Potato Gene Research Articles

BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans.

We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC–mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.

Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base

The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including potato production. Only a small part of the information reaches formalized databases (for example, Uniprot, NCBI Gene, BioGRID, IntAct, etc.). One of the main sources of reliable biological data is the scientific literature. The well-known PubMed database contains more than 18 thousand abstracts of articles on potato. The effective use of knowledge presented in such a number of non-formalized documents in natural language requires the use of modern intellectual methods of analysis. However, in the literature, there is no evidence of a widespread use of intelligent methods for automatically extracting knowledge from scientific publications on cultures such as potatoes. Earlier we developed the SOLANUM TUBEROSUM knowledge base (http://www-bionet.sysbio.cytogen. ru/and/plant/). Integrated into the knowledge base information about the molecular genetic mechanisms underlying the selection of significant traits helps to accelerate the identification of candidate genes for the breeding characteristics of potatoes and the development of diagnostic markers for breeding. The article searches for new potential participants of the molecular genetic mechanisms of resistance to adverse factors in plants. Prioritizing candidate genes has shown that the PHYA, GF14, CNIH1, RCI1A, ABI5, CPK1, RGS1, NHL3, GRF8, and CYP21-4 genes are the most promising for further testing of their relationships with resistance to adverse factors. As a result of the analysis, it was shown that the molecular genetic relationships responsible for the formation of significant agricultural traits are complex and include many direct and indirect interactions. The construction of associative gene networks and their analysis using the SOLANUM TUBEROSUM knowledge base is the basis for searching for target genes for targeted mutagenesis and marker-oriented selection of potato varieties with valuable agricultural characteristics.

Molecular characterization of a sweet potato stress tolerance-associated trehalose-6-phosphate synthase 1 gene (IbTPS1) in response to abiotic stress

Trehalose-6-phosphate synthase (TPS) plays an important regulatory role in the response of plants to multiple abiotic stresses. However, our knowledge of the stress tolerance functions of TPS genes in sweet potato (Ipomoea batatas [L.] Lam) remains limited. In the present study, we isolated and functionally characterized the sweet potato gene encoding TPS1, IbTPS1. Sequence analysis showed that IbTPS1 belongs to class I TPS proteins and harbors highly conserved acceptor (glucose-6-phosphate [Glc6P]) and donor (uridine diphosphoglucose [UDP-Glc]) binding sites. The IbTPS1 gene showed the highest level of constitutive expression in leaves and storage roots of sweet potato plants and was induced by several environmental stresses including drought, salt, and heat shock. The IbTPS1 protein might be localized to the cytosol. Complementation assay of yeast tps1Δ and tps1Δtps2Δ growth-defective mutants confirmed the TPS activity of IbTPS1, and truncation of the N-terminal extension of IbTPS1 (ΔNIbTPS1) increased the catalytic activity of the protein. Additionally, expression of IbTPS1 in yeast conferred abiotic stress tolerance to dehydration, salinity, and oxidation, and expression of ΔNIbTPS1 further enhanced the tolerance to abiotic stresses. The results of this study advance our understanding of the functions of IbTPS1 under abiotic stress conditions. Our results suggest that the IbTPS1 gene is an excellent candidate for improving the stress tolerance of different crop plants.

Cloning and expression analysis of the StCUL1 gene in potato

The Cullin-RING E3 ubiquitin ligase (CRL) complex is the most common E3 ligase, and the SCF complex (CRL1) has the most diverse functions. Cullin1(CUL1) is a scaffolding protein for assembly of the complex. SCF has been shown to participate in the non-biological stress response pathways. In this study, a classic CUL1 protein was identified in Solanum tuberosum, StCUL1. A full-length cDNA of the StCUL1 gene was obtained from ED13 (a potato variety) by Ralstonia solanacearum inoculation using the RACE method. Sequence analysis indicated that the gene comprised 2662 bp, with an open reading frame of 2229 bp encoding 743 amino acids. The expression levels of the StCUL1 gene in potato treated with R. solanacearum and exogenous hormones (such as salicylic acid, jasmonic acid methyl ester and abscisic acid) at different time points were determined by real-time PCR. The results indicated that StCUL1 was induced not only by pathogenic bacteria, but also by exogenous hormones, with sustained high expression. However, there were some differences in the modes of expression. Tissue localization analysis indicated that its expression was tissue specific, and it was mainly in the phloem of the vascular system of stems and leaves.

