The central problem that Vavilov was investigating was the overall concept of global plant genetic resources. The theoretical basis of this concept consisted of the law of homologous series in variation, research on the problem of species as a system, botanical and geographical bases of plant breeding, and the key theory of the centers of origin of cultivated plants. The VIR global collection of plant genetic resources collected by Vavilov and his associates from all over the world reflects the fullness of botanical, morphological and genetic diversity, and can be used for historical, evolutionary, phylogenetic and applied breeding research aimed at unlocking the potential of all the collection material. The whole diversity of cultivated oats, as was proved by Vavilov, had originated from segetal weeds. This process can be clearly traced in Spain on the example of the cultivated diploid species A. strigosa, A. abyssinica in Ethiopia, A. byzantina in Turkey and Iran, and on segetal forms of A. sativa. The studies of the morphological features as a whole do not yield a complete picture of the evolutionary and systematic status of some oat species and forms. The methods and approaches that use DNA markers and genomic technologies, and are promising for the study of oat polymorphism and phylogeny have been actively researched recently. A number of works devoted to the molecular aspects of the evolution and phylogeny of the genus Avena have recently appeared. The research uses various markers of genes, gene regions, intergenic spacers (internal and external), both nuclear and chloroplast and mitochondrial, genomic approaches and other modern methods. On the basis of a comprehensive study of the complete intraspecific diversity from different zones of the distribution range of cultivated oat species as well as on the basis of an analysis of data on the geography of forms and species distribution ranges, it was established that the process of hexaploid species formation also took place in the western part of the Mediterranean, and subsequently, when moving eastward, these forms started occupying all the vast spaces in the region of the Southwest Asian center, forming a large intraspecific diversity of wild forms and weedy ones in transit to cultivated hexaploid oat species. An analysis of the intraspecific diversity of landraces has specified the centers of morphogenesis of all cultivated oat species. The phylogenetic analysis of the representative intraspecific diversity of cultivated and wild Avena species carried out using next generation sequencing (NGS) showed that diploid species with A-genome variants are in fact not primary diploids, but a peculiar Mediterranean introgressive hybridization complex of species that sporadically enter into interspecific hybridization. It was established that the tetraploid cultivated species A. abyssinica had most likely originated from the wild A. vaviloviana. An analysis of the ways of A. sativa and A. byzantina domestication showed that the most widespread ribotype of the A. sativa hexaploid was inherited from A. ludoviciana, and the second most widespread one, from A. magna, while A. byzantina has two unique ribotype families, most likely inherited from an extinct oat species or a still undiscovered cryptospecies.

Wheat is one of three main food crops around the world, which has the largest distribution area due to its adaptation to the different environments. This review considers polymorphisms and allelic variation of the vernalization response genes Vrn controlling the major adaptation traits in wheats (the genus Triticum L.): growth habit (spring vs. winter) and length of vegetative period (earliness). The review summarizes available information on the allelic diversity of the Vrn genes and discusses molecular-level relationships between Vrn polymorphisms and their effect on growth habit (spring vs. winter) and earliness (length vegetative period in spring plants) in di-, tetra- and hexaploid wheat species. A unique attempt has been made to relate information on mutations (polymorphisms) in dominant Vrn alleles to the values of the commercially most important trait “length of plant vegetative period (earliness)”. The effects of mutations (polymorphisms) in the recessive vrn genes on vernalization requirement in winter wheats are considered, and this trait was formalized. The evolution of the winter/spring growth habit in the genus Triticum  species is discussed. A scheme of phylogenetic interactions between Vrn alleles was constructed on the basis of these polymorphisms; the paper considers the possibilities to enhance the diversity of polymorphisms for the dominant Vrn genes and their alleles using wheat related species and rarely used alleles and discusses the prospects of breeding for improved earliness for concrete agroecological zones.

