Rapid development of high-performance genomic, transcriptomic, proteomic and metabolic technologies led to an information explosion in the field of plant biology and agrobiology. To date, the number of scientific publications on only one of the most important agricultural crops of Solanum tuberosum L. (potato) has exceeded 1.5 million. Effective access to knowledge distributed over such a multitude of non-formalized natural language textual sources requires the use of special computer-assisted intelligent methods of data mining (text-mining). However, in the literature, there is no data on the application of intellectual methods of automatic knowledge extraction from publications on agricultural crops, such as potato. Previously we have developed a pilot version of the SOLANUM TUBEROSUM knowledge base. SOLANUM TUBEROSUM is a computer platform for complex intellectual processing of large data bodies, including (1) automatic analysis of scientific publications and databases for extraction of information on genetics, markers, breeding, diagnostics, protection and storage technologies for potato, (2) formalized representation of extracted information in the knowledge base, (3) user access to these data, (4) analysis and visualization of query results. The ontology of the SOLANUM TUBEROSUM knowledge base contains dictionaries of molecular genetic objects (proteins, genes, metabolites, microRNAs, biomarkers); phenotypic characteristics of potato varieties; potato diseases and pests; biotic/abiotic environmental factors; potato agrobiotechnologies. This article describes the current version of the SOLANUM TUBEROSUM knowledge base developed from an extensive analysis of scientific publications on the moleculargenetic regulation of metabolic pathways in potatoes, as well as model plant organisms (maize, rice, Arabidopsis  thaliana). In total, about 9,000 full-text articles and more than 130,000 abstracts of PubMed were analyzed. With the help of automatic analysis of scientific publications, more than 59,000 facts on molecular genetic interactions and genetic regulation were identified, and the analysis of factual databases revealed more than 380,000 such interactions in the examined organisms. It turned out that about 3 % of extracted facts about molecular genetic interactions and genetic regulation were related to Solanum tuberosum L. Thus, the inclusion of information on well-studied model species during the extraction of information on the molecular-genetic regulation of metabolic processes is important. It allows prediction of orthologous genes in potato and their further identification and analysis based on homology. An associative network of genetic regulation of starch biosynthesis in potatoes, including 33 metabolites, 36 proteins, 6 metabolic pathways and 132 interactions between them, 86 of which describe catalytic reactions, and the rest – regulatory events, was reconstructed. The reconstructed network is the basis for the search for target genes for directed mutagenesis and marker-oriented selection of potato varieties with specified starch properties. The trial version of the SOLANUM TUBEROSUM knowledge base is available at http://www-bionet.sysbio.cytogen.ru/and/ plant/.

The development of phytopathogen-resistant varieties is the most reliable and economic way to reduce potato yield losses. Breeding of such varieties is possible by using genetic sources of resistance. The use of DNA markers for identification of valuable genotypes, including forms with several resistance genes, makes it possible to significantly improve breeding efficiency. The development of a multiplex PCR technique and using it to simultaneously test varieties and breeding lines for several genes that control the resistance to viruses and nematodes is a new approach to using DNA markers. This study is aimed at screening samples from the collection of the Narym Department of  Breeding and Seed Production of the Siberian Research Institute of Agriculture and Peat (the Branch of the Siberian Federal Agrobiotechnology Research Center, the Russian Academy of Sciences) using the multiplex PCR technique, for genes for resistance to Globodera rostochiensis and Globodera pallidas, potato wart disease, viruses X and Y. 40 samples were tested by means of genetic markers to identify genes for resistance to potato wart disease (Sen1), virus X (Rx), virus Y (Ryadg, Rychc, Rysto), Globodera rostochiensis (H1, Gro1-4) and Globodera pallida (Gpa2), in the genome. The sample included two varieties, three populations produced by self-pollination of the Ideal variety, and 35 individually selected potato hybrids. As a result, we identified marker NL25 (Sen1) in 19 samples; marker PVX (Rx) in 13 samples; marker RYSC³³¹² (Ryadg) in 10 samples; marker YES3-3A341 (Rysto) in 5 samples; markers TG 689¹⁴¹, 57R⁴⁵⁰, N195³³⁷ (H1) in 12 samples; marker Gro1-4-1⁶⁰² (Gro1-4) in 6 samples; marker Gpa2-2⁴⁵² (Gpa2) in 13 samples. In terms of economically valuable traits, sample С-31-15 is noted for high yield and quality indicators. It carries genes for resistance to potato virus X (Rx), Y (Rysto), Globodera rostochiensis (H1, Gro1-4), and Globodera pallida (Gpa2).