Genome-wide identification and characterization of HD-ZIP genes in potato

HD-ZIP (Homeodomain leucine zipper) transcription factors play an important regulatory role in stress resistance in plants. The purpose of this study was to analyze the characteristics of the HD-ZIP genes/proteins and to study their expression profiles under high and low temperature conditions in potato (Solanum tuberosum L.). A strict homology search was used to find 43 HD-ZIP genes located on potato chromosomes 1–12. Exons/introns, protein features and conserved motifs were analyzed, and six segment duplications were identified from 43 HD-ZIP genes. Then, we analyzed the data from the PGSC (Potato Genome Sequencing Consortium) database regarding the expression of 43 HD-ZIP genes that were induced by biotic and abiotic stresses and phytohormone treatments and conducted an expression analysis for these genes across all potato life stages. Additionally, the expression levels of 13 HD-ZIP genes were analyzed under high temperature (37 °C) and low temperature (4 °C) conditions. The results showed that the transcript levels of all 13 genes changed, which indicated that these genes respond to heat and cold in plants. Especially for StHOX20, the expression significantly upregulated in roots at 37 °C and 4 °C. Our findings laid the foundation and provided clues for understanding the biological functions of HD-ZIP family genes.

Genome-wide Identification, Expression Profiling and Evolutionary Analysis of Auxin Response Factor Gene Family in Potato (Solanum tuberosum Group Phureja)

Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.

Transgene-Free Genome Editing in Tomato and Potato Plants Using Agrobacterium-Mediated Delivery of a CRISPR/Cas9 Cytidine Base Editor.

Genome editing tools have rapidly been adopted by plant scientists for gene function discovery and crop improvement. The current technical challenge is to efficiently induce precise and predictable targeted point mutations valuable for crop breeding purposes. Cytidine base editors (CBEs) are CRISPR/Cas9 derived tools recently developed to direct a C-to-T base conversion. Stable genomic integration of CRISPR/Cas9 components through Agrobacterium-mediated transformation is the most widely used approach in dicotyledonous plants. However, elimination of foreign DNA may be difficult to achieve, especially in vegetatively propagated plants. In this study, we targeted the acetolactate synthase (ALS) gene in tomato and potato by a CBE using Agrobacterium-mediated transformation. We successfully and efficiently edited the targeted cytidine bases, leading to chlorsulfuron-resistant plants with precise base edition efficiency up to 71% in tomato. More importantly, we produced 12.9% and 10% edited but transgene-free plants in the first generation in tomato and potato, respectively. Such an approach is expected to decrease deleterious effects due to the random integration of transgene(s) into the host genome. Our successful approach opens up new perspectives for genome engineering by the co-edition of the ALS with other gene(s), leading to transgene-free plants harboring new traits of interest.

Virus resistance of potato genetic diversity under climate change

Aim. To determine the resistance of potato gene pool accessions to viruses in the southern forest-steppe of Ukraine and to select starting material for breeding. Results and Discussion. Our analysis of the climate changes for the period of 1955–2018 revealed that the unfavorable weather/climatic conditions during spring planting of tubers, as a result of which weakened plants were more easily depressed by viral infections, were the primary cause of potato cacogenesis in the southern forest-steppe of Ukraine. It was found that significant deviations from the multi-year average temperature and amount of precipitation contributed to the intense mass manifestation of symptoms of viral diseases or under favorable weather/climatic conditions, on the contrary, viral diseases were not visually detected. Studies have shown that the main factor in resistance to viral degeneration of potato varieties is the genotype, and its development and expression depend on growing conditions. It is also important to take into account emergence of new strains of viruses requiring continuous monitoring. Virus resistance of the varieties was visually determined. In order to identify viruses and study their morphology, electron microscopy, EIA and PCR were used. Conclusions. As a result of the study, sources of high field resistance to leaf-rolling, potato rugose and streak mosaics, which are valuable starting material for further practical use in breeding, as well as in scientific and educational programs, were identified.