Satellite repeats are a significant component of the genome of Triticeae and play a crucial role in the speciation. They are a valuable tool for studying these processes. Pseudoroegneria species play a special role among grasses, as they are considered putative donors of the St-genome in many polyploid species. The aim of this study was to compare the copy number of satellite repeats in the genomes of Triticeae species. Quantitative real-time PCR was applied to determine the copy numbers of 22 newly discovered satellite repeats revealed in the whole-genome sequences of Pseudoroegneria species and one additional repeat previously identified in the genome of Aegilops crassa. The study focused on seven species of Pseudoroegneria, three species of Thinopyrum, Elymus pendulinus, Ae. tauschii, Secale cereale, and Triticum aestivum. Based on the copy number level and coefficients of variation, we identified three groups of repeats: those with low variability between species (medium-copy CL82), those with medium variability (low- and medium-copy CL67, CL3, CL185, CL119, CL192, CL89, CL115, CL95, CL168), and those with high coefficients of variation (CL190, CL184, CL300, CL128, CL207, CL69, CL220, CL101, CL262, CL186, CL134, CL251, CL244). CL69 exhibited a specific high copy number in all Pseudoroegneria species, while CL101 was found in both Pseudoroegneria and Th. junceum, CL244 in Th. bessarabicum, CL184 in P. cognata and S. cereale. CL95, CL128, CL168, CL186, CL207, and CL300 exhibited higher copy numbers in P. cognata compared to other species; CL3, CL95, CL115, CL119, CL190, CL220, CL207, and CL300 in P. kosaninii; CL89 in P. libanotica; CL134 in P. geniculata. Our assessment of the copy number of new satellite repeats in the St-genome and the analysis of their amplification specificity between species can contribute to the molecular-genetic and chromosome markers used for evolutionary, phylogenetic, and population studies of Triticeae species.

Substitution lines of the cotton Gossypium hirsutum L. involving chromosomes of the tetraploid species G. bar ba dense L., G. tomentosum Nutt. ex Seem., and G. mustelinum Miers ex Watt. are a valuable source for breeding, increasing the genetic diversity of G. hirsutum. The substitution of certain G. hirsutum L. chromosomes with G. barbadense chromosomes affect fibre elongation, fibre yield, fibre strength, and micronaire. To increase the efficiency of creating lines, it is necessary to study the nature of the introgression of alien chromosomes into the G. hirsutum L. genome. As a result of molecular genetic analysis of BC₂F₁ hybrids obtained from crossing monosomic lines of the cotton G. hirsutum from the cytogenetic collection of Uzbekistan with monosomic backcross hybrids BC₁F₁ G. hirsutum × G. barbadense on the same chromosomes, genetic differences between the hybrids in the profile of chromosome-specific microsatellite SSR markers were found. The predominant introgression of chromosomes 4, 6 and 12 of the A_t-subgenome and 22 of the D_t-subgenome of G. barbadense was revealed, while chromosomes 2 and 7 of the A_t-subgenome and 18 of the D_t- subgenome of G. barbadense were characterized by elimination. Among them, chromosomes 7 of the A_t- sub genome and 18 of the D_t-subgenome of G. barbadense were eliminated in the first backcross generation. In this work, two lines, CS- B06 and CS-B07, from the American cytogenetic collection with a putative substitution involving chromosomes 6 and 7 of the A_t-subgenome were analysed. The presence of only polymorphic alleles from the species G. hirsutum and the absence of polymorphic alleles from the species G. barbadense were revealed, which showed the absence of substitution involving these chromosomes. BC₂F₁ hybrids with monosomy for both G. barbadense and G. hirsutum chromosomes were characterized by regular pairing of chromosomes and high meiotic indexes. However, many hybrids were characterized by a decrease in pollen fertility. Two hybrids with monosomy for chromosome 7 of the A_t-subgenome of G. hirsutum and chromosome 6 of the A_t-subgenome of G. barbadense had the greatest reduction in pollen viability (70.09 ± 1.57 and 75.00 ± 1.66 %, respectively). Thus, this work shows a specific feature in the introgression of individual chromosomes of the cotton species G. barbadense into the cotton G. hirsutum genome.