Potato steroidal glycoalkaloids (SGAs) compose a part of plant immunity. Some of their modified variants are toxic to humans. In the course of potato domestication, plants with a lower SGA level were selected. The advent of approaches for manipulation with the regulation of metabolic pathways provides an opportunity to overcome the undesirable direct relationship between the potato resistance to pests and the toxicity of its tubers. However, for such a fine regulation, a deep knowledge of the regulatory network of potato SGA biosynthesis is required. The purpose of this review is to summarize the information on the known SGA biosynthesis genes in plants and the results of the investigation of these genes in potato, as well as to consider the mechanisms of the SGA protective toxic action against pathogens and pests. The SGA biosynthesis is realized via the cytosolic mevalonate pathway and consists of three stages. The first two stages are required for the synthesis of primary metabolites, and lead to cycloartanol and cholesterol, respectively. Twelve enzymes are involved in the biosynthesis, and the half of them are involved in the biosynthesis of phytosterols, which is a branch of the first stage of this metabolic pathway. In the potato leaves with an excess of phytosterols, the synthesis switches to SGAs, increasing the content of the latter. In tubers, with an excess of SGA precursors, they are involved in the synthesis of lanosterol, supporting in this way the stable level of SGA. The importance of structural genes encoding the enzymes of the first two stages of biosynthesis does not allow us to consider them as a target for knockout in order to reduce the level of SGAs. However, information about the tissue-specific mechanisms of switching between the pathways of synthesis of SGA and other compounds having common precursors with SGAs can be used to manipulate the tissue-specific level of steroidal glycoalkaloids. At the third stage (the synthesis of glycoalkaloids from cholesterol), about 20 enzymes participate. In the potato genome, 14 corresponding genes were identified, 8 of which were studied in detail using reverse genetics approaches. As a promising target for reducing SGA levels in tubers, the genes encoding PGA enzymes (belonging to the CYP72 subfamily cytochrome-P450-dependent monooxygenases catalyzing the conversion of hydrocholesterol to trihydrocholesterol) and SGT (SGA glycosyltransferases that catalyze the conversion of solanidine to its toxic glycosylated derivatives α-solanine and α-chaconine) are considered. Cis-regulatory elements in the promoter regions of some glycoalkaloid biosynthesis genes, including elements responsible for tissue-specific expression, are described. The accumulated information provides the base for creating potato genotypes with tissue-specific regulation of SGAs, in which high levels of SGAs in leaves will remain to protect against pathogens and pests and, at the same time, the synthesis of toxic substances in tubers will be suppressed

Increasing the resistance of varieties to diseases and pests is a priority in potato breeding. Many potato varieties created in the Leningrad Scientific Research Institute of Agriculture “Belogorka” are multi-species hybrids possessing complex resistance to the most spread pathogens in combination with a high plasticity, which determined their zoning in many regions of the Russian Federation. Potato varieties and hybrids created in different periods of time in this institute and in the Ltd Breeding company “LiGa” were included in marker-assisted selection with 22 markers of 14 R genes conferring extreme resistance to viruses PVY and PVX, resistance to cyst nematodes Globodera pallida (patotypes Pa2, Pa3) and G. rostochiensis (pathotype Ro1) and resistance to late blight. The data of molecular screening were compared with the results of the State Test of Varieties for Disease Resistance, as well as with other published sources. Markers of sterile and fertile cytoplasm types were also used in the study. Based on the results of molecular screening, varieties and hybrids with different combinations of markers of R genes conferring resistance to the most harmful pathogens (Ry_sto, Ry-f_sto, Rx1, Rx2, Gro1-4, H1, Gpa2, R1, R3a, Rpi-blb1, Rpi-sto1) were detected. Among them, genotypes with sterile D-, T-, W/gamma cytoplasmic types were selected. Analysis of their pollen fertility, crossability and pedigree data showed that breeders succeed in obtaining fertile forms with the D- and T-types of cytoplasm carrying genetic material of Mexican polyploid species Solanum stoloniferum and S. demissum. The information about the presence of markers of R genes and about cytoplasm types of hybrids and varieties will allow an effective implementation of further breeding programs for resistance to a complex of pathogens, including pyramiding of R genes. The data of molecular screening made it possible to specify the pedigrees of several varieties and hybrids that have been created over several decades.