Genome-wide identification and expression analysis of StTCP transcription factors of potato (Solanum tuberosum L.)

The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redundant TCP transcription factors of potato were identified and divided into two subfamilies including three distinct subclades. The various orthologous TCP genes in Arabidopsis, rice, potato and tomato were identified using synteny and phylogenetic analysis. Protein motif analysis demonstrated that StTCPs in the same subclade shared similar conserved motif structures. Gene structure analysis showed that almost all StTCPs displayed highly conserved exon-intron organization. The analysis of StTCP gene promoter regions revealed that multiple cis-acting elements were involved in plant growth, development, hormone responses as well as stress responses. The result of StTCP gene expression profiles showed they had tissue-specific expression patterns which implied their differentiated functions. According to the results of quantitative RT-PCR (qRT-PCR), 7 StTCP genes were dramatically up-regulated during the release of tuber dormancy and some specific StTCP genes were strongly responding to different abiotic stresses and multiple hormones, which suggested they had important roles in potato growth and development processes. The results of our findings could provide comprehensive insights in StTCP family genes of potato for further functional investigations.

Genome-wide analysis of the MATE gene family in potato.

The multidrug and toxic compound extrusion (MATE) protein family is a newly discovered family of secondary transporters that extrude metabolic waste and a variety of antibiotics out of the cell using an electrochemical gradient of H+ or Na+ across the membrane. The main function of MATE gene family is to participate in the process of plant detoxification and morphogenesis. The genome-wide analysis of the MATE genes in potato genome was conducted. At least 48 genes were initially identified and classified into six subfamilies. The chromosomal localization of MATE gene family showed that they could be distributed on 11 chromosomes except chromosome 9. The number of amino acids is 145-616, the molecular weight of proteins is 15.96-66.13 KD, the isoelectric point is 4.97-9.17, and they were located on the endoplasmic reticulum with having 4-13 transmembrane segments. They contain only two parts of the exons and UTR without introns. Some members of the first subfamily of potato MATE gene family are clustered with At2g04070 and they may be related to the transport of toxic compounds such as alkaloids and heavy metal. The function of the members of the second subfamily may be similar to that of At3g23560, which is related to tetramethylammonium transport. Some members of the third subfamily are clustered with At3g59030 and they may be involved in the transport of flavonoids. The fifth subfamily may be related to the transport of iron ions. The function of the sixth subfamily may be similar to that of At4g39030, which is related to salicylic acid transport. There are three kinds of conserved motifs in potato MATE genes, including the motif 1, motif 2, and motif 3. Each motif has 50 amino acids. The number of each motif is different in the gene sequence, of which 45 MATE genes contain at least a motif, but there is no motif in ST0015301, ST0045283, and ST0082336. These results provide a reference for further research on the function of potato MATE genes.

MicroR408 regulates defense response upon wounding in sweet potato.

MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.

Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance.

Sweet potato (Ipomoea batatas [L.] Lam.) is an important subsistence crop in Sub‐Saharan Africa, yet as for many crops, yield can be severely impacted by drought stress. Understanding the genetic mechanisms that control drought tolerance can facilitate the development of drought‐tolerant sweet potato cultivars. Here, we report an expression profiling study using the US‐bred cultivar, Beauregard, and a Ugandan landrace, Tanzania, treated with polyethylene glycol (PEG) to simulate drought and sampled at 24 and 48 hr after stress. At each time‐point, between 4,000 to 6,000 genes in leaf tissue were differentially expressed in each cultivar. Approximately half of these differentially expressed genes were common between the two cultivars and were enriched for Gene Ontology terms associated with drought response. Three hundred orthologs of drought tolerance genes reported in model species were identified in the Ipomoea trifida reference genome, of which 122 were differentially expressed under at least one experimental condition, constituting a list of drought tolerance candidate genes. A subset of genes was differentially regulated between Beauregard and Tanzania, representing genotype‐specific responses to drought stress. The data analyzed and reported here provide a resource for geneticists and breeders toward identifying and utilizing drought tolerance genes in sweet potato.

