Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis.

BACKGROUND: Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants. RESULTS: This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs' abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the 'Atlantic' (drought-sensitive cultivar, DS) and the 'Qingshu NO.9' (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants. CONCLUSION: In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.

Integrated transcriptomic and metabolomic analysis revealed altitude-related regulatory mechanisms on flavonoid accumulation in potato tubers.

Not least because it is adaptable to a variety of geographies and climates, potato (Solanum tuberosum L.) is grown across much of the world. Pigmented potato tubers have been found to contain large quantities of flavonoids, which have various functional roles and act as antioxidants in the human diet. However, the effect of altitude on the biosynthesis and accumulation of flavonoids in potato tubers is poorly characterized. Here we carried out an integrated metabolomic and transcriptomic study in order to evaluate how cultivation at low (800 m), moderate (1800 m), and high (3600 m) altitude affects flavonoid biosynthesis in pigmented potato tubers. Both red and purple potato tubers grown at a high altitude contained the highest flavonoid content, and the most highly pigmented flesh, followed by those grown at a low altitude. Co-expression network analysis revealed three modules containing genes which were positively correlated with altitude-responsive flavonoid accumulation. The anthocyanin repressors StMYBATV and StMYB3 exhibited a significant positive relationship with altitude-responsive flavonoid accumulation. The repressive function of StMYB3 was further verified in tobacco flowers and potato tubers. The results presented here add to the growing body of knowledge regarding the response of flavonoid biosynthesis to environmental conditions, and should aid in efforts to develop novel varieties of pigmented potatoes for use across different geographies.

Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation.

Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.

Expression of Potato StDRO1 in Arabidopsis Alters Root Architecture and Drought Tolerance.

Potato (Solanum tuberosum L) is the third important crop for providing calories to a large human population, and is considered sensitive to moderately sensitive to drought stress conditions. The development of drought-tolerant, elite varieties of potato is a challenging task, which can be achieved through molecular breeding. Recently, the DEEPER ROOTING 1 (DRO1) gene has been identified in rice, which influences plant root system and regulates grain yield under drought stress conditions. The potato StDRO1 protein is mainly localized in the plasma membrane of tobacco leaf cells, and overexpression analysis of StDRO1 in Arabidopsis resulted in an increased lateral root number, but decreased lateral root angle, lateral branch angle, and silique angle. Additionally, the drought treatment analysis indicated that StDRO1 regulated drought tolerance and rescued the defective root architecture and drought-tolerant phenotypes of Atdro1, an Arabidopsis AtDRO1 null mutant. Furthermore, StDRO1 expression was significantly higher in the drought-tolerant potato cultivar "Unica" compared to the drought-sensitive cultivar "Atlantic." The transcriptional response of StDRO1 under drought stress occurred significantly earlier in Unica than in Atlantic. Collectively, the outcome of the present investigation elucidated the role of DRO1 function in the alternation of root architecture, which potentially acts as a key gene in the development of a drought stress-tolerant cultivar. Furthermore, these findings will provide the theoretical basis for molecular breeding of drought-tolerant potato cultivars for the farming community.

Potential of an endophytic bacteria Bacillus amyloliquefaciens 3-5 as biocontrol agent against potato scab.

To obtain a potential biocontrol agent for potato scab, 75 endophytic bacteria were isolated from the healthy potato tubers and strain 3-5 was selected as an optimal antagonistic bacterium against Streptomyces griseoplanus (Streptacidiphilus griseoplanus) causing potato scab. Strain 3-5 was identified as Bacillus amyloliquefaciens based on its morphological characteristics, 16S rDNA and gyrB gene sequence analysis. B. amyloliquefaciens 3-5 has biological functions of indole-3-acetic acid (IAA) production and nitrogen fixation. Polymerase chain reaction (PCR) detection revealed that B. amyloliquefaciens 3-5 had 6 diverse antibacterial substance synthesis genes, named bacD, bacAB, ituD, ituC, sfP and albF, which resulted in the production of bacilysin, iturin, surfactin and subtilosin. Field efficacy evaluation revealed that B. amyloliquefaciens 3-5 (solid fermentation) was successful in controlling potato scab with a 38.90 ± 3.2140% efficiency which is higher than other chemical bactericides except zhongshengmycin·oligosaccharins and kasugamycin·zhongshengmycin. The endophytic bacterium B. amyloliquefaciens 3-5 could be used as a biocontrol agent against potato scab due its control efficacy and environmental safety.

Genome-Wide Identification and Analysis of the NF-Y Gene Family in Potato (Solanum tuberosum L.).

