Vol 60, No 7 (2024)

The article analyses basic methods of population genetics and animal breeding, as well as mathematical methods of machine learning used in animal breeding. The training of cat boost library models was carried out on the example of two domesticated species – domestic horse (Equus caballus) and reindeer (Rangifer tarandus). Data from microsatellite panels of 16 and 17 loci, 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 to determine the success of the model. Confusion matrices were constructed. New possibilities of identification of animal breed affiliation were shown.

Reparative chromatin assembly is an important step in maintaining genome stability. The correct assembly of chromatin is provided by histone chaperones, whose dysfunction can lead to the development of various forms of cancer and a number of hereditary diseases in humans. The effect of remodeling factors completes chromatin repair. The yeast chromatin remodeling complex INO80 plays an important role in chromatin architecture. We used induced mutagenesis and real-time PCR to study the role of INO80 in chromatin repair assembly. In double mutants ies5Δ hsm3Δ(hif1Δ), defects in the structure of nucleosomes caused by mutations hsm3Δ and hif1Δ lead to hypersensitivity of cells to UV radiation and the disappearance of hsm3- and hif1-specific mutagenesis. Double mutants carrying the nhp10Δ mutation and hsm3Δ or hif1Δ mutations were indistinguishable from a single mutant in terms of the lethal effect of UV irradiation, however, the high UV-induced mutagenesis characteristic of all mutations disappeared. Thus, we found that mutations in the genes controlling the subunits of the INO80 complex can exhibit strong interactions with mutations in histone chaperone genes. We have confirmed the hypothesis that the Him1 protein performs a chaperone function in the process of reparative chromatin assembly.

We describe the results of analysis of genetic structure and spatial autocorrelation in the populations of grey wolf (Canis lupus Linnaeus, 1758) on the territory of the Russian Federation and the Republic of Kazakhstan, based on 20 autosomal microsatellite markers. With the use of molecular markers, we uncovered hidden genealogical patterns reaching as far as 700–1600 km and having the most pronounced effect on distances up to 150 km. Our research has shown that identification and exclusion of closely related genotypes has limited effect on the results of analysis of intrapopulation genetic diversity. Meanwhile, such procedure is recommended for researching population structure, as it allows for streamlining some statistical approaches. Results of our work demonstrate integral effect of natal migration, working against the differentiation effect of philopatry. Finally, we also show that the exclusion of closely related individuals can lead to underestimation of values of genetic distances between populations.

Based on the analysis of a fragment of the cytochrome b (cytb) gene of mitochondrial DNA (mtDNA), the genetic diversity of the little ground squirrel Spermophilus pygmaeus Pallas, 1779 of the Central and Eastern Caucasus was studied. Phylogenetic analysis revealed the existence of two clusters A and B within the western clade of S. pygmaeus 2. Cluster A is formed by haplotypes of ground squirrels from the Eastern Caucasus and the right bank of the river. Volga (Ermakov et al., 2023), and B – only haplotypes of Central Caucasian animals. The distance between clusters A and B reaches 1.3%. The relatively isolated position on the phylogenetic tree of the ground squirrel population of the Central Caucasus, the absence of identical haplotypes in Central and East Caucasian animals, and the distances obtained indicate genetic heterogeneity of the ground squirrel in the North Caucasus. A decrease in haplotypic and nucleotide variability was noted in the Central Caucasian populations of the lesser gopher as compared to those from the Eastern Caucasus, which in general indicates the low viability of S. pygmaeus inhabiting the mountains of the Central Caucasus.

Atrial fibrillation (AF) is one of the most frequent cardiac arrhythmias and leads to heart failure. Excessive sympathetic activity aggravates arrhythmogenic processes at the cellular and tissue levels. Hypersympathicotonia leads to desensitization of β1-adrenoreceptors (β1-AR), negative regulation develops until the synthesis of new receptors stops. Desensitization processes may be indirectly reflected in an increase or decrease in the expression of the ADRB1 gene encoding β1-AR. The level of relative expression of the β1-AP ADRB1 gene in leukocytes of 52 patients with different forms of AF was analyzed in dynamics: before treatment, 3 days, 3 and 12 months after ablation. Before ablation, expression was reduced in patients with persistent AF compared to groups with other forms of AF (р = 0.026). The study of dynamics revealed a significant decrease in the level of expression in patients with paroxysmal AF at the point of 3 days compared with the level before ablation (p = 0.003), with a further increase in values to the baseline at the point of 12 months (p = 0.021) relative to the point of 3 days. In patients with persistent AF, the expression level significantly increased 3 months after ablation (p = 0.046) compared to the level before surgery. Patients with long-term persistent AF after ablation had a tendency to decrease expression.

When combining imputed and sequenced data in a single gene-based association analysis, the problem of reconstructing genetic correlation matrices arises. It is related to the fact that for a gene, we know the correlations between genotypes of all imputed variants and the correlations between genotypes of all sequenced variants, but we do not know the correlations between genotypes of variants, one of which is imputed and the other is sequenced. To recover these correlations, we propose an efficient method based on maximising the determinant of the matrix. This method has a number of useful properties and has an analytical solution for our task. Approbation of the proposed method was performed by comparing reconstructed and real correlation matrices constructed on individual genotypes from the UK biobank. Comparison of the results of gene-based association analysis performed by the SKAT, BT and PCA methods on reconstructed and real matrices, using modelled summary statistics and calculated summary statistics on real phenotypes, showed high quality of reconstruction and robustness of the method to different gene structures.

We found hypomethylation of 5 CpG sites in the 5’region of TBX20 gene (7p14.2) in the tissues of atherosclerotic aortic plaque compared to dilated part of aorta in patients with ascending aortic aneurysm. Using GEO database, we found that the DNA methylation level in the chr7:35253926-35262250 region changes in opposite direction in aortic dissection and aortic atherosclerosis. The results suggest an alteration in epigenetic regulation both in aortic atherosclerosis andaortic aneurysm.

Flax seeds are the richest plant source of lignans, which prevent the development of many diseases. Secoisolariciresinol diglucoside (SDG) is the predominant lignan in seeds of the cultivated species Linum usitatissimum. We sequenced transcriptomes of flax seeds at five developmental stages for 8 varieties differing in lignan content grown under three different conditions and evaluated the expression of PLR1 and UGT74S1 genes, which play a key role in SDG synthesis. The co-expression of PLR1 and UGT74S1 genes was detected, and the expression level of these genes was observed to change tens and hundreds of times during seed development, confirming their role in SDG synthesis in flax seeds. Low temperature (16 °С) and abundant watering resulted in a shift of the maximum expression level of both genes to later dates (14th day after flowering) compared to poor watering and high temperature (24 °С) and optimal conditions (20 °С) (7th day after flowering). Meanwhile, the expression level of PLR1 and UGT74S1 genes was lower under high temperature and poor watering than under optimal conditions. No association was found between lignan content in seeds of the studied flax varieties and the expression level of PLR1 and UGT74S1 genes. Our results provide important information on the contribution of genotype and environment to the expression of key genes of SDG synthesis, which is also necessary for the development of optimal approaches to obtain lignan-rich flax seeds.