Finding RB/Rpi-blb1/Rpi-sto1-like sequences in conventionally bred potato varieties

The main objectives in potato breeding are increasing yield abilities and improving resistance to numerous pathogens and pests. Among them, the late blight caused by the Phytophthora infestans oomycete is one of the most destructive potato diseases both in Russia and worldwide. Wild relatives of cultivated potato are traditionally used in breeding as the source of valuable R genes conferring resistance to pathogens. Of particular interest are Mexican wild species because Mexico is the centre of origin and diversity of P. infestans and at the same time, it is the centre of potato species diversity. Mexican wild potato species S. bulbocastanum and S. stoloniferum are an important source of the R genes conferring broad-spec trum resistance against various isolates of P. infestans (Rpi-blb1, Rpi-blb2, Rpi-sto1). Recently these genes have been transferred into cultivated potato gene pool using the cisgene approach. At the same time there is a high probability of finding geno types with the Rpi-sto1 gene (functional homologues of Rpi-blb1) among conventionally bred varieties because for about 40 years S. stoloniferum has been used in breeding as a source of the Rysto and Ry-fsto genes of the extreme resistance to the most important viral pathogen PVY. In this study 188 potato varieties bred in Russia and in near-abroad countries were screened for the presence of six gene-specific markers of the RB/Rpi-blb1 = Rpi-sto1 and Rpi-blb2 genes conferring broad-spectrum resistance against P. infestans, and for the markers linked to the Rysto and Ry-fsto genes conferring extreme resistance to PVY. In addition, a marker for detecting male sterile mitochondrial DNA type gamma derived from S. stoloniferum was used. The genotypes selected through the molecular markers were divided into four groups: (A) 13 PVY resistant varieties carrying diagnostic markers of the Rysto, Ry-fsto genes and having sterile mt-type gamma; (B) four varieties possessing mt-type gamma and not having the markers of the R genes introgressed from S. stoloniferum; (C) eight genotypes carrying five gene-specific markers for the RB/Rpi-blb1/= Rpi-sto1; (D) the rest 166 (86.9 %) varieties not possessing any of the diagnostic markers associated with the S. stoloniferum genetic material. The sequences of the Rpi-sto1- and BLB1 F/R-amplicons were identical in all the genotypes of group ‘C’ and showed respective 99 % and 100 % similarity to the corresponding fragments of the Rpi-sto1 and Rpi-blb1 genes from the GenBank database. Among the genotypes of group ‘C’ various mt-types were detected, and some of them were male fertile.

Expression of the Arabidopsis ABF4 gene in potato increases tuber yield, improves tuber quality and enhances salt and drought tolerance.

In this study we show that expression of the Arabidopsis ABF4 gene in potato increases tuber yield under normal and abiotic stress conditions, improves storage capability and processing quality of the tubers, and enhances salt and drought tolerance. Potato is the third most important food crop in the world. Potato plants are susceptible to salinity and drought, which negatively affect crop yield, tuber quality and market value. The development of new varieties with higher yields and increased tolerance to adverse environmental conditions is a main objective in potato breeding. In addition, tubers suffer from undesirable sprouting during storage that leads to major quality losses; therefore, the control of tuber sprouting is of considerable economic importance. ABF (ABRE-binding factor) proteins are bZIP transcription factors that regulate abscisic acid signaling during abiotic stress. ABF proteins also play an important role in the tuberization induction. We developed transgenic potato plants constitutively expressing the Arabidopsis ABF4 gene (35S::ABF4). In this study, we evaluated the performance of 35S::ABF4 plants grown in soil, determining different parameters related to tuber yield, tuber quality (carbohydrates content and sprouting behavior) and tolerance to salt and drought stress. Besides enhancing salt stress and drought tolerance, constitutive expression of ABF4 increases tuber yield under normal and stress conditions, enhances storage capability and improves the processing quality of the tubers.