Pubescence is one of the important biotic factors in plants related to protection from stressful environmental factors. In potato, the interest in the study of pubescence is associated primarily with the fact that it plays a significant role in the protection of plants from insect pests. The review focuses on the functional role and genetic control of leaf pubescence in potato. The review describes morphological features of pubescence of potatoes, which consists of simple and glandular trichomes of several types. The ratio of trichomes of different types in potato species potato is diverse, especially for wild species. Therefore, the pubescence may serve as a classifying trait. The role of trichomes as “factories” of secondary metabolites of potatoes, among which are the esters of sucrose and terpene derivatives that serve as insect repellents. Trichomes also synthesize polyphenol oxidases, which lead to the biosynthesis of compounds which are harmful to the insects. The review presents information about the currently known genes responsible for pubescence. These are genes involved in the formation of a complex of MYB-bHLH-WD40, which controls the differentiation and development of trichomes in plants. The proteins of this complex in potatoes are primarily studied in connection with the regulation of the biosynthesis of anthocyanins. The fundamental basis for identification of genes controlling pubescence in potato is currently sequence data from complete genome sequencing. By analysis of homology with the genes of model organisms, it allows candidate genes that control important traits in potato to be identified. Work in this direction is already underway, but at the initial stage. In the final section, the review describes the methods ofphenotyping trichomes, based on the visual analysis of microscopic images (obtained both with optical and electron microscopes). The urgency of developing new high-performance approaches to the study of the morphology of the trait in potatoes has been demonstrated.

Nowadays there is much tension in the Russian modern vine growing industry around the issue of enhancing the range of grape varieties, which is aimed at production of highly adaptive grape plants and sustainable production of competitive grape varieties in the unstable stressing weather conditions of the moderate continental climate in the south of Russia. In this view, we believe it important to carry out research into the origin, generation and preservation of genetic resources so that they can be involved in the selection process and reach most important objectives of the national economy. The role of a variety and ampelographic collections becomes more important. The Anapa ampelographic collection (http://azosviv.info/category/osnovnye_razdely/anapskaya_ampelograficheskaya_kollekciya) is Russia’s largest gene pool depository of grape varieties brought from various countries of Europe, Asia and America, and Russia’s regions as well. It contains 4921 grape varieties, including Vitis vinifera L. (2975), V. amurensis Rupr. (40), V. labrusca L. (50), the interspecies varieties V. vinifera L.×V. amurensis Rupr. (210), V. vinifera L.×V. labrusca L. (168), blended interspecies hybrids V. vinifera L.× hybrids SV (220), V. vinifera L.×V. amurensis Rupr.×hybrids SV (70), and other samples. We carry out extensive research into collection varieties for their production and selection. We select varieties and forms showing good agronomic characters in productivity, quality of grapes and wine products, winter hardiness, drought resistance, and resistance to pests. We have identified, preserved and now use in selection, as sources of good agronomic characters of resistance to low temperatures in winter, such varieties as Riesling of the Rhine, Rkatsiteli, Aligoté, Riesling of Italy, Traminer Pink, Pinot Noir, Rara Neagra, Cabernet Sauvignon, Coarna Neagra, Pinot Gris, Gamay Freaux, Saperavi, Muscat Ottonel, Madeleine Angevine, Cabernet Franc, Khikhvi, Pearl of Csaba, Chardonnay, Krasnostop of Anapa, Dostoiniy, Krasnostop AZOS, etc. The collection has given birth to twenty seven varieties and elite forms, of which twelve varieties have been sent to the State Committee for the Testing of New Varieties of Agricultural Plants (Pluto, Muzhestvenniy (Courageous), Gordiy (Proud), Maran, Varvarovsky, Harmony, Progress, Gorniy (Mountaneous), Saturn, Dimitry, Vladimir, Kurchansky). We carry out a molecular genetic testing of the accumulated gene pool and DNA-classification of varieties. We have studied the microsatellite polymorphism in the genotypes of autochthonous grape varieties of the Don River and the Republic of Dagestan. We are performing the DNA-classification of varieties selected by the North Caucasian Regional Research Institute of Horticulture and Viticulture (Krasnodar), which is advantageous for the identification of pure varieties in planting material and vineyards and specifying of the parent forms of grape varieties, as well as when any disputes arise as to the variety authorship.

