All-Russian Research Institute of Genetics and Farm Animal Breeding

Abstract Machine learning (ML) models with stochastic and non-deterministic characteristics are increasingly used for genomic prediction in plant breeding, but evaluation often neglects important aspects like prediction stability and ranking performance. This study addresses this gap by evaluating how two hyperparameters of a Gradient Boosting Machine (GBM), learning rate (v) and boosting rounds (ntrees), impact stability and multi-objective predictive performance for cross-season prediction in a MAGIC wheat population. Using a grid search of 36 parameter combinations, we evaluated four agronomic traits with a comprehensive suite of metrics: Pearsons r, R², Area Under the Curve (AUC), Normalized Discounted Cumulative Gain (NDCG), and the Intraclass Correlation Coefficient (ICC) and Fleiss’ Kappa for stability. Our findings demonstrate that a low learning rate combined with a high number of boosting rounds substantially improves prediction stability (ICC > 0.98) and selection stability (Fleiss Kappa ≈ 0.90), while also improving generalizability. This combination improved predictive accuracy (r, R²) and ranking efficiency (NDCG) without a trade-off, though optimal settings were trait-dependent. Conversely, classification accuracy (AUC) was poor and performed relatively better with higher learning rates, revealing a conflict in optimization hyperparameters. Despite low absolute performance for most metrics in the challenging cross-environment prediction, NDCG was high (> 0.85), indicating the models excelled at ranking top-performing entries. This research demonstrates that multi-objective hyperparameter tuning, with a specific focus on stability, is useful for developing reliable genomic prediction models suitable for practical breeding applications.

Abdominal fat deposition in chickens is an important trait that affects meat quality, reproductive performance, and overall production efficiency. This review analyses key aspects of the genetic regulation of this process, including the role of transcription factors, microRNAs, and key metabolic pathways. The prospects for applying knowledge of molecular mechanisms in breeding programs to achieve an optimal balance between production performance, product quality, and reduced feed costs are discussed. Detailed attention is given to genetic studies, including GWAS, transcriptomics, and the use of genome editing technologies, which reveal the polygenic nature of fat deposition. Mechanisms regulating lipogenesis and adipocyte differentiation are described, as well as interactions between signaling pathways such as PPAR and SREBP. The findings emphasize the importance of molecular approaches to improve the environmental sustainability of the industry and meet consumer demands for high quality meat products.

Reindeer husbandry is a historically established main branch of animal husbandry in the northern regions of the Russian Federation. Despite the active of domestic reindeer breeding within the northern latitudes of our country, the features of the biological processes of this animal species remain incompletely understood. The importance is a detailed study the reproductive system physiology, which is relevant in light of the prospects for introducing assisted reproductive technologies into reindeer husbandry practice in order to intensify the selection process. Assisted reproductive technologies in reindeer husbandry are currently not used even in breeding herds due to the low level of development, although their introduction can significantly reduce the time and financial costs of selection and breeding work carried out to improve the productive qualities of domestic reindeer breeds. In mammals, the sexual process is under the complex subordinate control of neurohumoral mechanisms, which are based on changes in hormonal status, that is, the levels and ratios of the hormones in accordance with the physiological cycle. Reindeer are the least studied productive farm animals in terms of reproduction. The current trend is to study the hormonal regulation of reproductive processes in female reindeer in different physiological states, such as anestrus, rut, pregnancy, and the post-calving period. We studied the concentration of estradiol, progesterone, and luteinizing hormone (LH) in the blood of female reindeer before the rut (early summer, early autumn, and at the beginning of the rut). The levels of hormones were determined using enzyme immunoassay. The study determined the level hormones in physiologically healthy female domestic reindeer in the early summer and early autumn periods and at the beginning of the rut. The results obtained showed a statistically significant decrease in the concentration of progesterone and estradiol. A decrease in LH was recorded in the warm period with an increase towards the breeding period.

