The characterization of genetic diversity is one of the main components of the genetic resources collection and management. Molecular markers are the most effective tool for characterizing and assessing genetic diversity in plant collections. IRAP (inter-retrotransposons amplified polymorphism) markers have proven to be some of the most effective for characterizing and evaluating germplasm, confirming the genetic fidelity of in vitro preserved cultivars and species. In this regard, the aim of this work is to test several IRAP primers to identify genetic polymorphism and study the genetic fidelity of three rare and endemic flora species of the Western Caucasus during in vitro conservation. Approbation of 16 IRAP-primers on the investigated species was carried out for Eryngium maritimum L., Galanthus woronowii Losinsk. and Campanula sclerophylla Kolak. The results made it possible to select the most efficient of them for genetic fidelity analysis of micropropagated plants. Out of 16 IRAP primers 8 amplified PCR products in Eryngium maritimum. In Galanthus woronowii as well 8 of 16 IRAP primers resulted in the amplification with the number of DNA fragments ranging from 2 to 12. In Campanula sclerophylla 9 of 16 IRAP primers amplified 1 to 11 fragments, depending on the marker. The results of the genotyping of regenerants were compared with data on stock in situ plants, which were the source of explants for in vitro conservation. In total, 60 regenerants for each species of the natural flora of the Western Caucasus were involved in the study. The results obtained demonstrated no genetic changes of the regenerants in all the studied species. These results were confirmed using ISSR analysis of an extended sample set of microplants for each species. The results obtained can serve as evidence of a low probability of genetic disorders during in vitro propagation and conservation of the species Eryngium maritimum L., Galanthus woronowii Losinsk. and Campanula sclerophylla Kolak.

There was an increase and intensification of droughts in connection with global climate change in recent decades. Not all plant organisms are able to adapt to changing environmental conditions. Therefore, the question of stressresistant (drought-resistant) genotypes selection for breeding is quite urgent. This problem also concerns forest tree plants, including Scots pine, which is one of the main foresters in the Voronezh region. The results of vegetative and generative sphere analysis of individual Scotch pine trees with the help of biotechnology, molecular-genetic and cytogenetic method are given in this study. The possibility of applying the tissue culture method in vitro for testing initial plants for stress resistance, including drought resistance, is explained by the interconnection of cells, tissues and the whole plant properties. It is shown that the cytogenetic characteristics of the seed progeny and the indicators of callusogenic reactions do not always coincide in different genotypes: in some cases energy resources are spent on ontogeny protection, while, in other cases, to reproductive function maintain. There are trees, in which the state the generative sphere in arid years is at the level of optimal years, and their callus cultures reaction remains unchanged even under simulated conditions of drought. Based on the results obtained for the selection of Scots pine drought-resistant genotypes we suggest applying a system of criteria characterizing both the ability of the vegetative sphere to survive in drought conditions on the basis of the tissue culture method in vitro (callus tissue formation speed, its viability, frequency of callusogenesis), and the state of the generative sphere with the help of cytogenetic analysis of seed progeny (frequency of mitosis pathologies, the proportion of cells with micronuclei, mitotic activity). The expediency of applying the biotechnological approach was proved by analysis of the gene expression level of stress proteins: the level of AbaH gene expression correlates greatly with the indicator of the viability of callus cultures, including ones on a nutrient medium with an additional stress agent (NaCl). Trees that can be assigned to drought-resistant ones, according to the results of the analysis, should be recommended for use in breeding.

The main problems of establishment a slow growth in vitro collection of citrus and other tree crops cultivars are high degree of fungal contamination of bud explants and low growth potential of shoots. In this regard, the aim of current research is to assess the efficiency of decontamination procedure and the possibility of tissue culture initiation and slow growth conservation of valuable lemon cultivars. The best results of surface sterilization were obtained using immersion solutions of 0.3 % Veltolen – 25 minutes or 10 % Domestos – 25–30 minutes. In these treatments, 27.7–33.0 % of aseptic explants were obtained, respectively. However, after the third subculture, the yield of aseptic viable explants decreased till 10 % as a result of secondary contamination by endophytic fungi. The addition of biocide (“Gavrish”) in a nutrient medium at a concentration of 1 ml/l helped to increase the yield of aseptic viable explants till 50 %. However, after the third subculture the photosynthetic activity and the pigments content as well as growth rate decreased. Plants dropped yellowish leaves and eventually died. Thus, 37.35 % of plantlets survived after 8 months of conservation, and only 14.6 % survived after 10 months. Even after the third month of conservation significant decrease in the viability index and the coefficient of photosynthetic activity occurred in plants. Chlorophyll a in leaves decreased from 1.59 to 1.14 mg/g during 12 months in vitro conservation. The similar tendency observed on clorophyll b and carotenoids content. The experiments were carried out for 5 years using different lemon cultivars and other citrus varieties and cultivars. Thus, micropropagation and slow growth in vitro conservation of valuable lemon cultivars are still problematic and requires new technical solutions due to the low growth potential of plantlets raised from the mature buds that is consistent with the data of other researchers.