Mobilization and preservation of genetic sources of diversity of the cultivated pear varieties and their wild relatives is one of the main aspects of new cultivars breeding for modern intensive horticulture. The crucial matter during a new cultivar creation goes to the selection of parental pairs, which obtain a complex of positive features. The aim of this work is to study the Gene Fund collection of pear plantings from Nikitsky Botanical Gardens in accordance with the main economically important traits and to select the most valuable genotypes for using them in breeding programs as a starting material, as well as to conduct a DNA-fingerprinting and the analyses of genetic polymorphism of promising cultivars from the collection of pear with implementing of microsatellite analyses. As a result of long-term studies the following cultivars were selected in accordance with the complex of features promising for the breeding program: Gvardeiskaya Zimnyaya, Izuminka Kryma, Izumrudnaya, Kelmenchanka, Krymskaya Aromatnaya, Krymskaya Medovaya, Lazurnaya, Maria, Mriya, Nadezhda Stepi, Nezabudka, Novosadovskaya, Oreanda Kryma, Otechestvennaya, Tauschaya, Yakimovskaya. The samples of these cultivars were forwarded for genotyping. For the genetic polymorphism analyses of the studied cultivars, seven microsatellite DNA-markers – EMPc108, EMPc117, EMPc115, CH04e03 and CH01d09, CH01f07a, CH01d08 – grouped into 2 multiplex sets were used. The SSR-markers were significantly different according to their level of polymorphism – from 3 (CH04e03 marker) to 11 (EMPc115) alleles per a gene locus were revealed, the effective number of alleles varying from 1.37 to 4.65. Based on SSR-markers polymorphism analysis data, the rate of genetic similarity of the studied pear cultivars was estimated. This evaluation research helped estimate genetic relations inside the studied sample collection of genotypes. The SSR-fingerprints of the cultivars obtained will be used as a starting material for the creation of DNA-passports database of the “NBG – NSC” Gene Fund collection of pear cultivars.

The most common and harmful disease of the agricultural crop rice is a “burn” caused by the fungus Magnoporthe grisea (Hebert) Barr, the causative agent of rice blast. The important direction of modern domestic rice breeding is the development of high-yielding varieties resistant to blast. To solve the problem, it is important to search for sources and donors of resistance to the Krasnodar population of the pathogen among ecotypes of different ecological and geographical origin. Evaluation of the rice collection diversity for resistance to blast was carried out both on a natural background and on an infectious-provocative one. Immunological evaluation and phenotyping were carried out in 2015–2017 on 154 varieties of the Oryza sativa L. species from 7 ecological and geographical cultivation zones. Over the years of research, the range of variation in the intensity of the disease development in varieties was in the range from 1.1 to 77.8 %. The differences in the resistance of rice varieties to the pathogen between ecological groups and countries have been found. Most of the studied samples have shown medium resistance, there were isolated 51 resistant forms. Most often stable forms were found among the germplasm from China, Italy, the Philippines and Korea, and the unstable ones were from African countries, Japan, Primorye and Vietnam. Introduced samples resistant to the disease were identified and adapted to soil and climatic conditions and rice cultivation technologies of the Kuban, they were included in the breeding scheme for developing pathogen-resistant rice varieties with the extension of their genetic basis. The article presents data on the variation of morphological traits and the rate of development of plants of international varieties from 24 countries in the conditions of the south of Russia. The results of the comparison of germplasm of domestic and foreign varieties according to the degree of resistance to the pathogen in conditions of natural infection in the field experiment for five years are presented. As a result of the evaluation of plant resistance to the Krasnodar population of the pathogen, the effective genes for resistance to the pathogen for breeding programs of the south of Russia and the molecular genetic analysis of the rice collection variety were determined: Pi-1, Pi-z, Pi-ta, Pi-z5, Pi-9, Pi-5(t), Pi-t, Pi-19.