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which is composed of three subunits (NF-YA, NF-YB, and NF-YC). NF-Y has been identified as a key regulator of multiple pathways in plants. Although the NF-Y gene family has been identified in many plants, it has not been reported in potato (Solanum tuberosum). In the present study, a total of 41 NF-Y proteins in potato (StNF-Ys) were identified, including 10 StNF-YA, 22 StNF-YB, and nine StNF-YC subunits, and their distribution on chromosomes, gene structure, and conserved motif was analyzed. A synteny analysis indicated that 14 and 38 pairs of StNF-Y genes were orthologous to Arabidopsis and tomato (Solanum lycopersicum), respectively, and these gene pairs evolved under strong purifying selection. In addition, we analyzed the expression profiles of NF-Y genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the Potato Genome Sequencing Consortium (PGSC) database. Furthermore, we performed RNA-seq on white, red, and purple tuber skin and flesh of three potato cultivars at the tuber maturation stage to identify genes that might be involved in anthocyanin biosynthesis. These results provide valuable information for improved understanding of StNF-Y gene family and further functional analysis of StNF-Y genes in fruit development, abiotic stress tolerance, and anthocyanin biosynthesis in potato.

ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review.

Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of "superweeds" and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes.

Integration of mRNA and miRNA analysis reveals the molecular mechanism of potato (Solanum tuberosum L.) response to alkali stress.

The continuing increase in the global saline-alkali land area has made saline-alkali stress the principal abiotic stress limiting plant growth. Potato is the most important non-grain crop, and its production is also severely limited by saline-alkali stress. However, few studies have addressed the mechanism of saline-alkali tolerance of potato with a focus on its response to neutral salt NaCl stress, or its response to alkali stress. Recently, miRNA-mRNA analyses have helped advance our understanding of how plants respond to stress. Here, we have characterized the morphological, physiological, and transcriptome changes of tissue culture seedlings of potato variety "Qingshu No. 9" treated with NaHCO3 (for 0, 2, 6, and 24 h). We found that the leaves of tissue culture seedlings wilted and withered under alkali stress, and the contents of ABA, BRs, trehalose, and lignin in roots increased significantly. The contents of GAs decreased significantly. Subsequently, miRNA-seq analysis results identified 168 differentially expressed miRNAs (DEMIs) under alkali stress, including 21 exist miRNAs and 37 known miRNAs from 47 families and 110 novel miRNAs. The mRNA-seq results identified 5731 differentially expressed mRNAs (DEMs) under alkali stress. By miRNA-mRNA integrated analysis, were obtained 33 miRNA-target gene pairs composed of 20 DEMIs and 33 DEMs. Next, we identified the "phenylpropanoid biosynthesis", "plant hormone signal transduction", and "starch and sucrose metabolism" pathways as necessary for potato to respond to alkali stress. miR4243-x and novel-m064-5p were involved in the response of potato to alkali stress by their negative regulatory effects on shikimate O-hydroxycinnamoyltransferase (HCT) and sucrose-phosphate synthase (SPS) genes, respectively. The expression results of miRNA and mRNA were verified by quantitative real-time PCR (qRT-PCR). Our results clarify the mechanism of potato response to alkali stress at the miRNA level, providing new insights into the molecular mechanisms of potato's response to alkali stress. We report many candidate miRNAs and mRNAs for molecular-assisted screening and salt-alkali resistance breeding.

Genomic survey and gene expression analysis of the MYB-related transcription factor superfamily in potato (Solanum tuberosum L.).

The MYB transcription factors (TFs) comprise a major TF family in the plant kingdom. Studies increasingly show that MYB-related genes drive physiological functions in plants. However, little is known regarding their regulatory networks and downstream pathways in potato. We conducted a genome-wide analysis of MYB TFs and related proteins in potato (Solanum tuberosum, abbreviated as St), and identified 138 StMYB-related TFs that were phylogenetically classified into three distinct subgroups based on highly conserved gene structures, consensus motifs and protein domain architecture. Segmental duplication events were detected in the StMYB-related gene family by collinearity analysis, which likely contributed to the expansion of this family. Synteny analysis indicated that 41 StMYB-related genes were orthologous to Arabidopsis and 24 to wheat. In addition, RNA-seq analysis identified several tissue-specific and abiotic stress-responsive StMYB-related genes. To determine a potential role of these genes in anthocyanin biosynthesis and drought response, we analyzed the transcriptomes of the white, pigmented, drought-sensitive ('Atlantic') and drought-resistant ('Qingshu No.9') tetraploid potato cultivars from three flowering stages: early, peak (full blooms) and late (foliage falling). The interaction networks of StMYB-related proteins that were differentially expressed between pigmented versus white, as well as the drought-tolerant versus sensitive cultivars were also predicted. Our findings lay the foundation for prospective functional studies of potato StMYB-related TFs.

Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.).

