Abstract: Traits associated with body weight at different ages correlate strongly with the productivity, health, and longevity of cattle. At the same time, body weight is a trait with high heritability in cattle. Genome-wide association study can identify genetic variants and potential candidate genes that control the trait of interest. However, there are practically no reviews of genome-wide association studies of body weight traits in dairy cattle breeds. The aim of the review was to identify potential candidate genes associated with body weight traits in dairy cattle based on genome-wide association studies. Literature search was conducted using the query “Cattle AND Dairy AND Weight AND Genome-wide AND Association AND Study”. The criterion for inclusion in the review was the identification of at least one candidate gene significantly associated with a trait associated with body weight in dairy cattle. A web tool Venn was used to calculate the number of intersections between lists of candidate genes. Gene/protein interactions were analyzed using the GeneMANIA web resource. Overrepresented gene ontology terms were identified using the DAVID web tool. Twenty genes were identified that were associated in one publication with different weight traits, or with the same trait, but in several publications. We identified 20 genes that were associated in one publication with different weight traits, or with the same trait but in several publications. The genes TNNT3, DYRK4, AKAP3, GALNT8, NDUFA9, and KCNA1 had the highest number of intersections among them. Shared biochemical pathways and protein-protein interactions have been identified between TNNT3–TNNI2 and FGF6–FGF23 gene pairs. Shared protein domains were found in the pairs TNNT3–TNNI2, FGF6–FGF23 and KCNA1–KCNA6. Functional annotation of the above-mentioned list of 20 genes revealed overrepresented gene ontology terms, indicating the enrichment of the list with genes encoding troponin complex proteins (TNNT3 and TNNI2), proteins of delayed rectifier potassium channels (KCNA1 and KCNA6), as well as fibroblast growth factor receptor proteins (FGF6 and FGF23).
Key words: cattle; dairy breed; body weight; genome-wide association study; candidate gene
For citation: Yudin N.S., Igoshin A.V., Larkin D.M. Weight-associated candidate genes in dairy cattle. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):5-11. doi 10.18699/letvjgb-2025-11-02 (in Russian)
Funding: This study was supported by a budget project No. FWNR-2022-0039.

Abstract: The aim of this work is to identify polymorphic loci in Daphnia genomes using genome sequence analysis and experimental analysis of real accessions of samples collected in nature. We use primers predicted by an algorithm for DNA amplification from Daphnia samples and capillary electrophoresis to detect polymorphic loci. This was done to detect polymorphic loci in a single experiment, when the presence of polymorphic loci with a frequency sufficient for genetic studies is detected as the appearance of multiple peaks on the electrophoregram. Thus, we evaluate the effectiveness of the capillary electrophoresis method and refine population parameters, including the proportion of sexual reproduction and the effective population size. Studying polymorphic loci becomes especially relevant in the context of climate change and anthropogenic impacts on ecosystems, as these factors can significantly affect genetic diversity and adaptation in populations. Polymorphic loci can serve as indicators of genetic stability and the ability of species to adapt to changing environmental conditions. In the face of global climate change and increasing anthropogenic impacts, such as pollution, urbanization, and landscape changes, populations face new challenges that require rapid adaptation. Polymorphic loci, due to their high variability, can provide valuable information about the genetic structure of populations and their potential for adaptation. In the context of our research, studying polymorphic loci in Daphnia becomes particularly important, given their ecological role and sensitivity to environmental changes. Daphnia, as key components of freshwater ecosystems, can serve as model organisms for studying genetic adaptation to climate change and anthropogenic impacts. Understanding polymorphic loci in Daphnia can provide valuable data for assessing genetic stability and adaptive potential in these populations, which is particularly important in the face of rapidly changing environmental conditions.
Key words: polymorphic loci; capillary electrophoresis; agent-based modeling; microsatellites; Daphnia; genetic diversity; adaptation; climate change; anthropogenic impacts
For citation: Poroshina A.A., Sherbakov D.Yu. Experimental analysis of polymorphic microsatellite loci in Cladocera: mixed breeding strategy and population dynamics. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):12-16. doi 10.18699/letvjgb-2025-11-03
Funding: The study was carried out within the framework of the state budget theme No. 0279-2021-0010 “Genetics of Baikal organism communities: genofond structure, conservation strategies”.