The phenomenon of DNA import into mitochondria has been shown for all major groups of eukaryotes. In plants and animals, DNA import seems to occur in different ways. It has been known that nucleic acids enter plant organelles through alternative channels, depending on the size of the imported molecules. Mitochondrial import of small DNA (up to 300 bp) partially overlaps with the mechanism of tRNA import, at least at the level of the outer membrane. It is noteworthy that, in plants, tRNA import involves components of the protein import apparatus, whose role in DNA transport has not yet been studied. In this work, we studied the role of individual components of the TIM inner membrane translocase in the process of DNA import into isolated Arabidopsis mitochondria and their possible association with the porin VDAC1. Using knockout mutants for the genes encoding Tim17 or Tim23 protein isoforms, we demonstrated for the first time the involvement of these proteins in the import of DNA fragments of different lengths. In addition, inhibition of transport channels with specific antibodies to VDAC1 led to a decrease in the level of DNA import into wild-type mitochondria, which made it possible to establish the specific involvement of this porin isoform in DNA import. In the tim17-1 knockout mutant, there was an additional decrease in the efficiency of DNA import in the presence of antibodies to VDAC1 compared to the wild type line. The results obtained indicate the involvement of the Tim17-1 and Tim23-2 proteins in the mechanism of DNA import into plant mitochondria. At the same time, Tim23-2 may be part of the channel formed with the participation of VDAC1, while Tim17-1, apparently, is involved in an alternative DNA import pathway independent of VDAC1. The identification of membrane carrier proteins involved in various DNA import pathways will make it possible to use the natural ability of mitochondria to import DNA as a convenient biotechnological tool for transforming the mitochondrial genome.

Many crops require not only leaf photosynthesis for their seed development but also the photochemical reactions that occur in the seeds. The purpose of this work was a comparative analysis of light transmittance and photochemical activity in the leaves of Pisum sativum L. and its pericarp, seed coat, and cotyledons at the early, middle, and late maturation stages. The spectral composition of light was measured using a spectroradiometer in the range of 390–760 nm. We assessed the light transmittance of plant tissues by placing the plant tissue between the light source and the spectroradiometer’s sensor. PAM fluorometry was used to quantify the photochemical activity in plant tissues: this technique is handy for evaluating the efficiency of converting light energy into chemical energy through the analysis of the kinetics of chlorophyll fluorescence excitation and quenching. On average, a photochemically active green leaf of pea transmitted 15 % of solar radiation in the 390–760 nm, blue light was delayed entirely, and the transmitted red light never exceeded 5 %. Photochemically active radiation passing through the pericarp and coat and reaching the cotyledons at the early and middle seed maturation stages manifested a high proportion of green and far-red light; there was no blue light, and the percentage of red light was about 2 %. However, the cotyledons were photochemically active regardless of low irradiance and spectral ranges untypical of leaf photosynthesis. At the early and middle maturation stages, the maximum quantum yield of photosystem II (Fv/Fm) averaged 0.5 at the periphery of cotyledons and 0.3 at their center. Since the intensity of embryonic photochemical reactions significantly affects the efficiency of reserve nutrient accumulation, this parameter is a promising marker in pea breeding for seeds with improved nutritional qualities. 

The relationship between a variety’s genotype, environmental conditions and phytopathogenic load are the key factors contributing to high yields that should be taken into account in selecting donors for resistance and high manifestation of valuable traits. The study of leaf rust resistance in 49 common wheat varieties was carried out in the field against the natural pathogen background and under laboratory conditions using single-pustule isolates with virulence to Lr9 and Lr24. It has been shown that the varieties carrying alien genes Lr6Agi2 (Tulaikovskaya 10) and Lr6Agi1 (Voevoda) were resistant to leaf rust infection both in the field and in the laboratory. Varieties KWS Buran, KWS Akvilon, KW 240-3-13, and Etyud producing crop yields from 417 to 514 g/m2 comparable to the best standard variety Sibirskaya 17 can be reasonably used as Lr24 resistance gene donors under West Siberian conditions. Oms kaya 44 variety showing crop yield of 440g/m2 can be used as a donor for Lr19 and partially effective Lr26. Varieties Tuleevskaya and Altayskaya 110 with Lr9 in their genomes are recommended for the development of resistance gene-pyramided genotypes. The highest protein and gluten contents were observed in the CS2A/2M sample, while KWS Buran, Altayskaya 110, Volgouralskaya, and KWS Akvilon showed the lowest values. Varieties CS2A/2M, Tulaikovskaya 10, Pavon, and Tuleevskaya were ranked the highest in micro- (Cu, Mn, Zn, Fe) and macronutrient (Ca, Mg, K) contents among the common wheat samples from the collection, while the lowest values for most elements were observed in KWS Buran, Novosibirskaya 15, and Volgouralskaya. Winter varieties demonstrating leaf rust resistance against the infectious background typically carry adult plant resistance genes (Lr34, Lr12, and Lr13), particularly combined with the juvenile Lr26 gene. The presence of Lr41 in a winter type line (KS 93 U 62) allowed it to maintain resistance against a leaf rust pathogen clone kLr24, despite the presence of Lr24 in the genotype. Varieties Doka and Cheshskaya 17 may act as donors of resistance genes Lr26 + Lr34 and Lr9 + Lr12 + Lr13 + Lr34, as well as sources of dwarfing without losses in winter hardiness and yield under West Siberian conditions.