During all periods of male ontogenesis, physiological processes responsible for the correct functioning of reproductive organs and spermatogenesis are under the influence of various factors (neuro-humoral, genetic, and paratypical). Recently, the attention of researchers has increasingly turned to the study of epigenetic factors. In scientific publications, one can increasingly find references to the direct role of microRNAs, small non-coding RNAs involved in post-transcriptional regulation of gene expression, in the processes of development and functioning of reproductive organs. Although the role of microRNAs in the reproduction of mammals, including humans, has been intensively studied, this area of knowledge in birds remains under-researched and limited to single experiments. This is likely due to the unique features of embryogenesis and the structure of the avian reproductive system. This review summarizes the current state of knowledge on the role of microRNAs in avian reproduction. Insight into the molecular basis of spermatogenesis in Gallus gallus domesticus is provided. Data on the functions and mechanisms by which microRNAs influence the processes of growth, development, and formation of rooster germ cells that determine the necessary morphofunctional qualitative characteristics of mature spermatozoa are summarized. Particular attention is paid to miRNA biogenesis as an important step affecting the success of spermatogenesis, as well as the role of miRNAs in avian sex differentiation during early embryogenesis. The modern literature sources systematized in this review, revealing the questions about the role of miRNAs in the reproductive function of birds, create a theoretical basis and define new perspectives and directions for further research in this field.

In this article the results of genotyping of tumor necrosis factor (TNF) and Toll-like receptor 2 (TLR2) genes among 644 head of cattle of six breeds belonging to four different genetic roots are presented. The Kholmogory and Holstein breeds of black-and-white root, the Ayrshire breed of red root, the Kostroma and Brown Swiss breed of brown root, and the fawn Simmental breed were studied. The PCR-RFLP method was used to identify alleles and genotypes. Significant differences in allele frequency of the TNF and TLR2 genes were observed between breeds of different genetic roots (p < 0.001) and between breeds of dairy and dairy-meat productivity (p < 0.001). In five of the six cattle breeds studied, the predominance of the TLR2T allele was revealed. The highest frequency of the TLR2T allele (0.99) was found in the Ayrshire breed. The herd of Ayrshire cows is close to being monomorphic for the TLR2 gene; 98% of the animals have the homozygous TLR2TT genotype. A more uniform distribution of alleles and genotypes for the TLR2 gene was found in black-and-white animals: in Holstein cattle, the average frequency of the TLR2T allele was 0.78; in Kholmogory cattle, it was 0.83. The TLR2TT genotype was detected in the majority of Holstein (61%) and Kholmogory (69%) cows. The frequency of the TLR2T allele in the Simmental breed was 0.62; in the Kostroma breed, it was 0.67. In Simmental and Kostroma cows, the heterozygous TLR2TG genotype is more common (54 and 47% respectively). A different picture of the distribution of allele and genotype frequencies was revealed in Brown Swiss animals. The TLR2T allele frequency averages 0.26. More than half of Brown Swiss cows (55%) are homozygous for TLR2GG. In all breeds, the TNFB allele predominated with a frequency of occurrence ranging from 0.61 in Holstein cattle to 0.98 in the Brown Swiss breed. A high frequency of the TNFB allele was found in the Kostroma (0.94), Ayrshire (0.885), and Simmental (0.80) breeds. In the Kholmogory breed, the average frequency of the TNFB allele was 0.72. The highest frequency of the TNFBB genotype was found in Brown Swiss herds (96%). The predominance of the homozygous TNFBB genotype was revealed in Kholmogory (53%), Simmental (62%), Ayrshire (77%), and Kostroma cattle (87.5%). In Holstein cows, the majority of animals (53%) carry the heterozygous TNFАВ genotype. In three breeds, Ayrshire, Kostroma, and Brown Swiss, the TNFAA genotype was not detected.

