LEAF HAIRINESS IN POTATO Solanum tuberosum: MORPHOLOGY, FUNCTION AND METHODS OF ANALYSIS

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

A protocol for analysis of the quantitative characteristics of leaf pubescence in potato

Plant leaf pubescence is one of the important features, which is responsible for microclimate formation near the epidermis. It is involved in protection against adverse biotic and abiotic environmental factors. In Solanaceae, to which belongs the potato Solanum tuberosum L., leaf pubescence appears as multicellular unbranched trichomes of diverse size and morphology. Pubescence of this plants promotes resistance to insect pests, in particular, Colorado potato beetle and aphid, which is a carrier of viral diseases. During the process of breeding and genetic experiments, there is a need to assess the intensity of leaf pubescence of potato plants. For this task, micrographs taken under a microscope are commonly used. They are used to count different types of trichomes on the leaf surface to characterize the intensity of potato leaf pubescence. This approach requires visual counting of trichomes under a microscope and is fairly laborious. This protocol describes a rapid technology for quantitative assessment of the characteristics of potato pubescence (the number of trichomes on the leaf surface and the average length of trichomes) to solve the problems of genetics and breeding of this plant. It consists of a preparation technology, digital imaging of leaf folds with an optical microscope in transmitted light and subsequent automatic processing of images using the LHDetect2 software

Analysis of color and texture characteristics of cereals on digital images

The color of the grain shell of cereals is an important feature that characterizes the pigments and metabolites contained in it. The grain shell is the main barrier between the grain and the environment, so its characteristics are associated with a number of important biological functions: moisture absorption, grain viability, resistance to pre-harvest germination. The presence of pigments in the shell affects various technological properties of the grain. Color characteristics, as well as the appearance of the grain shell are an important indicator of plant diseases. In addition, the color of the grains serves as a classifying feature of plants. Genetic control of the color formation of both grains and other plant organs is exerted by genes encoding enzymes involved in the biosynthesis of pigments, as well as regulatory genes. For a number of pigments, these genes are well understood, but for some pigments, such as melanin, which causes the black color of grains in barley, the molecular mechanisms of biosynthesis are still poorly understood. When studying the mechanisms of genetic control of grain color, breeders and geneticists are constantly faced with the need to assess the color characteristics of their shell. The technical means of addressing this problem include spectrophotometers, spectrometers, hyperspectral cameras. However, these cameras are expensive, especially with high resolution, both spatial and spectral. An alternative is to use digital cameras that allow you to get high-quality images with high spatial and color resolution. In this regard, recently, in the field of plant phenotyping, methods for evaluating the color and texture characteristics of cereals based on the analysis of two-dimensional images obtained by digital cameras have been intensively developed. This mini-review is devoted to the main tasks related to the analysis of color and texture characteristics of cereals, and to methods of their description based on digital images

Online resources on gene networks containing human and animal data

Gene networks are molecular genetic systems that ensure the formation of phenotypic characteristics of organisms (molecular, biochemical, structural, morphological, behavioral, etc.) based on  information encoded in their genomes. Reconstruction of gene networks provides a methodological basis for modern systems biology. In this regard, the information on the structural and functional organization of gene networks accumulated in modern databases is extremely valuable. This review characterizes a number of Internetaccessible information resources oriented to humans and animals and containing data on gene networks and their functional modules. Without pretending to fully cover all information resources containing data related to humans and animals on the subject, the current review was created to report the current status of the problem and to present the criteria according to which we propose to evaluate the utility of webresources for specific research tasks. On this basis, we compiled and characterized a collection of databases containing information on metabolic and signaling pathways, as well as pathways of regulation of biological processes at the cellular and organismal levels. In addition, we observed the characteristics of several well­known databases containing data on interactions between biomolecules of various types. The following characteristics of databases were considered: (1) the types of information accumulated in the databases; (2) methods of data presentation; (3) methods of data collection; (4) data sources; (5) special search tools and options for data analysis. A comparison of the above characteristics showed that the databases are very heterogeneous according to their scopes, sources and types of data, interfaces, as well as according to their search options and data analysis tools. It was concluded that at the first step of the gene network reconstruction it is important to form a full set of information resources from which the data can be obtained. The web portals accumulating information about the databases that may be useful for the reconstruction and analysis of gene networks are specified

INFORMATIONAL RESOURCES ON POTATO GERMPLASM COLLECTIONS

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

Determination of the quantitative content of chlorophylls in leaves by reflection spectra using the random forest algorithm

Determining the quantitative content of chlorophylls in plant leaves by their reflection spectra is an important task both in monitoring the state of natural and industrial phytocenoses, and in laboratory studies of normal and pathological processes during plant growth. The use of machine learning methods for these purposes is promising, since these methods allow inferring the relationships between input and output variables (prediction model), and in order to improve the quality of the prediction, a researcher may modify predictors and selects a set of method parameters. Here, we present the results of the implementation and evaluation of the random forest algorithm for predicting the total concentration of chlorophylls a and b from the ref lection spectra of plant leaves in the visible and infrared wavelengths. We used the ref lection spectra for 276 leaf samples from 39 plant species obtained from open sources. 181 samples were from the sycamore maple (Acer pseudoplatanus L.). The ref lection spectrum represented wavelengths from 400 to 2500 nm with a step of 1 nm. The training set consisted of the 85 % of A. pseudoplatanus L. samples, and the performance was evaluated on the remaining 15 % samples of this species (validation sample). Six models based on the random forest algorithm with different predictors were evaluated. The selection of control parameters was performed by cross-checking on five partitions. For the f irst model, the intensity of the ref lection spectra without any transformation was used. Based on the analysis of this model, the optimal ranges of wavelengths for the remaining f ive models were selected. The best results were obtained by models that used a two-point estimation of the derivative of the ref lection spectrum in the visible wavelength range as input data. We compared one of these models (the two-point estimation of the derivative of the ref lection spectrum in the range of 400–800 nm with a step of 1 nm) with the model by other authors (which is based on the functional dependence between two unknown parameters selected by the least squares method and two ref lection coeff icients, the choice of which is described in the article). The comparison of the results of predictions of the model based on the random forest algorithm with the model of other authors was carried out both on the validation sample of maple and on the sample from other plant species. In the f irst case, the predictions of the method based on a random forest had a lower estimate of the standard deviation. In the second case, the predictions of this method had a large error for small values of chlorophyll, while the third-party method had acceptable predictions. The article provides the analysis of the results, as well as recommendations for using this machine learning method to assess the quantitative content of chlorophylls in leaves