In Russia, only low amylose short grain varieties were previously grown, but recently, because of the growth of consumption of this cereal, domestic varieties with various quality have become necessary. Absence of information on the genetics of this trait constrains selection in the given direction. Despite a considerable number of foreign works on localisation of genes defining quality of rice grain, there are no similar Russian works yet. Definition of the possibility of using loci identified from studying foreign samples, for marker assisted selection of domestic germplasm became the purpose of our research and possible localisation before the unknown loci defining the quality of rice grain. We used both neutral markers and those associated with quality. Polymorphism of the allocated groups of varieties with the contrasting quality trait was studied using 57 markers. Polymorphism of domestic varieties of rice with contrasting quality traits such as “weight of 1000 grains”, “translucency”, “husk content”, “the maintenance of the whole kernel in a croup” was studied with use of the SSR markers to reveal chromosomal regions associated with the division of Russian rice varieties into groups based on the traits being studied. It was shown that 12 markers authentically divided groups with the various grain form, 3, with a various exit of the whole kernel, and 1 marker group, with various translucency and husk content. The markers authentically dividing groups of varieties with various weight of 1000 grains, groats exit, the protein and amylose content were not revealed. Data about the association of markers RM3276, RM5707, RM5508, RM7110, RM509, RM600, RM136 with the quality trait in references were not revealed. Probably, the genes defining the quality of rice grain, specific for domestic gemplasm, are located around the given markers.

The study of seed mineral composition of wheat and its wild relatives revealed higher content of all elements in Aegilops ovata and Ae. triuncialis, as well as an overall increased background in relatives compared to modern varieties of Triticum aestivum (standards). By content of macro- and microelements, synthetic forms of wheat occupy an intermediate position between wild relatives and modern varieties. Transitional forms with the level of mineral composition typical of wild forms (Zhetysu×T. militinae; Zhetysu×T. kiharae; Bezostaya 1×Ae. cylindrica) have been identified. All genotypes have been differentiated into 3 clusters. The first consists predominantly of introgressive forms, Ae. triaristata and the Komsomolskaya 1 variety, which has wild forms in its origin. The second cluster includes mainly varieties (parental forms), T. timopheevii and the introgressive form (Steklovidnaya 24×T. militinae). The third cluster consists largely of T. militinae, T. kiharae, Ae. cylindrica species and introgressive forms originated from them: Zhetysu×T. militinae and Bezostaya 1× Ae. cylindrica. Such division allows us to classify genotypes according to the level of metabolism: wild relatives (3rd cluster), varieties (2nd cluster) and an intermediate group – introgressive forms (1st cluster). In general, inclusion of cultural forms (backcrossing with varieties) to crosses with introgressive forms is usually accompanied by a decrease in the total metabolic level, but it varies in cultivars and wild species characterized by polymorphism. Sources of high content of elements have been revealed: wild relatives and introgressive forms, some of which are donors. According to the results of topcross breeding with testers – commercial common wheat varieties Steklovidnaya 24, Almali, Zhetysu – inheritance of this trait by progenies in F₂–F₃ generations has been revealed in two constant lines: (Bezostaya 1×Ae. cylindrica)×T. kiharae and Zhetysu×T. kiharae.

The synthetic forms of Triticum miguschovae (GGAADD), Triticum palmovae (A^bA^bDD), T. durum (M. it.)/Ae. Tauschii (BBAADD) and the introgressive lines of common wheat created on their basis were evaluated for resistance to leaf rust. All synthetic forms have a high resis­tance to leaf rust. Twenty-two lines of common wheatresistant to leaf rust with genetic material from T. miguschovae, 10 lines with genetic material from T. du­rum (M. it.)/Ae. tauschii and 4 lines obtained on the basis of T. palmovae were identified. A screening with the use of molecular markers for the presence of leaf rust resistance genes Lr21, Lr26, Lr32, Lr39 was done. The GDM35 marker linked to the Lr39 gene was identified in the synthetic forms. Molecular markers Lr21F/R and BARC135 linked to the genes Lr21 and Lr32, respectively, were not identified. Resistance to leaf rust in lines 729, 1555, 2203, 2289, 2295, 2296, 4155, 4171, obtained on the basis of T. miguschovae, lines 3261, 3265, obtained on the basis of T. palmovae, and in line 4141 with the genetic material from T. durum (M. it.)/Ae. Tauschii is controlled by the presence of the Lr39 gene. The SCM9 marker indicating the presence of translocation of 1BL.1RS with the Lr26 gene was detected in 15 lines obtained on the basis of T. miguschovae, in 2 lines with genetic material from T. durum (M. it.)/Ae. tauschii, and in 1 line created on the basis of T. palmovae. Lines 729, 1555, 2203, 2289, 2295, 2296, 4155, 4171 obtained with the participation of T. miguschovae and line 3261 with the participation of T. palmovae carry a combination of genes (Lr39+Lr26).

