Ecological genetics

Domestication of rice (Oryza sativa L.), one of the five earliest cereal crops, gave rise to a characteristic “domestication syndrome” marked by loss of natural seed dispersal, enlargement and colour change of the caryopsis, shortening of seed dormancy, and transition to an annual life cycle. Archaeological, physiological-genetic and molecular evidence is synthesised here to summarise the mechanisms underlying these key agronomic traits. Reduced seed shattering is linked to mutations andallelic diversification at loci SH4, qSH1, SH5, SHAT1, CPL1, OsSh1/ObSH3, ObSH11, NPC1, OSH15, GRF4 and OsLG1/SPR3, which govern formation and degradation of the spikelet abscission layer. Grain size is determined by QTL GW2, GS3, GS5 and TGW6, modulating cell division and endosperm development and thus shaping thousand-grain weight and yield. Pericarp pigmentation is controlled by Rc and Rd together with the Kala1–Kala3–Kala4 cassette; structural rearrangements in theKala4 promoter trigger ectopic expression of a bHLH factor and anthocyanin accumulation, whereas a 14-bp deletion in Rc converted most cultivars to the white-grained type and was later functionally restored via CRISPR/Cas9. Collectively, these findings provide a genetic foundation for targeted improvement of yield, harvestability and nutritional quality in modern rice breeding.

BACKGROUND: Legumes can play a key role in the formation of highly productive pasture phytocenoses and have significant potential for introduction in the Arctic regions of the Russian Federation for the purpose of sustainable development of northern livestock farming. One of the key properties of legumes is the formation of a mutually beneficial nitrogen-fixing symbiosis with nodule bacteria (rhizobia), which facilitates the fixation of atmospheric nitrogen and provides plants with available nitrogen compounds, thereby increasing the productivity of phyto- and agrocenoses. Oxytropis czekanowskii Jurtz. is a rare subendemic species of perennial legume growing in Yakutia and Taimyr.

AIM: The aim of the work was to create a collection and study the rhizobial endophytes from nodules of O. czekanowskiigrowing in Norilsk (Krasnoyarsk Territory).

MATERIALS AND METHODS: Rhizobial strains were isolated from root nodules of plants by a standard technique using mannitol-yeast nutrient medium YMA after sterilization of nodules for 1 min in 96% ethanol. The taxonomic position of the isolates was studied using sequencing and phylogenetic analysis of 16S rDNA and ITS region sequences.

RESULTS: A high genetic diversity of the isolates was shown, assigned to six genera and four families of the order Hyphomicrobiales: Mesorhizobium (family Phyllobacteriaceae), Neorhizobium, Pararhizobium and Agrobacterium (family Rhizobiaceae), Bosea (family Boseaceae) and Tardiphaga (family Bradyrhizobiaceae). Based on the analysis of 16S rRNA genes and the ITS region, isolates P10/4-1 and P10/5-2 were assigned to the species Neorhizobium vignae, isolates P10/1-1 and P10/5-1 to the species Pararhizobium herbae, while isolate P10/3-1 was identified as Mesorhizobium qingshengii. At the same time, the strains Bosea sp. P10/2-3, P10/1-3 and P10/4-4, which showed a low level of similarity with the closest type strain, can potentially be attributed to a new species of microorganisms.

CONCLUSION: Thus, wild northern legumes are a unique source of valuable genetic resources of cold-resistant nodule and endophytic bacteria, promising for the creation of highly productive perennial pasture and hay cereal-legume phytocenoses in the extreme soil and climatic conditions of the Arctic.

BACKGROUND: Bacteria of the genus Lactobacillus possessing a number of positive properties on the human body are a promising source for the creation of functional nutrition. The study of antimutagenic activity of lactobacilli will substantiate the use of these bacteria to prevent the effects of genotoxic environmental factors.

AIM: To comparative analysis the antimutagenic potential of four Lactobacillus strains.

MATERIALS AND METHODS: Four bacterial strains Lactobacillus casei 3184, L. casei MB, L. plantarum AB, L. plantarum B578 were used in this work. The antimutagenic activity of cells suspension and supernatant of Lactobacillus culture was evaluated using Ames test.

RESULTS: The supernatant of L. plantarum B578 in the stationary growth phase most effectively suppressed the mutagenic effect of sodium azide (45.6%) and 2-nitrofluorene (43.5%). Substantial antimutagenic activity was also observed for the cell suspension of the strains L. casei 3184 and L. plantarum AB in the exponential growth phase against sodium azide(40.8% and 39.9%, respectively), and for the supernatant of these strains in the stationary growth phase against 2-nitrofluorene (39.8% and 37.5%, respectively). L. casei strain MB did not significantly reduce the effect of known mutagens: the antimutagenic activity of all tested samples for this strain in different growth phases ranged from 15.9% to 23.4% against sodium azide, and from 15.6% to 28.5% against 2-nitrofluorene.

CONCLUSION: Analysis of the results obtained suggests that the antimutagenic effect of L. casei 3184 and L. plantarum AB strains against sodium azide is due to direct binding of the mutagen by lactobacilli cells, and that of L. plantarum B578 strain — by exometabolites accumulating in the tested culture media during the stationary growth phase. Reduction of 2-NF mutagenicity by L. casei 3184, L. plantarum AB and L. plantarum B578 strains can also be associated with direct binding of the mutagen, with inhibition of biotransformation enzymes of this compound, and with the antioxidant effect of exometabolites of lactobacilli strains. The data obtained emphasize the dependence of the antimutagenic potential of lactobacilli on the growth phase and indicate the promising application of the strains L. plantarum B578, L. casei 3184 and L. plantarum AB to reduce the negative effects of genotoxic agents.