With the advent of the new genome editing tool of target-specifically customizable endonucleases, a huge variety of novel opportunities have become feasible. The crop improvement is one of the main applications of genome editing in plant science and plant biotechnology. The amount of publications referring to genome editing and CRISPR/Cas system based molecular tools application in crops is permanently growing. The aim of this study is the systematization and cataloging of these data. Earlier we published the first catalog of targeted crop genome modifications as of February 10, 2017. The current review is an update of the catalog; it covers research papers on crop genome modifications from February 10, 2017 to August 17, 2018, found by searching 47 crop names in the Scopus database. Over one year and a half, 377 articles mentioning CRISPR/Cas and crop names have been published, of which 131 articles describe an experimental application of this tool for editing 193 genes in 19 crops, including rice with the largest number of genes modified (109 genes). Editing 50 of 193 genes was aimed at crop improvement. The catalog presented here includes these 50 genes, specifying the cultivars, each gene and gene product function, modification type and delivery method used. The current full list of genes modified with CRISPR/Cas with the aim of crop improvement is 81 in 16 crops (for 5 years from August 2013 to August 2018). In this paper, we also summarize data on different modifications types in different crops and provide a brief review of some novel methods and approaches that have appeared in crop genome editing research over the reviewed period. Taken together, these data provide a clear view on current progress in crop genome modifications and traits improvement using CRISPR/Cas based genome editing technology.

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an agricultural crop species new to Russia and is in demand by the gas, oil and food industries. Due to the progress of “omics” technologies and the marker-assisted selection, there is a huge interest in the studies that compare the metabolites of various guar varieties, employing metabolomics as a method of functional genomics. For a large-scale screening of guar germplasm from the VIR collection, it is important to choose an efficient method to extract metabolites from samples. The accuracy of the assessment of the content of metabolites in samples is crucial for distinguishing varieties within the crop, since the metabolome profiles of plants within the same species differ mainly in the quantitative ratio of metabolites, and not in their qualitative composition. In metabolome practice, two methods of extracting polar compounds are usually employed in the preparation of samples for GC-MS analysis. One of the widely used methods of sample preparation is the long-term extraction of metabolites from whole tissues with the aid of a methanol solvent. Another method of sample preparation is based on the short-term methanol extraction of metabolites from frozen and homogenized material. The advantages and disadvantages of these two methods revealed in the course of our work have prompted us to develop a new approach that avoids some difficulties in analyzing the metabolic profiles of leaves of various guar varieties. The method we suggested combines the advantages of the two above-mentioned approaches of sample preparation, namely eliminates the loss of metabolites due to centrifugation and ensures the complete destruction of all cell walls, ensuring the maximum extraction level of polar metabolites. The essence of the new method is that the leaf is rapidly frozen in liquid nitrogen with subsequent thawing in cold methanol. Thus, leaf tissues retain morphological integrity, and subsequent centrifugation, necessary for homogenization, is skipped. We have checked the effectiveness of this improved method by experiments with leaf samples of three guar genotypes. It has been shown that the amount of extracted metabolites increases more than 5-fold compared to extraction with methanol from fresh unfrozen leaf tissues and more than 2-fold compared to extraction with methanol after freezing and homogenization. Extraction of metabolites using the new method allows the GC-MS analysis of guar samples to be conducted with the least loss and high accuracy required to distinguish varieties.