Progress in plant genome sequencing: research directions

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

Computational structural and functional proteomics 235 IDENTIFICATION AND STRUCTURE-FUNCTIONAL ANALYSIS OF THE SPECIFICITY DETERMINING RESIDUES OF THE ALPHA SUBUNITS OF THE PROTEOSOMAL COMPLEX

SUMMARY Motivation: Proteosomes are polyenzymatic proteolytic structures that provide the degradation of the bulk of cytoplasmic proteins to oligopeptides. The proteosomal genes in the eukaryotes all arose by duplication of a single ancestral gene encoding the proteosomal subunits in the bacteria. The analysis of evolutionary events after duplication may be useful for discovering new information about proteosomal structural and functional properties. Results: We confine our study here to the detection of the positions of the α-subunits whose amino acid substitutions are specific to particular subunits of the proteosomal alpha-rings. We detected a set of the α-subunit positions whose substitutions are specific to the genes that encode the various proteosomal subunits. It was demonstrated that these specific amino acid substitutions are the features of residues that form the subunit contacts in the α-ring of the proteosomes. Availability: The proteosomal sequences, multiple sequence alignments and phylogenetic tree used in analysis are available upon request

Human phospholipases A2: a functional and evolutionary analysis

Phospholipases A2 (PLA2) are capable of hydrolyzing the sn-2 position of glycerophospholipids to release fatty acids and lysophospholipids. The PLA2 superfamily enzymes are widespread and present in most mammalian cells and tissues, regulating metabolism, remodeling the membrane and maintaining its homeostasis, producing lipid mediators and activating inflammatory reactions, so disruption of PLA2-regulated lipid metabolism often leads to various diseases. In this study, 29 PLA2 genes in the human genome were systematically collected and described based on literature and sequence analyses. Localization of the PLA2 genes in human genome showed they are placed on 12 human chromosomes, some of them forming clusters. Their RVI scores estimating gene tolerance to the mutations that accumulate in the human population demonstrated that the G4-type PLA2 genes belonging to one of the two largest clusters (4 genes) were most tolerant. On the contrary, the genes encoding G6-type PLA2s (G6B, G6F, G6C, G6A) localized outside the clusters had a reduced tolerance to mutations. Analysis of the association between PLA2 genes and human diseases found in the literature showed 24 such genes were associated with 119 diseases belonging to 18 groups, so in total 229 disease/PLA2 gene relationships were described to reveal that G4, G2 and G7-type PLA2 proteins were involved in the largest number of diseases if compared to other PLA2 types. Three groups of diseases turned out to be associated with the greatest number of PLA2 types: neoplasms, circulatory and endocrine system diseases. Phylogenetic analysis showed that a common origin can be established only for secretory PLA2s (G1, G2, G3, G5, G10 and G12). The remaining PLA2 types (G4, G6, G7, G8, G15 and G16) could be considered evolutionarily independent. Our study has found that the genes most tolerant to PLA2 mutations in humans (G4, G2, and G7 types) belong to the largest number of disease groups

Potato spindle tuber viroid

Viroids belong to a very interesting class of molecules attracting researchers in phytopathology and molecular evolution. Here we review recent literature data concerning the genetics of Potato spindle tuber viroid (PSTVd) and the mechanisms related to its pathological effect on the host plants. PSTVd can be transmitted vertically through microspores and macrospores, but not with pollen from another infected plant. The 359 nucleotidelong genomic RNA of PSTVd is highly structured and its 3D-conformation is responsible for interaction with host cellular factors to mediate replication, transport between tissues during systemic infection and the severity of pathological symptoms. RNA replication is prone to errors and infected plants contain a population of mutated forms of the PSTVd genome. Interestingly, at 7 DAI, only 25 % of the newly synthesized RNAs were identical to the master copy, but this proportion increased to up to 70 % at 14 DAI and remained the same afterwards. PSTVd infection induces the immune response in host plants. There are PSTVd strains with a severe, a moderate or a mild pathological effect. Interestingly, viroid replication itself does not necessarily induce strong morphological or physiological symptoms. In the case of PSTVd, disease symptoms may occur due to RNA-interference, which decreases the expression levels of some important cellular regulatory factors, such as, for example, potato StTCP23 from the gibberellic acid pathway with a role in tuber morphogenesis or tomato FRIGIDA-like protein 3 with an early flowering phenotype. This association between the small segments of viroid genomic RNAs complementary to the untranslated regions of cellular mRNAs and disease symptoms provides a way for new resistant cultivars to be developed by genetic editing. To conclude, viroids provide a unique model to reveal the fundamental features of living systems, which appeared early in evolution and still remain undiscovered