RNA interference is a gene silencing mechanism that plays an important role in genetic regulation in a number of eukaryotes. Argonaute (AGO) proteins are central to the complex RNA interference system. However, their role in this mechanism, both in the host plant organism and in the pathogen, has not yet been fully elucidated. In this work, we identified and phylogenetically analyzed the SnAGO1, SnAGO2, SnAGO3, and SnAGO18 genes of the pathogenic fungus Stagonospora nodorum Berk., and analyzed their expression under conditions of infection of plants with varying degrees of resistance to the pathogen. The expression level against the background of plant immunization with the resistance inducers salicylic and jasmonic acids was assessed. In addition, the activity of these genes in the culture of the fungus in vitro was studied under the direct influence of resistance inducers on the mycelium of the fungus. Earlier activation of the SnAGO genes in in vitro culture under the influence of salicylic and jasmonic acids suggests their sensitivity to it. In an in vivo system, plant immunization to induce the accumulation of pathogen SnAGO transcripts was found. At the same time, the SnAGO genes of the fungus S. nodorum, when interacting with plant cells, reacted depending on the degree of host resistance: the highest level of transcripts in the resistant variety was observed. Thus, our data prove that the SnAGO genes of the fungus S. nodorum effectively interact with the host defense system in direct proportion to the degree of resistance of the latter to the pathogen. It was proposed to use the ratio of the transcriptional activity of the fungal reference gene SnTub to the host TaRLI gene as a marker of disease development in the initial period of the infectious process.

In modern conditions, the increase in the yield of agricultural crops is provided not by expanding the areas of their cultivation, but mainly by introducing advanced technologies. The most effective strategy for this purpose is the development of genetically resistant and productive cultivars in combination with the use of a variety of plant protection products (PPPs). However, traditional, chemical PPPs, despite their effectiveness, have significant drawbacks, namely, pollution of environment, ecological damage, toxicity to humans. Recently, biological PPPs based on natural compounds have attracted more attention, since they do not have these disadvantages, but at the same time they can be no less effective. One of such agents is chitosan, a deacetylation product of chitin, one of the most common polysaccharides in nature. The high biological activity, biocompatibility, and safety of chitosan determine the breadth and effectiveness of its use in medicine, industry, and agrobiology. The review considers various mechanisms of action of chitosan as a biopesticide, including both a direct inhibitory effect on pathogens and the induction of plant internal defense systems as a result of chitosan binding to cell surface receptors. The effect of chitosan on the formation of resistance to the main classes of pathogens: fungi, bacteria, and viruses has been shown on a variety of plant objects. The review also discusses various ways of using chitosan: for the treatment of seeds, leaves, fruits, soil, as well as its specific biological effects corresponding to these ways. A separate chapter is devoted to protection products based on chitosan, obtained by its chemical modifications, or by means of combining of a certain molecular forms of chitosan with various substances that enhance its antipathogenic effect. The data presented in the review generally give an idea of chitosan and its derivatives as very effective and promising plant protection products and biostimulants.