Decrease in natural illumination in fall/winter months causes depressive-like seasonal affective disorders in vulnerable individuals. Obesity is another risk factor of depression. The lethal yellow (AY) mutation causes ectopic expression of agouti protein in the brain. Mice heterozygous for AY mutation (AY/a) are obese compared to their wild-type littermates (a/a). The main aims of the study were to investigate the effects of AY mutation, photoperiod and the interaction between these factors on daily activity dynamics, feeding, locomotor and exploratory activities, anxiety-related and depressive-like behaviors in mild stress condition. Six weeks old mouse males of AY/a and a/a lines were divided into four groups eight animals each and exposed to long- (14 h light and 10 h darkness) or short- (4 h light and 20 h darkness) day conditions for 28 days. Then the behavior of these mice was successively investigated in the home cage, open field, elevated plus-maze and forced swim tests. We did not observed any effect of AY mutation on the general activity, water and food consumption in the home cage; locomotion and exploration in the open field test; anxiety-related behavior in the open field and elevated plus-maze tests. At the same time, AY mutation increased depressive-like immobility time in the forced swim test (F1.28 = 20.03, p = 0.00012). Shortday conditions decreased nocturnal activity in the home cage, as well as locomotion (F1.28 = 16.33, p = 0.0004) and exploration (F1.28 = 16.24, p < 0.0004) in the open field test. Moreover, short-day exposition decreased time spent in the center of the open field (F1.28 = 6.57, p = 0.016) and in the open arms of the elevated plus-maze (F1.28 = 12.08, p = 0.0017) tests and increased immobility time in the forced swim test (F1.28 = 9.95, p = 0.0038). However, no effect of the interaction between AY mutation and photoperiod on immobility time in the forced swim test was observed. Therefore, short-day photoperiod and AY mutation increased depressive-like behavior in the forced swim test by means of different mechanisms.

Fasting has become increasingly popular for treatment and prevention of obesity. Sex differences in the mechanisms of adaptation to fasting may contribute to choosing a therapeutic strategy for correction of metabolic disorders. Hepatokine fibroblast growth factor 21 (FGF21) is involved in the adaptation to fasting. Muscles are assumed to be the main energy-consuming tissue in the body, as muscle metabolism plays an important role in the adaptation to nutritional deficit. However, there is still little information on sex differences in muscle and FGF21 physiological response to fasting. Our aim was to find out whether there were sex differences in hormonal regulation and the expression of genes controlling glucose and lipid metabolism in skeletal muscles in response to fasting. We estimated the effect of 24-hour fasting on the expression of genes involved in lipid (Ucp3, Cpt1) and carbohydrate (Slc2a4) metabolism in muscles and evaluated changes in body weight and blood plasma levels of glucose, insulin, free fatty acids (FFA), adiponectin, and FGF21 in male and female C57BL/6J mice. None of the genes studied (Ucp3, Cpt1 and Slc2a4) showed sex-related changes at mRNA levels in control groups, but females exposed to fasting demonstrated a significant increase in the expression of all genes as compared to control. Fasting significantly decreased body weight and glucose blood plasma levels in animals of both sexes but exerted no effect on the levels of insulin or FFA. The adiponectin and FGF21 levels were increased in response to fasting, the increase in females being significant. We were first to show sex dimorphism in muscle gene expression and FGF21 blood level in response to fasting. In females, the greater increase in FGF21 and adiponectin blood levels was positively associated with the greater upregulation of lipid oxidation and glucose uptake gene expression.

Osteoporosis is one of multifactorial diseases, it develops from interactions between the genetic component and the environment. However, the universal epigenetic markers of osteoporosis are not yet defined. Finding the risk factors will predict the risk of osteoporosis at the preclinical stage, help define the course and severity of the disease, and develop preventive measures based on them to reduce the risk of fractures. Expanding knowledge in the field of bone biology, especially in the genetics of osteoporosis and osteoimmunology, showed that osteoporosis is a disease that occurs not only due to hormonal or mechanical disorders, but also as a clinically and genetically heterogeneous disease, and there are still unknown pathogenetic links in its structure. Decreases in bone mass and matrix mineralization as well as changes in bone microarchitecture can have different pathogenetic patterns of development and, moreover, there are unknown links of the pathogenesis of osteoporosis. It is possible that DNA methylation is one of these links and a mechanism for epigenetic regulation of gene expression. Evidence exists that this mechanism alongside regulatory miRNAs and post-translational modifications makes a significant contribution to the central processes of bone remodeling; however, the results of various studies vary greatly, and, therefore, there is a need to understand the significance of the accumulated data and to make them consistent. The purpose of this review is to compile and systematize data on the role of DNA methylation in bone metabolism in normal and pathological conditions, in the formation of osteoporosis, and to assess achievements and trends in this field of research and technologies for studying DNA methylation.