The effect of titanium tetrapolyethylene glycolate dissolved in polyethylene glycol (ratio 1:10) (abbreviated TTPEG*10PEG) on granulosa cells (GC) of the antral ovarian follicles of Sus scrofa domesticus in the dynamics of in vitro culture was assessed. Granulosa cells aspirated from post mortem ovarian porcine follicles (ø 3-5 mm) obtained at the Tosnensky Meat Processing Plant, were cultured without and in the presence of 0.1, 0.01 and 0.001 % TTPEG*10PEG. After 22 and 44 hours, the GC were analyzed by flow cytometry. A comprehensive analysis of viability indicators (mitochondrial activity, apoptosis), as well as the generation of reactive oxygen species (ROS) in the GC after exposure to TTPEG*10PEG, revealed that the addition of 0.1 % TTPEG*10PEG to the culture medium after 22 and 44 hours causes disturbances in the functional activity of the GC, accompanied by a decrease of mitochondrial membrane potential compared to control (by 8 and 9 %, respectively, p&lt;0.05) and cell death (the proportion of cells in apoptosis was 45 and 41 %, respectively, p&lt;0.001). In the groups cultured in the presence of 0.01 % and 0.001 % TTPEG*10PEG, no significant differences in the level of GC in the state of apoptosis were detected when cultured for either 22 or 44 hours. At the same time, an increase in mitochondrial activity was shown in these groups in comparison with the control and the group containing 0.1 % TTPEG*10PEG (by 11 and 13 %, respectively, after 22 hours, p&lt;0.001 and by 15 and 27 % after 44 hours, p&lt; 0.001). No significant differences were found between the study groups in the rate of ROS generation in cells. In general, a dose-dependent negative effect of TTPEG*10PEG (0.1 %) was identified. TTPEG*10PEG at concentrations of 0.01 and 0.001% did not have a destructive effect on the studied cell population, which indicates the possibility of using TTPEG*10PEG at the above concentrations (0.01 and 0.001 %) to simulate the composition of media used in porcine granulosa cells culture systems.

In recent years, increasing attention has been paid to the problem of preserving the genetic diversity of farm animals and poultry. However, an indispensable condition for the economic feasibility of preserving any breed is not only its uniqueness, but also the possibility of practical use. An example is the Russian snow-white breed of chickens in the VNIIGRZh bioresource collection. It was developed by breeding of Russian white chickens for thermal resistance at low temperature conditions, as well as for resistance to neoplastic diseases. Currently, this breed is specialized for the purposes of the bio-industry (raw materials for the production of embryonic viral vaccines). The change in the direction of breeding work led to a modification of the genetic structure of the population. Constant selective pressure on one particular trait can lead to a decrease in variability around the genomic regions associated with that trait. Therefore, understanding the genetic mechanisms leading to phenotypic differentiation requires the identification of regions in the genome that were under selection pressure. The study of runs of homozygosity (ROH) rates can provide useful information about the history of population selection, as well as allow for a better understanding of the genotype-phenotype relationship by discovering genes that are or were under selection pressure. In ROH islands specific to two generations of chickens, the most relevant candidate genes associated with adaptive traits are annotated. It has been established that genetic analysis based on changes in ROH can be used to characterize the genetic profile of chickens and to change the structure of the population under the influence of selection pressure. These data are especially important to take into account when evaluating qualitative phenotypic features, such as the adaptive capabilities of chickens.

Siberian cedar, Siberian cedar pine (Pinus sibirica du Tour.)- a species that, in the conditions of the forest-steppe region of the European part of Russia, is able to increase the productivity of forests and their biodiversity. The purpose of this work is to examine Siberian cedar pine under conditions of introduction in the Lipetsk region. In a comparative analysis of the growth of the species in its natural range with its introduction results, it was concluded that Siberian cedar can be grown on fertile soils of the Central Chernozem region, taking into account the decision on the conditions of its placement on the area. In gardening, you can practice the creation of initially wings and curtains from it when watering, eliminating competition from fast-growing breeds.

The performance of two artificial intelligence (AI) platforms, ChatGPT 3.5 (OpenAI, California, United States) and Gemini (Google AI, California, United States) was assessed by answering 200 questions of microbiology drawn from validated sources. The questions were selected from topics such as General Microbiology, Immunology, and Microbiology Applied to Infectious Diseases. The study was conducted from December 2023 to March 2024, and the responses of the different AI platforms were compared with an answer key. Statistical analysis was performed to assess accuracy. ChatGPT 3.5 and Gemini had comparable accuracy with correct response scores of 71% and 70.5%, respectively. Their performance varied across different sections. Gemini performed better in General Microbiology and Immunology, and ChatGPT 3.5 had a better score in the Applied Microbiology section. The study's findings highlight that AI platforms such as ChatGPT and Gemini can be utilized in microbiology and medical education.The evolution and continuous updating of AI platforms are required to improve their performance.

The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.