Plant Q-type C2H2 zinc finger proteins play an important role in plant tolerance to abiotic stresses. Although the Q-type C2H2 gene family has been identified in many plants, little is known about it in potato (Solanum tuberosum). In the present study, a total of 79 Q-type C2H2 proteins in potato (StZFPs) were identified and their distribution on chromosomes, gene structure, and conserved motifs was assessed. According to their protein structural and phylogenetic features, these 79 StZFPs were classified into 12 distinct subclasses. Collinearity analysis showed that tandem and segmental duplication events played a crucial role in expansion of the StZFP gene family. Synteny analysis indicated that 11 and 21 StZFP genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively. RNA-seq data were used to analyze the tissue-specific expression and abiotic stress responses of the StZFP genes. Furthermore, we analyzed the expression of StZFP genes in drought-sensitive and drought-tolerant potato cultivars under drought stress. Subsequently, we used qPCR (Quantitative real-time-PCR) to calculate the relative expression of candidate genes in potato plantlets treated with NaCl (100 mM) and PEG 6000 (10% w/v) for 24 h. Such candidate genes could provide valuable information for abiotic stress resistance research in potato.

Genome-wide analysis and expression profiles of the StR2R3-MYB transcription factor superfamily in potato (Solanum tuberosum L.).

MYB transcription factors comprise one of the largest families in plant kingdom, which play a variety of functions in plant developmental processes and defence responses, the R2R3-MYB members are the predominant form found in higher plants. In the present study, a total of 111 StR2R3-MYB transcription factors were identified and further phylogenetically classified into 31 subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that the segmental duplication events played a crucial role in the expansion of StR2R3-MYB gene family. Synteny analysis indicated that 37 and 13 StR2R3-MYB genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively, and these gene pairs have evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-preferential and abiotic stress-responsive StR2R3-MYB genes. We further analyzed StR2R3-MYB genes might be involved in anthocyanin biosynthesis and drought stress by using RNA-seq data of pigmented tetraploid potato cultivars and drought-sensitive and -tolerant tetraploid potato cultivars under drought stress, respectively. Moreover, EAR motifs were found in 21 StR2R3-MYB proteins and 446 pairs of proteins were predicted to interact with 21 EAR motif-containing StR2R3-MYB proteins by constructing the interaction network with medium confidence (0.4). Additionally, Gene Ontology (GO) analysis of the 21 EAR motif-containing StR2R3-MYB proteins was performed to further investigate their functions. This work will facilitate future biologically functional studies of potato StR2R3-MYB transcription factors and enrich the knowledge of MYB superfamily genes in plant species.

Improving salt tolerance in potato through overexpression of AtHKT1 gene.

BACKGROUND: Survival of plants in response to salinity stress is typically related to Na+ toxicity, but little is known about how heterologous high-affinity potassium transporter (HKT) may help alleviate salt-induced damages in potato (Solanum tuberosum L.). RESULTS: In this study, we used the Arabidopsis thaliana high-affinity potassium transporter gene (AtHKT1) to enhance the capacity of potato plants to tolerate salinity stress by decreasing Na+ content and improving K+/Na+ ratio in plant leaves, while maintaining osmotic balance. Seven AtHKT1 transformed potato lines (namely T1, T2, T3, T5, T11, T13 and T15) were compared with non-transgenic control plant at molecule and whole-plant levels. The lines T3 and T13 had the highest AtHKT1 expression with the tolerance index (an quantitative assessment) being 6.8 times that of the control. At 30 days under 100 and 150 mmol L- 1 NaCl stress treatments, the T3 and T13 lines had least reductions in net photosynthetic rate, stomatal conductance and transpiration rate among the seven lines, leading to the increased water use efficiency and decreased yield loss. CONCLUSIONS: We conclude that the constitutive overexpression of AtHKT1 reduces Na+ accumulation in potato leaves and promotes the K+/Na+ homeostasis that minimizes osmotic imbalance, maintains photosynthesis and stomatal conductance, and increases plant productivity.

StMYB44 negatively regulates anthocyanin biosynthesis at high temperatures in tuber flesh of potato.