Psoriasis (PS) and psoriatic arthritis (PsA) are multifactorial diseases determined by the result of complex combined interaction of genetic and environmental factors. The study of genetic polymorphism of PS and PsA will allow identification of common diagnostic criteria for the progression of pathology. The aim was to analyze the frequency of distribution of genotypes of the promoter region of the C-590T (rs2243250) gene IL4 in patients with psoriasis and psoriatic. The study included patients with psoriasis (n = 49) and psoriatic arthritis (n = 48), which, taking into account the carriage of certain genotypes, are divided into groups: 1, PS, carriers of the C/С genotype (n = 31); 2, PS, carriers of the C/T and T/T genotype (n = 18); 3, PsA, carriers of the C/С genotype (n = 30); and 4, PsA, carriers of the C/T and T/T genotype (n = 18). DNA extraction from whole venous blood was performed using a standard kit with a sorbent. Genotyping allelic variants was carried out by the method of restriction analysis of amplification products (RFLP-analysis) of specific regions of the genome. In PS carriers of the C/С IL4 (rs2243250), the value of the PASI index is statistically significantly lower relative to the carriers of the C/T and T/T genotypes. A possible association of the carriage of the C/T and T/T genotypes in PsA with nail psoriasis was noted in comparison with the C/C genotype. When studying intergroup differences, it was determined that the carriage of the C/C genotype in PsA can influence the clinical course of the psoriatic process with frequent exacerbations and involvement of more than 30 % of the hairy part in the pathological process. The carriage of the C/T and T/T genotypes in PsA may be associated with the Koebner phenomenon and the metabolic disorders in comparison with PS. Differences in the carriage of the C/C genotypes relative to C/T and T/T IL4 (rs2243250) in psoriasis and psoriatic arthritis were determined. Given the extremely low number of patient groups, the results should be considered as preliminary and require further testing on much larger samples.

Gliomas are the most common type of malignant brain tumors. Standard treatment of gliomas consists of surgical excision of the tumor with subsequent chemotherapy and radiotherapy. Tumor cells are characterized by rapid division with an increased uptake of glucose and its catabolism during glycolysis. To maintain rapid division, the level of glycolysis of the tumor cell is significantly increased, compared with normal cells. It is known that some nanoparticles (NP) have the property of accumulating in tumors. In particular, NPs of manganese oxide can penetrate into the brain and, with considerable accumulation, cause toxic effects. These facts served as a prerequisite for studying the effects of manganese oxide NPs on the viability of glioma cells. The purpose of this work was to study the effects of manganese oxide NPs, as well as their combination with gamma irradiation on the glycolysis of glioma cells. The cells were irradiated using the research radiobiological gamma-installation IGUR-1 based on 137Cs. The level of cell glycolysis was determined using the standard glycolytic stress test on a Seahorse XFp platform. Cell viability was determined using the ViaCount reagent staining of living and dead cells. Their count was performed using flow cytometry. We showed that the glycolysis of U-87 MG glioma cells was significantly reduced when incubated for 48 hours with manganese oxide NPs. Irradiation in combination with NPs or alone did not have significant effects on glycolysis of gliomas. Glioma incubation with manganese oxide NPs for 72 hours led to a significant reduction in cell viability. This study may be useful for the development of new therapies and diagnosis of gliomas.

Gametic embryogenesis is one form of totipotency of plant cells, in which either male or female gametes are induced to form embryoids (sporophytes). Regeneration of haploid plants from embryoids and subsequent chromosome duplication result in doubled haploids and DH-lines. The production of haploids and doubled haploids (DHs) through gametic embryogenesis allows a single-stage development of complete homozygous lines from heterozygous plants. The development of effective haploid protocols to produce homozygous plants has a significant impact on plant breeding, shorting the time and costs required to establish new cultivars. There are several available methods to obtain haploids and DHs-lines, of which anther or isolated microspore culture in vitro are the most effective. Microspore embryogenesis is more commonly applied. This is in part because more male gametophytes are contained in a single anther compared to the single female gametophyte per embryo sac. Microspore embryogenesis is regarded as one of the most striking examples of plant cell totipotency. The switch of cultured microspores from gametophytic to sporophytic mode of development has been induced by stress treatments of various kinds applied to donor plants, inflorescences, buds, anthers or isolated microspores both in vivo and in  vitro. Physical or chemical pretreatments (cold and heat shock, sugar starvation, colchicine, n-butanol, gametocydes) act as a trigger for inducing the sporophytic pathway, preventing the gametophytic pathway development of microspore. The recent investigations have revealed that cold pretreatment during microspore reprogramming acts rather as an anti-stress factor alleviating the real stress caused by nutrient starvation of anthers or microspores isolated from donor plants. Under stress pretreatment a vacuolated and polarized microspore transformed into a depolarized and dedifferentiated cell, which is an obligatory condition for reprogramming their development. We summarize data concerning the role of various stresses in the induction of microspore embryogenesis and possible mechanisms of their action at cellular and molecular levels. Identification of new stresses allows creating efficient protocols of doubled haploid production for end-user application in the breeding of many important crops.