Krim-saghyz (Taraxacum hybernum Steven) is an alternative to Hevea brasiliensis as a source of natural rubber. In Russia, krim-saghyz is common only in the Crimean Peninsula and is traditionally named after it. In spite of its potential for economical use, the genetic structure of the Crimean population of this plant is still unexplored. In this regard, the purpose of our work was a comparative molecular-genetic characterization of T. hybernum from various habitats of the Crimean Peninsula using SSR, RAPD and ISSR markers. According to the plan, we collected achenes, leaves and roots of krim-saghyz in 10 spots all over the Crimean Peninsula. We found the plants in the western part of the southern Crimean coast and the western part of the Crimean foothills, which are two general regions of the area of this species. Total DNA was extracted from dry leaves of krim-saghyz with cetyltrimethylammonium bromide (CTAB). For the first time 12 SSR, 3 RAPD and 3 ISSR markers were tested on krim-saghyz. To observe polymorphism of RAPD- and ISSR-fragments, we used analytical electrophoresis in 1.7 % agarose gel. To compare the length of SSR amplicons, we used gel-electrophoresis in 8 % polyacrylamide gel. We found that the Crimean population of krim-saghyz appears to be genetically homogeneous. This could be due to a small geographic range and apomictic reproduction of this species. However, the phenotypical diversity within the population of T. hybernum is well known from the literature. Consequently, the study of the DNA polymorphism of this species should be continued, in particular, with the help of high-resolution techniques.

The pea Pisum sativum is widely cultivated in Russia as well as over the world. Pea productivity depends on the ability of the pea plant to get into a symbiosis with nodule bacteria. It was previously shown that the strength of the symbiotic activity depends on the activity of plant sucrose cleavage enzymes. Sucrose synthase Sus1 is one of the most important enzymes involved in carbohydrate metabolism. Sucrose synthase cleaves sucrose into UDP-glucose and fructose. This paper is devoted to characterization of Sus1 gene intraspecific variability in 14 Pisum sativum accessions. The length of the identified Sus1 gene varied from 3514 bp to 3532 bp. All identified genes had a similar structure and contained 13 exons and 12 introns. According to their structure, they were assigned to the SUS1-group of dicotyledonous plants. In nucleotide sequences, 125 SNPs were identified. In addition to SNPs, intron sequences contained six indels, thus their length varied from 1093 bp to 1111 bp. The most variable was the intron III. In coding sequences, 47 SNPs were found, wherein the most variable was the exon II. 16 exon SNPs led to amino acid substitutions. Six of them were deleterious and may potentially influence protein folding and stability. All the conservative motifs and active sites were detected in the translated amino acid sequences. It was shown that their sequences were invariable in all the tested accessions. Computational analysis of the amino acid sequences has predicted Sus1 tertiary structure. The protein is a tetramer and each subunit in its turn consists of three domains. The phylogenetic analysis using identified Pisum Sus1 sequences and homologous sucrose synthase genes revealed that the Sus1 and Sus3 genes are closer to each other than to Sus2. It was also proposed that the sucrose synthase family genes had diverged before legumes split into species.