Molecular characterization of nine sweet potato (Ipomoea batatas Lam.) MADS‐box transcription factors during storage root development and following abiotic stress

AbstractSweet potato is an important plant for researchers to study storage root development and resistance. MADS‐box proteins are a group of important transcription factors which play a crucial role in plant development as well as stress response. However, the investigation regarding sweet potato MADS‐box genes remains limited up to now. In this study, nine MADS‐box genes, named as IbMBP1˜IbMBP9, were cloned and characterized. Nine genes exhibited different tissue‐specific expression profiles. IbMBP2, IbMBP3, IbMBP4 and IbMBP9 showed high expression during storage roots development and were upregulated by storage roots development‐related hormones. Varying degrees of induction was observed in the transcript level of these MADS‐box genes under multiple abiotic stresses, as well as stress‐related hormones. The present results revealed that nine MADS‐box genes exhibited different tissue‐specific expression profiles and were impacted by multiple abiotic stresses and/or hormones, which lay a good foundation for further exploring the function of MADS‐box genes in sweet potato.

Multiplex PCR for detection and quantification of GM potato event EH92-527-1 in food

Aim - the elaboration of the protocol for the quantitative detection of genetically modified (GM) potato event EH92-527-1 in the format of duplex real-time polimerase chain reaction (RT-PCR) with TaqMan® PCR technology. Material and methods. The duplex system included two types of specific DNA primers and fluorescent probes: the 1st was for identifying of the event-specific EH92-527-1 DNA, the 2nd was for identifying of the taxon-specific potato gene Stp23. The selection of PCR parameters was carried out by empirical assortment of primers and probes, Mg2+-ions, deoxyribonucleotides and polymerase stabilizing agent, primers annealing temperature and incubation time for the each cycle stage. The results of this research was the optimization of the reaction mixture composition for EH92-527-1 event and Stp23 gene fragment identification in the duplex system: 2.5× RT-PCR buffer in the presence of ROX, primers specific for the GM potato (EH92- f/EH92-r) and target taxon (GРF3/GРR3) in the amount of 250/250 and 100/100 nM, probes - 200 and 200 nM, respectively; bovine serum albumin - 0.04%; MgCl2 - 3.5 mM, deoxynucleoside triphosphates - 0.3 mM, as well as the temperature-time reaction profile (initial denaturation at 95°C - 5 minutes, the next 45 cycles: 95 °C - 20 seconds, 58 °C - 20 seconds, 62 °C - 40 seconds). Conclusion. The method for the quantitative detection of genetically modified (GM) potato event EH92-527-1 in the format of duplex RT-PCR has been elaborated. The linearity, precision, accuracy and limit of the method definition are confirmed with in vitro studies, that results testify to the method's reliability.

Identification of multiple genes encoding SnRK1 subunits in potato tuber.

BackgroundMany studies have proven the importance of SnRK1 in the regulation of carbohydrate metabolism and plant development. Compared to Arabidopsis, much less is known about SnRK1 complexes in crop plants, and therefore, more work needs to be done to identify SnRK1 genes and to investigate their function in crop plants.MethodsIn this study we identified five SnRK1-related genes in potato by analyzing the potato genome through BLAST, which encode one α-subunit isoform (stKIN), two β-subunit isoforms (stKINβ1 and stKINβ2) and two γ-subunit isoforms (stKINγ and stKINβγ). To investigate the functions of SnRK1 in the tuber development of potato, we further made overexpression and RNAi transgenic plants of these five genes. Based on these overexpression transgenic plants, the Fast protein liquid chromatography (FPLC) were employed to purify SnRK1 complexes, which were tracked by western-blot.ResultsExperiments in vivo and in vitro showed that these five proteins in potato are functional SNF1/AMPK/SnRK1-related proteins. The SnRK1 activity decreased by 60% in the RNAi transgenic lines of stKIN; the starch content increased by 25% in the overexpression transgenic lines of stKIN, compared to that in the wild-type lines, whereas there is no significant difference in SnRK1 activity and starch content in the RNAi transgenic or overexpression lines of stKINβ1, stKINβ2, stKINγ and stKINβγ. In addition, we found that a few different SnRK1 complexes are present in potato by partially purifying SnRK1 complexes from these overexpression transgenic plants.ConclusionsFive functional SnRK1-related genes were identified in potato, including three novel genes, which encode one α-subunit isoform (stKIN), two β-subunit isoforms (stKINβ1 and stKINβ2) and two γ-subunit isoforms (stKINγ and stKINβγ). We found that a few SnRK1 related genes are present in potato tuber, which form several different SnRK1 isoenzymes. We found that stKIN is the primary α subunit of SnRK1 in potato tuber and plays important roles in the development of potato tubers.