A totipotent zygote has unlimited potential for differentiation into all cell types found in an adult organism. During ontogenesis proliferating and maturing cells gradually lose their differentiation potential, limiting the spectrum of possible developmental transitions to a specific cell type. Following the initiation of the developmental program cells acquire specific morphological and functional properties. Deciphering the mechanisms that coordinate shifts in gene expression revealed a critical role of three-dimensional chromatin structure in the regulation of gene activity during lineage commitment. Several levels of DNA packaging have been recently identified using chromosome conformation capture based techniques such a Hi-C. It is now clear that chromatin regions with high transcriptional activity assemble into Mb-scale compartments in the nuclear space, distinct from transcriptionally silent regions. More locally chromatin is organized into topological domains, serving as functionally insulated units with cell type – specific regulatory loop interactions. However, molecular mechanisms establishing and maintaining such 3D organization are yet to be investigated. Recent focus on studying chromatin reorganization accompanying cell cycle progression and cellular differentiation partially explained some aspects of 3D genome folding. Throughout erythropoiesis cells undergo a dramatic reorganization of the chromatin landscape leading to global nuclear condensation and transcriptional silencing, followed by nuclear extrusion at the final stage of mammalian erythropoiesis. Drastic changes of genome architecture and function accompanying erythroid differentiation seem to be an informative model for studying the ways of how genome organization and dynamic gene activity are connected. Here we summarize current views on the role of global rearrangement of 3D chromatin structure in erythroid differentiation.

Currently, studies on the mechanisms of the pathogenesis of plant diseases and their distribution in crops are intensively conducted in Russia and the world. First of all, this interest is associated with a significant effect of pathogens on the harvest. In Western Siberia, brown rust and powdery mildew are almost annually recorded in the crops of spring and winter wheat, reaching in some years up to the epiphytotic level. In this regard, methods for monitoring the condition of crops in order to predict their dynamics and plan agrotechnological events to control the state of plants in crops, including the development of fungal infection are developing. Models of fungal infections development on the wheat leaf (for example, brown rust) are used to monitor, predict and control the state of crops in order to optimize the growing process. Mathematical models allow computational experiments to make predictions about the risk dynamics of infections in different scenarios of global weather changes. Such designation of models assumes their hierarchical structure characteristic of multilevel modeling systems. This review presents models for the development of foliar fungal infections in crops, and formulates the methodological aspects of system modeling that can be used for adapting existing models and their units, and developing new models based on them. The article presents the structure of the hierarchical system for modeling the development of leafy infection, provides an overview of the units constituting the system, and discusses the issues of parametric adaptation of submodels. We demonstrated that, to date, plant growth and development models have been developed with varying degrees of detail. Currently, to develop a system for modeling the development of an infection in a crop, it is necessary to determine a large body of available experimental data and, by taking into account this data, we can put together a model as a system consisting of model modules, for which the models of basic processes have already been developed and described.

Due to current global climate changes, the issue of improving adaptive capacity of crops is of high importance. It is important to create winter crop varieties with both ecological adaptability and yield stability in years with different hydrothermal conditions. In order to develop winter barley varieties with a combination of yield and stability, 14 promising breeding lines have been evaluated in the conditions of the V.M. Remeslo Myronovka Institute of Wheat of NAAS of Ukraine in 2012/2013–2014/2015 using four different sowing dates. The ANOVA revealed a reliable part in yield variation: 64.59 % for environment, 16.84 % for genotype–environment interaction, and 15.57 % for genotype. The sowing dates significantly increased the yield variation of the breeding lines. The differences between the average yields of the lines depending on sowing date within the year were 1.05 t/ha in 2012/2013, 0.90 t/ha in 2013/2014, and 1.25 t/ha in 2014/2015. For genotype–environment interaction interpretation and ranking lines by yield a number of the most known statistical parameters of adaptability, stability, and plasticity and GGE biplot were applied. The use of different sowing dates at the final stage of the winter barley breeding process is a simple but effective approach that allows a more detailed assessment of the adaptive potential of breeding lines in various growing conditions. As compared to statistical parameters, GGE biplot has some advantages for interpretation of genotype–environment interaction. This graphic model allows ranking environments to be visualized for their discriminating ability and representativeness, as well as both specifically adapted genotypes and the ones with the optimal combination of yield potential and stability to be identified in a set of environments (mega-environment). The breeding line Pallidum 4816 with the optimal combination of yield and stability, as well as the high-yielding breeding lines Pallidum 4857 and Pallidum 4659 were identified and submitted to the State Variety Testing of Ukraine as the new winter barley varieties MIP Yason, MIP Oskar and MIP Hladiator.