The potato (Solanum tuberosum L.) is one of the most important food crops, the advantage of which is the ability to give a high yield in a wide range of agroecosystems, high specific production of dry weight per unit of cultivated area. Nowadays potato is considered a source of vitamins, minerals, dietary fiber and other nutrients. Potato cultivars are characterized by low genetic diversity, which reduces their potential to produce varieties with improved properties. Wild potato relatives retain a high degree of genetic diversity, which can be used to find the superior alleles and for their further transfer to cultural genotypes. To this end, there is an intense development of potato gene banks, with the help of the information technology to access the data. The present review is devoted to global information resources in potato. It describes the most relevant information portals and databases of genetic resources for potatoes. Analysis of information in the Internet shows that the main information resources on potato collections are concentrated in the United States and Europe. Information portals provide a wide variety of information useful to producers, consumers and breeders. On such portals, there is an intensive information support of the latest technologies in the field of potato growing and breeding. An interesting direction is the provision of services to determine the DNA prints (markers) of potato varieties, involvement of potato growers in the process of operational monitoring of diseases and pests of potatoes. Integration of data on potato collections plays an important role at the present stage. In line with this, European collections and databases are being developed. However, despite the existence of pan-European potato collection, national collections are still given support. An important collection-related trend in recent years has been inclusion of samples with a large number (more than a hundred) characteristics, which are evaluated by constantly testing varieties within the framework of foreign state breeding programs. As a result of access to such information, the breeder can effectively plan an experiment with the purpose of directed selection for key features of plants. These trends confirm the effectiveness of the use of the latest technologies (including information) in the maintenance and dissemination of potato genetic resources.

Reactive oxygen species (ROS) are some of the most damaging factors for living systems. Cells produce ROS during normal metabolism reactions, but ROS production increases under stressful conditions. Improving the antioxidant system in cultivated plants will increase their tolerance to abiotic stresses, such as salinity, drought and cold. However, the biochemical components of the system are redundant, for each reaction is catalyzed by a series of enzymes encoded by different genes. Choosing the most perspective components of this system will help speed up evaluating the optimal breeding strategy for improving abiotic stress tolerance in economically valuable plants. In the present research article, we present the results of an integrative analysis of evolution- and expressionrelated characteristics. The work was carried out on a series of genes that belong to 4 functional groups (APX, GPX, SOD and CAT) of enzymatic components of the antioxidant defense system in six species of C₃ cereal plants and 3 species of C₄ cereal plants. As a result, 25 groups of orthologous genes were evaluated and described. The highest gene expression level and the greatest pressure of purifying selection were found to characterize six groups. These genes were chosen for further verification and use in breeding. Because these genes undergo the most conservative evolution and have the highest level of mRNA expression, we may assume that they contribute a lot to the antioxidant system functioning of the C₃ and C₄ cereal plants studied. We have shown that the integration of evolutionary characteristics and expression data represents a promising approach to predict target genes for plant breeding.

The structure of the ear is one of the most important features of cereals associated with such agronomically important traits as productivity, resistance to environmental factors and pests, threshebility. Ears differ in shape, size, density, awnedness, color, etc. Analysis of the ear traits requires visual inspection, manual measurements and is very time-consuming. The effectiveness of ears’ phenotyping can be improved by the introduction of an automated image processing technology, storage of information in databases, use of machine learning algorithms to analyze this information. This paper presents a new approach for collecting, storing and analyzing of information about morphometric characteristics of ears of wheat. Two protocols for obtaining digital images of the ear have been developed. The computer-aided information system SpikeDroidDB has been developed, which allows you to store digital images of the ear, annotate their phenotypic features (14 features, including plant variety description, links to parent genotypes, generation, planting number, ear morphology description). The interface provides a flexible query system to access the data. SpikeDroidDB represents an interconnected representation between genotype, phenotype, location, and growing conditions. The web interface of SpikeDroidDB is available at http://spikedroid.biores. cytogen.ru/ and allows you to work with the system as with desktop computers or mobile devices. We used SpikeDroidDB for the digitization and annotation of a collection of ears of F₂ hybrids from crosses between the Australian cultivar of common wheat Triple Dirk and accession KU506 of Chinese wheat Triticum yunnanense. This experiment includes analysis of 104 plants, 230 spike images. The analysis of the variability of ears in form, length, and other traits allowed determination of the type of their genetic control: compactness is controlled by two recessive genes, awn type and hairi ness at the site of attachment of the spikelet to the axis is controlled by single dominant gene type, hairiness on the axis of the spike is controlled by two dominant genes.

