many studies. Principal component analysis on DQA1 variability united wild and domestic reindeer in Yakutia, which implies gene flow between local breeds of domesticated reindeer and wild populations and the formation of similar adaptation mechanisms. However, significant differences were found between wild and Evenki reindeer of Amur oblast, which may reflect the influence of domestication processes on the Evenki breed.
Analysis of the Calpastatin (CAST) and Androgen Receptor (AR) Gene Polymorphisms as Biomarkers for Meat Quality Traits in Reindeer Rangifer tarandus E. A. Konorov, K. A. Kurbakov, M. T. Semina, Yu. A. Stolpovsky, K. A. Layshev Russian Journal of Genetics, 2024 Abstract— 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.
Artificial Intelligence and Classical Methods in Animal Genetics and Breeding A. D. Soloshenkov, E. A. Soloshenkova, M. T. Semina, N. N. Spasskaya, V. N. Voronkova, Y. A. Stolpovky Russian Journal of Genetics, 2024 Abstract— Basic methods of population genetics and animal breeding and mathematical methods of machine learning used in animal breeding are analyzed. CatBoost library models were trained on the example of two domesticated species—horse (Equus caballus) and reindeer (Rangifer tarandus). Data from microsatellite panels of loci 16 and 17, respectively, were used to train the model using data on domesticated and wild reindeer, European and Russian horse breeds. The standard indicators (Accuracy, Precision, Recall, and F1) were calculated, and confusion matrices were constructed to assess the success of the model. New possibilities for identifying animal breed affiliation are shown.
Genetic Structure of Domesticated Reindeer (Rangifer tarandus) Populations in the Central Siberian Plateau and Adjacent Areas S. N. Kashtanov, E. S. Zakharov, M. T. Semina, N. V. Vinokurov, A. V. Vinokurov, A. A. Onokhov, P. A. Filimonov, E. A. Soloshenkova, A. A. Yuzhakov, O. K. Sergeeva, M. M. Somova, K. A. Layshev, Yu. A. Stolpovsky Russian Journal of Genetics, 2024 Abstract On the basis of 16 microsatellite markers, the genetic structure of the domesticated reindeer of two breeds, Evenk and Even, bred on the territory of the Central Siberian Plateau and adjacent territories, was studied. Genetic flows between modern domesticated reindeer populations of the two breeds were analyzed. Significant differences were found between the Evenk taiga and Even breeds of domestic deer. Using a historical sample from the middle of the last century, a high degree of stability in time of the gene pool of domesticated populations was revealed. It has been established that genetic flows between wild and domesticated forms in the study area are insignificant. Statistically significant genetic differences between wild and domesticated reindeer populations are shown.
Identification and worldwide populational distribution of personality-related candidate genes in goat (Capra Hircus) using a translational approach Aleksei Piskunov, Valeriya Voronkova, Elina Nikolaeva, Magdalena Semina, Yuri Stolpovsky Bio Web of Conferences, 2023 Biodiversity of farm animals is a highly valuable resource for sustainable development of humanity especially when faced environmental and economic changes. Intensification of farm industry destabilizes animal’s genetic diversity. Farm animals’ behaviour shaped during the long period off domestication might be of the specific risk being poorly investigated due to the difficulties in measuring behavioural traits. Here we use translational approach by identifying goat orthologues of human personality-related genes as in the recent study of Tamu Yokomori et al. (2023) that dealt with racing horses’ personality. We extended this approach by using a huge dataset covering goat populations through all the World, that allowed to investigate populational distribution of alleles in personality related genes. We identified 41 SPN in 18 genes that were previously shown to be polymorphic both in human and horses in the study of Yokomori et al. Many of them showed highly asymmetric distribution that suggest an important role for these genes in goat evolution and domestication.