Abstract: L.P. Osipova’s life in science lasted half a century and was closely connected with the establishment, organization and development of complex and large-scale studies of the genetic structure of human populations in Northern Eurasia. Her research was initiated and conducted in various areas of human population and evolutionary genetics, molecular genetics and immunogenetics, demography and biomedicine of indigenous peoples; the mechanisms of human adaptation to environmental factors were studied, as well as the impact of technogenic factors on the environment and human health. The totality of the results of large-scale genomic studies of international consortiums with the participation of L.P. Osipova’s team made it possible to reconstruct ancestral genomes and recreate human migration routes in the historical past.
Key words: population genetics; genetic demography; genetic variation; adaptation; indigenous peoples; Northern Eurasia; ethnogenetics; L.P. Osipova
For citation: Zakharov I.K., Posukh O.L. Half a century of population genetics of the peoples of Siberia: research by Lyudmila P. Osipova. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):17-28. doi 10.18699/ letvjgb-2025-11-04 (in Russian)

Abstract: Sexual polymorphism of a gynodioecious plant Geranium sylvaticum L. were investigated in meadow and forest phytocoenoses in subtaiga of the Ob right riverside (surroundings of Novosibirsk). In the populations of G. sylvaticum depending on the combination of bisexual, pistillate and intermediate flowers of one individual, three sexual phenotypes are distinguished: hermaphrodite, female and gynomonoecious. In hermaphrodite phenotypes, flowers with 5 staminodes and 5 normal stamens prevailed among intermediate flowers. Gynomonoecious phenotypes are presented in two variants: initially a female individual with single intermediate flowers and initially hermaphrodite individuals with several pistillate flowers. Intermediate flowers are few in number and are formed in the upper and/or lower part of the inflorescence, at the beginning and/or end of flowering plants. Females produce approximately 2 times fewer flowers and 1.6 times fewer fruits than hermaphrodite phenotypes; the differences are statistically significant (p < 0.05); however, fruit formation per flower in females is 1.4 times higher than in hermaphrodites. In low-light conditions, hermaphrodites with intermediate flowers occur 2.2 times more than in high-light conditions; the ratio of two forms of hermaphrodites (with and without intermediate flowers) between meadow and forest phytocenoses differs statistically significantly (p = 0.0247 < 0.05). At a high level of light, hermaphrodites produce 1.6 times more fruits than at a low level of light; the differences are statistically significant (p < 0.05). A low proportion of G. sylvaticum females was detected in both meadow and forest communities: 7.1 and 4.7 %, respectively. Gynomonoecious phenotypes in cenopulations are rarely observed only once: 0.8–1.6 %. G. sylvaticum is characterized by a relatively low frequency of females and gynomonoecious phenotypes and a noticeable participation of hermaphrodites with intermediate flowers in the European and Asian parts of the species’ range. Key words: Geranium sylvaticum L.; gynodioecy; gynomonoecy; phenotype; sex ratio For citation: Gordeeva N.I. Sexual polymorphism of a gynodioecious plant Geranium sylvaticum (Geraniaceae). Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):29-35. doi 10.18699/letvjgb-2025-11-05 (in Russian) Funding: The work was carried out within the framework of the State task of the Central Siberian Botanical Garden, SB RAS No. АААА-А21-121011290026-9.[/expand]