This review presents data on studies of the intestinal microbiota of pigs, which plays a key role in the maintenance of animal health and physiology. The review summarizes to describe the effects of age, diet and antibiotics on the composition and functional activity of the intestinal microbiota of pigs and the distribution of antibiotic resistance genes under livestock production conditions. This review summarises research data on the composition of the intestinal microbiota of pigs, with special attention paid to the formation and dynamics of the composition of the microbiota of piglets in the neonatal period. The influence of different types of diet on the composition and functional activity of the intestinal microbiota of pigs, including the expression of glycosidohydrolase and glycosyltransferase genes and the possibility of modulating the composition of the microbiota through diet, which can minimise the effects of stress at weaning and increase animal performance. Particular attention is given to the role of the gut microbiota in the metabolism of amino acids, vitamins, lipids and bile acids, and to the functional metagenomics of the microbial community, allowing the identification of genes associated with adaptation to different diet types and pathological conditions. The review also discusses the role of pigs in the spread of antibiotic resistance genes, including using metagenomic and metatranscriptomic profiling, as well as the risks associated with their introduction into the environment and the potential impact on animal and human health.

BACKGROUND: Extra-pair paternity, where offspring are fathered by males outside of a primary pair bond, is common among avian species and challenges the idea of strict monogamy. It provides insights into sexual selection and reproductive strategies. While extra-pair paternity is frequently documented in species such as the Willow Warbler, its occurrence and population variability in the closely related Wood Warbler remains poorly studied.

AIM: To investigate the presence of extra-pair paternity in a Wood Warbler population in the Pskov Region, Northwest Russia.

MATERIALS AND METHODS: During fieldwork, we collected 124 DNA samples from 27 adult males, 14 adult females,and 83 chicks from 14 families. To analyze extra-pair paternity, we used three microsatellite loci (Ase5, Ase18, Ase27) suitable for this population.

RESULTS: Of the 14 socially monogamous families examined, extra-pair paternity was found in one brood, where two of five chicks (40%) were sired by a male outside the social pair bond. The overall extra-pair paternity rate was 2.5%, and 7.1% of nests contained extra-pair young. These rates are markedly lower compared to Central Russia, where extra-pair paternity in Wood Warblers has been documented at 25%, with 41% of nests containing extra-pair offspring. However, due to the small number of markers used, our estimates may be conservative. These results are therefore preliminary and require further investigation.

CONCLUSIONS: The reduced incidence of extra-pair paternity in the Pskov Region may be linked to lower breeding densities and fewer unmated males. It cannot be also ruled out that the extra-pair paternity estimate is underestimated due to the use of an insufficient number of markers. Further studies are essential to assess extra-pair paternity in various regions and to understand the ecological and behavioral factors that influence its prevalence.

BACKGROUND: Potato virus Y (PVY) is one of the most distributed plant RNA-viruses. PVY affects a wide host range including crops and wild plants from different families. Potato virus Y exists as a strain complex which produce a numerous recombinant variants. Usual diagnostic methods based on ELISA and PCR are able to define strain group at the best case, however not particular recombinant variant. Actually, only high-throughput sequencing of plant transcriptomes allow to obtain viral full-genome sequence and reveal all recombinant variants. However, the apply of this approach is limited by the relatively high cost of single sample analysis, which doesn’t allow to explore large-scale samples.

AIM: The aim was to develop an approach for the bulk examination of PVY strain diversity.

MATERIALS AND METHODS: Total RNA was isolated from potato leaves. cDNA was synthesized using different reverse transcriptases. PVY genome amplification was performed using different DNA polymerases. Amplicons were used for the sequencing libraries preparation, which were sequenced on MinION platform. Reads after processing were mapped on reference. SNP-calling was performed for the revealing different PVY isolates.

RESULTS: The possibility of different reverse transcriptases and DNA polymerases for PVY genome amplification for farther sequencing was evaluated. Among exterminated sample 10 PVY isolates were revealed. The isolates belong to 5 different recombinant variants, three of them belong to common variants, while two another haven’t been previously described.One of them, N-Wi(s) is similar to the N-Wi, however the recombination point in Hc-Pro gene is shifted to the 5'-end and matches the NO-short variant. Another, SYR-IIa is similar to the SYR-II, however the recombination point in NIb gene is shifted about50 nucleotides to the 5'-end.

CONCLUSION: Probably the diversity of PVY recombinant variants is still underestimated since even in the small exterminated sample two novel variants were found. Developed protocol allows to explore PVY strain diversity and has two main advantages: low cost of single sample and each read holds a whole viral genome allowing unambigously identify a recombinant variant.

Potato Bioinformatics is a rapidly growing discipline at the interface of biology, computer science, and mathematics.Recent scientific and technological advances in biological and biomedical sciences have led to a rapid increase in data generation. The analysis and interpretation of such data requires powerful computational tools and specialists with deep expertise in various fields, including molecular biology, genetics, programming, and mathematics. Currently, machine learning and deep learning methods are being rapidly integrated into various fields of biology and medicine, significantly transforming bioinformatic solutions and marking the advent of a new era in bioinformatics. The development of new algorithms and efficient data analysis methods using artificial intelligence forms the foundation for the future growth of this field. In this context, the demand for specialists capable of bridging the gap between biological and mathematical disciplines continues to grow, necessitating the adaptation of educational programs. This article reviews recent trends in bioinformatics, including the development of multi-omics approaches and the use of artificial intelligence, and highlights the importance of multidisciplinary education with advanced training in mathematics and statistics to prepare a new generation of scientists capable of driving innovation in this dynamic field.