Development and improvement of mathematical methods used in modeling biological systems represents a topical issue of mathematical biology. In this paper, we considered a general form of a system of first-order delayed differential equations, traditionally used for describing the function of biological systems of different hierarchical levels. The main feature of this class of models is that some inherent processes (for example, elongation of DNA, RNA, and protein synthesis) are described in a subtle form and can be explicitly specified only through delayed arguments. In this paper, we propose an algorithm for rewriting systems with constant delayed arguments in an equivalent form that represents a system of partial differential equations with transfer equations. The algorithm is universal, since it does not impose any special conditions on the form of the right-hand parts of systems with delayed arguments. The proposed method is a multivariant algorithm. That is, based on one system of differential equations with delayed arguments, the algorithm allows writing out a number of special systems of partial differential equations, which are equivalent to the original system with delayed argument in the entire solution set. The results obtained indicate that delayed arguments and transfer equations are equivalent mathematical tools for describing all types of dynamic processes of energy and/or matter transfer in biological, chemical, and physical systems, indicating a deep-level similarity between properties of dynamic systems, regardless of their origin. At the same time, those processes that are subtle when retarded argument is used can be explicitly described in the form of transfer equations using systems of partial differential equations. This property is extremely important for the modeling of molecular genetic systems in which processes of DNA, RNA, and protein synthesis proceed at variable rates and need to be considered in certain problems, what can easily be done in models constructed using the mathematical tool of partial derivatives.

Human genes HBB, HBD and F9 belong to the hematopoiesis system. The deficiency or excess of these genes’ products is the cause of hereditary thalassemias of various severity and haemophilia B Leyden. Previously, it was shown that a number of annotated single-nucleotide polymorphisms of TATA boxes of these genes associated with the occurrence of ß- and δ-thalassemia affect the interaction with the TATAbinding protein, the interaction changing proportionally with the change in the number of gene products. In the present work, we investigate the effect of rare not annotated single-nucleotide polymorphisms (SNPs) of TATA boxes of these genes with an unknown manifestation on the TATA-binding protein interaction. To study the kinetic characteristics of TBP/TATA complex formation in vitro, doublestranded oligodeoxynucleotides identical to the TATA-containing portions of the promoters of the HBB, HBD and F9 genes (“normal” and minor alleles) and recombinant human TBP were used. It was shown that the TATA-box SNP of –25A > C (rs281864525) and the deletion of the –25AA (rs63750953) TATA-box of the β-globin gene have the same effect on the TBP/TATA affinity, which decreases 3-folds in both cases. However, the effect of these substitutions on the rate of the TBP/TATA complex formation is significantly different: SNP –25A > C decreases the rate 5-fold, and the deletion decreases the rate more than 7-fold. The influence of substitutions on the strength of the TBP/TATA complexes has a different effect. If in the case of SNP –25A > C the strength of the complexes increases 1.8-fold, then in the case of the –25AA deletion, the strength of the complexes increases 2.4-fold, even though the affinity of the TATAbinding protein to the TATA box decreases. A comparison of experimental values of affinity (KD) of the TBP/T complexes of “normal” and minor alleles with the predicted has shown that data correlate well with each other. The coefficient of linear correlation r = 0.94 (α < 0.0001). A comprehensive approach to the study of rare polymorphisms may lead to the identification of the most sensitive markers of orphan diseases, which will contribute to the development of reliable and rapid methods for their diagnosis and treatment.

Parkinson’s disease (PD) affects an estimated 7–10 million people worldwide and 210000 people in Russia. PD is accompanied by degeneration of dopaminergic neurons and because of that neuronal apoptosis is an important factor in this disease. Analysis of gene networks is one of the key approaches in systems biology. We previously developed the ANDSystem tool, designed to automatically extract knowledge from scientific publications and reconstruct on this basis associative gene networks describing the molecular genetic mechanisms of biological processes. The aim of this work was prioritization of neuronal apoptosis genes by their involvement in PD pathogenesis, taking into account the structure of the PD associative gene network using ANDSystem. Analysis of the centrality of neuronal apoptosis genes, associated with PD, revealed that mean values of degree, closeness and betweenness centralities statistically significantly exceed such values of all nodes of the PD network. The APOE, CASP3 and GAPDH genes involved in neuronal apoptosis were among the most central genes. Prioritization of neuronal apoptosis genes for which there was no data in ANDSystem on their associations with PD was performed using standard methods (Endeavor and ToppGene) and the criteria of centrality and specificity of genes interactions with the PD gene network. Analysis revealed that genes involved in such processes as positive and negative regulation of neu ronal apoptosis, MAPK and ephrin receptor signaling pathways, are mainly represented among candidate genes with the highest priority (top 50, 70, 100 genes were considered). In particular, TP53, JUN, BCL2, PIK3CA and APP were among candidate genes with the highest priority.