Overexpression of PDX-II gene in potato (Solanum tuberosum L.) leads to the enhanced accumulation of vitamin B6 in tuber tissues and tolerance to abiotic stresses

Vitamin B6 is a vital metabolite required for living organisms as a cofactor in several metabolic biochemical reactions and recognized as a potent antioxidant molecule which modulates the expression of the proteins responsible for the scavenging of cellular reactive oxygen species. It is well established that the microorganisms and plants can synthesize the B6 de novo, therefore, all the animals including humans must acquire it from the plant dietary resources. However, the bioavailability of the vitamin in the edible portions of the commonly consumed plants is insufficient to meet the daily recommended doses. Genetic engineering techniques have proven successful in increasing the vitamin B6 content in the model plants. Present study describe the development of transgenic potato (Solanum tuberosum L. cv. Kufri chipsona) overexpressing key vitamin B6 pathway gene, the PDXII (NCBI database Ref. ID- NM_125447.2) isolated from Arabidopsis thaliana under the control of CaMV 35S constitutive promoter. The stable integration and expression of transgene in the transgenic lines were confirmed by PCR, Southern blot and RT-PCR analysis. Transgenic tubers exhibited considerably improved vitamin B6 accumulation (up to 107–150%) in comparison to the untransformed controls potato. This increase in vitamin B6 was also correlated with the increased mRNA expression of PDXII gene. The prominent increase in the B6 content of transgenic potato was also associated with the capability to survive under abiotic stresses, therefore, the transgenic lines were able to withstand various abiotic stresses imposed by salinity (NaCl) or methyl viologen (MV). We thus demonstrated that overexpression of PDXII gene under the control of a constitutive promoter enhanced the accumulation of the vitamin B6 which also augmented the tolerance under various abiotic stresses in potato (Solanum tuberosum L.).

Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network.

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper (Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L. NAC (CaNAC) proteins. In the present study, a comprehensive analysis of the CaNAC gene family in pepper was performed, and a total of 104 CaNAC genes were identified. Genome mapping analysis revealed that CaNAC genes were enriched on four chromosomes (chromosomes 1, 2, 3, and 6). In addition, phylogenetic analysis of the NAC domains from pepper, potato, Arabidopsis, and rice showed that CaNAC genes could be clustered into three groups (I, II, and III). Group III, which contained 24 CaNAC genes, was exclusive to the Solanaceae plant family. Gene structure and protein motif analyses showed that these genes were relatively conserved within each subgroup. The number of introns in CaNAC genes varied from 0 to 8, with 83 (78.9%) of CaNAC genes containing two or less introns. Promoter analysis confirmed that CaNAC genes are involved in pepper growth, development, and biotic or abiotic stress responses. Further, the expression of 22 selected CaNAC genes in response to seven different biotic and abiotic stresses [salt, heat shock, drought, Phytophthora capsici, abscisic acid, salicylic acid (SA), and methyl jasmonate (MeJA)] was evaluated by quantitative RT-PCR to determine their stress-related expression patterns. Several putative stress-responsive CaNAC genes, including CaNAC72 and CaNAC27, which are orthologs of the known stress-responsive Arabidopsis gene ANAC055 and potato gene StNAC30, respectively, were highly regulated by treatment with different types of stress. Our results also showed that CaNAC36 plays an important role in the interaction network, interacting with 48 genes. Most of these genes are in the mitogen-activated protein kinase (MAPK) family. Taken together, our results provide a platform for further studies to identify the biological functions of CaNAC genes.

THE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYS

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/.