Doubled haploid technology is a valuable biotechnological approach in plant breeding that enables one to quickly create new varieties through the single-stage production of homozygous lines. The aim of this study was to assess the indicators of in vitro androgenesis in the anther culture of the initial breeding material of varieties and combinations of F₁ and F₂ and to identify promising accessions with good responsiveness. For that purpose, the plant material that proved promising for the breeding programs of Siberian Research Institute of Plant Production and Breeding (SibRIPP&B) was used. Ten cultivars of common wheat and the F₁ and F₂ hybrids of nine combinations were evaluated for the main parameters of in vitro androgenesis such as the number of new formations, albino, green and all regenerated plants. Induction of androgenesis in vitro was carried out in anther culture in growth medium Chu (N6) containing 1 mg/l of growth regulator 2,4-D. The studied samples showed different responses to induction. The maximum level of new formations was found in F₂ hybrids Novosibirskaya 15 × Lutescens ShT-335. The largest number of green plants was found in F₁ Novosibirskaya 15 × Lutescens ShT-335. According to the results of variance analysis, a significant ( p < 0.01) influence of genotype on the studied traits was established. Varieties with good responsiveness to anther culture (Novosibirskaya 15) and lack of responsiveness to in vitro androgenesis (Novosibirskaya 31) were identified. Novosibirskaya 16 was characterized by a low regeneration capacity of new formations. A significant heterotic effect was revealed considering the number of new formations per 100 anthers among the hybrids of such combinations as Novosibirskaya 15 × Lutescens ShT-335, Novosibirskaya 15 × Lutescens 111/09, and Zagora Novosibirskaya × Obskaya 2. Novosibirskaya 15 was recommended for inclusion in crossings as a parental form that provides high hybrid responsiveness during in vitro androgenesis. The use of doubled haploid technology made it possible to quickly create DH-lines based on the breeding material.

The plant cell wall represents the outer compartment of the plant cell, which provides a physical barrier and triggers signaling cascades under the influence of biotic and abiotic stressors. Drought is a factor that negatively affects both plant growth and development. Cell wall proteins (CWP) play an important role in the plant response to water deficit. The adaptation mechanisms of the cell wall to water loss are of interest for identifying important genetic factors determining plant drought resistance and provide valuable information on biomarkers for further selection aimed at increasing the yield of crop plants. Using ANDSystem, a gene network describing the regulation of CWPs under water restriction conditions was reconstructed. The analysis of the gene network and the transcriptome data analysis allowed prioritizing transcription factors (TF) based on their enrichment of differentially expressed genes regulated by them. As a result, scores were calculated, acting as indicators of the association of TFs with water deficit. On the basis of the score values, eight most significant TFs were selected. The highest priority was given to the TF GBF3. CWPs were prioritized according to the criterion of summing up the scores of transcription factors regulating these genes. Among the most prioritized CWPs were the AT5G03350 gene encoding a lectin-like protein, AT4G20860 encoding BBE-like 22 required for the oxidation of cellulose degradation products, and AT4G37800 encoding xyloglucan endotransglucosy lase/hydrolase 7. Overall, the implemented algorithm could be used for prediction of regulatory interactions between transcription factors and target genes encoding cell wall proteins in plants.

Meta-analysis of transcriptomic data from different experiments has become increasingly prevalent due to a significantly increasing number of genome-wide experiments investigating gene expression changes under various conditions. Such data integration provides greater accuracy in identifying candidate genes and allows testing new hypotheses, which could not be validated in individual studies. To increase the relevance of experiment integration, it is necessary to optimize the selection of experiments. In this paper, we propose a set of quantitative indicators for a comprehensive comparative description of transcriptomic data. These indicators can be easily visualized and interpreted. They include the number of differentially expressed genes (DEGs), the proportion of experiment-specific (unique) DEGs in each data set, the pairwise similarity of experiments in DEG composition and the homogeneity of DEG profiles. For automatic calculation and visualization of these indicators, we have developed the program InterTransViewer. We have used InterTransViewer to comparatively describe 23 auxin- and 16 ethylene- or 1-aminocyclopropane-1-carboxylic acid (ACC)-induced transcriptomes in Arabidopsis thaliana L. We have demonstrated that analysis of the characteristics of individual DEG profiles and their pairwise comparisons based on DEG composition allow the user to rank experiments in the context of each other, assess the tendency towards their integration or segregation, and generate hypotheses about the influence of non-target factors on the transcriptional response. As a result, InterTransViewer identifies potentially homogeneous groups of experiments. Subsequent estimation of the profile homogeneity within these groups using resampling and setting a significance threshold helps to decide whether these data are appropriate for meta-analysis. Overall, InterTransViewer makes it possible to efficiently select experiments for meta-analysis depending on its task and methods.