Molecular biology

AbstractAbstract: Initiation of transcription by RNA polymerase II from TATA-containing promoters requires the assembly of a transcription complex, which begins with the interaction of TBP (TATA binding protein) or TFIID, of which it is a part, with the TATA box and the addition of other basal transcription factors to them. A large number of studies have been devoted to studying the interaction of TBP (TATA binding protein) with TATA boxes and TATA-like elements in mammals, which began to increase with the discovery of the effect of single nucleotide polymorphisms (SNPs) in TATA sequences on phenotype, in particular, on association with various human diseases. The interaction of TBP with the TATA boxes in plants, in particular, in Arabidopsis thaliana, has not been practically studied, with the exception of a few early studies. Large-scale prediction of promoter sequences and their constituent transcription factor binding sites using various in silico tools is successfully used due to advances in transcriptomic technologies and genome sequencing of many plant species (model plant A. thaliana, rice, tomato, beet, potato, wheat, cotton, etc.). However, predicted regulatory sequences may or may not be functional, and experimental verification of the contribution of a potential transcription factor binding site to promoter activity is required to confirm its functionality. This work uses a quantitative DNA gel retention method to determine the affinity of TBP for TATA boxes of A. thaliana gene promoters predicted using Plant_SNP_TATA_Z-tester, which correlates with the activity of transcription and gene expression. For the study, we used the genes of A. thaliana PUR7, TFL1, MLH1, FT, AOP2 transcribed in different tissues of the plant. We showed that oligodeoxyribonucleotides identical to the sequences of TATA boxes with flanking nucleotides of A. thaliana genes have an affinity for TBP that differs up to 66 times. Flanking sequences of TATA boxes of the promoters of the considered A. thaliana genes have a lower content of GC-nucleotides in the flanks (by 23 %) compared to human genes. Experiments have shown that for KD predicted by Plant_SNP_TATA_Z-tester and their experimental values expressed in nM, the linear correlation coefficient (r) = 0.97 at p< 0.05). The results obtained indicate the reliability of in silico assessment of the affinity of Arabidopsis TBP for promoters of the genes of this plant using the Plant_SNP_TATA_Z-tester service. Key words: Arabidopsis thaliana; TATA-box; A. thaliana genes promoters; TBP/TATA affinity For citation: Sharypova E.B., Ponomarenko M.P., Kolchanov N.A., Savinkova L.K. In vitro determination of TBP affinity to the TATA-box of promoters of Arabidopsis thaliana gene. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):36-42. doi 10.18699/letvjgb-2025-11-06 (in Russian) Funding: The work was carried out with the support of budget funding, No. FWNR-2022-0016. [/expand]

Mathematical biology

AbstractAbstract: The Student’s t-test for the statistical significance of the difference in the means of two samples, proposed by R. Fisher in 1925, is still one of the most popular methods of statistical analysis. Over almost a century of its use, a fairly stable system of recommendations and conditions for its application has developed, which is set out in textbooks and manuals on statistical data processing. As a rule, a preliminary check of the normality of the original sample distributions and the equality of their variances is urgently required. In case of abnormality, it is recommended to use nonparametric methods, for example, the Mann–Whitney test. The paper presents a more modern point of view on this problem, caused by several interrelated reasons. Firstly, a century of practical experience has accumulated in using the Student’s t-test, which makes one strongly doubt the necessity of checking normality and equality of variances, as well as the use of rank criteria in the absence of normality. Secondly, the theory has not stood still either. An alternative to the methods of the “normal theory” has appeared in the form of distribution-free procedures. Thirdly, over the past century, computing capabilities have increased dramatically, making it possible to model general distributions of initial samples on a computer without additional assumptions and use them to estimate the required p-values.
Key words: normal distribution; point-biserial correlation coefficient; free-distribution procedures; p-value; bootstrap
For citation: Efimov V.M. How to calculate the Student’s test for the statistical significance of the difference between the means of two samples. I. Testing for normality. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal of Genetics and Breeding. 2025;11(1):43-50. doi 10.18699/letvjgb-2025-11-07 (in Russian)
Funding: The work was supported by BP #FWNR-2022-0019.