High temperatures are known to reduce anthocyanin accumulation in a number of diverse plant species. In potato (Solanum tuberosum L.), high temperature significantly reduces tuber anthocyanin pigment content. However, the mechanism of anthocyanin biosynthesis in potato tuber under heat stress remains unknown. Here we show that high temperature causes reduction of anthocyanin biosynthesis in both potato tuber skin and flesh, with white areas forming between the vasculature and periderm. Heat stress reduced the expression of the R2R3 MYB transcription factors (TFs) StAN1 and StbHLH1, members of the transcriptional complex responsible for coordinated regulation of the skin and flesh pigmentation, as well as anthocyanin biosynthetic pathway genes in white regions. However, the core phenylpropanoid pathway, lignin, and chlorogenic acid (CGA) pathway genes were up-regulated in white areas, suggesting that suppression of the anthocyanin branch may result in re-routing phenylpropanoid flux into the CGA or lignin biosynthesis branches. Two R2R3 MYB TFs, StMYB44-1 and StMYB44-2, were highly expressed in white regions under high temperature. In transient assays, StMYB44 represses anthocyanin accumulation in leaves of Nicotiana tabacum and N. benthamiana by directly suppressing the activity of the dihydroflavonol reductase (DFR) promoter. StMYB44-1 showed stronger repressive capacity than StMYB44-2, with both predicted proteins containing the repression-associated EAR motif with some variation. StMYB44-1 conferred repression without a requirement for a basic helix-loop-helix (bHLH) partner, suggesting a different repression mechanism from that of reported anthocyanin repressors. We propose that temperature-induced reduction of anthocyanin accumulation in potato flesh is caused by down-regulation of the activating anthocyanin regulatory complex, by enhancing the expression of flesh-specific StMYB44 and alteration of phenylpropanoid flux.

AtHKT1 gene regulating K+ state in whole plant improves salt tolerance in transgenic tobacco plants.

The status of K+ is important for plant health. However, little is known about if high-affinity potassium transporter HKTs may help K+ retention under salt stress. Here, we determined the effect of Arabidopsis thaliana transporter gene (AtHKT1) on the K+ status, Na+-induced toxicity, and salt tolerance in tobacco (Nicotiana tabacum L.). Six AtHKT1 transformed tobacco lines (T1, T2, … T6) were contrasted with a non-transgenic plantlet at the whole-plant and molecule levels. AtHKT1 gene was expressed in the xylems of stem, root and leaf vein in the transgenic tobacco, with the line T3 having highest expression. At Day 15, in the 200 mmol L-1 NaCl stress treatment, the transgenic plants remained a healthy K+ status, while the control plants decreased K+ content by 70% and Na+ contents in leaves and stems were 1.7 times that in the transgenic line. The AtHKT1 expression enhanced the activities of SOD, CAT and POD, raised chlorophyll and soluble sugar contents and root activity, and decreased MDA and proline contents and electrolyte leakage destruction. The constitutive over-expression of AtHKT1 that helps maintain a healthy K+ status while reducing Na+ toxicity may serve as a possible mechanism in maximizing productivity of tobacco under salt stress.

Breaking continuous potato cropping with legumes improves soil microbial communities, enzyme activities and tuber yield.

This study was conducted to explore the changes in soil microbial populations, enzyme activity, and tuber yield under the rotation sequences of Potato-Common vetch (P-C), Potato-Black medic (P-B) and Potato-Longdong alfalfa (P-L) in a semi-arid area of China. The study also determined the effects of continuous potato cropping (without legumes) on the above mentioned soil properties and yield. The number of bacteria increased significantly (p < 0.05) under P-B rotation by 78%, 85% and 83% in the 2, 4 and 7-year continuous cropping soils, respectively compared to P-C rotation. The highest fungi/bacteria ratio was found in P-C (0.218), followed by P-L (0.184) and then P-B (0.137) rotation over the different cropping years. In the continuous potato cropping soils, the greatest fungi/bacteria ratio was recorded in the 4-year (0.4067) and 7-year (0.4238) cropping soils and these were significantly higher than 1-year (0.3041), 2-year (0.2545) and 3-year (0.3030) cropping soils. Generally, actinomycetes numbers followed the trend P-L>P-C>P-B. The P-L rotation increased aerobic azotobacters in 2-year (by 26% and 18%) and 4-year (40% and 21%) continuous cropping soils compared to P-C and P-B rotation, respectively. Generally, the highest urease and alkaline phosphate activity, respectively, were observed in P-C (55.77 mg g-1) and (27.71 mg g-1), followed by P-B (50.72 mg mg-1) and (25.64 mg g-1) and then P-L (41.61 mg g-1) and (23.26 mg g-1) rotation. Soil urease, alkaline phosphatase and hydrogen peroxidase activities decreased with increasing years of continuous potato cropping. On average, the P-B rotation significantly increased (p <0.05) tuber yield by 19% and 18%, compared to P-C and P-L rotation respectively. P-L rotation also increased potato tuber yield compared to P-C, but the effect was lesser relative to P-B rotation. These results suggest that adopting potato-legume rotation system has the potential to improve soil biology environment, alleviate continuous cropping obstacle and increase potato tuber yield in semi-arid region.

Roles of Plasmalemma Aquaporin Gene StPIP1 in Enhancing Drought Tolerance in Potato.

Survival and mortality of plants in response to severe drought may be related to carbon starvation, but little is known about how plasma membrane intrinsic proteins may help alleviate the drought-induced damage. Here, we determined the roles of plasmalemma aquaporin gene in improving plant water status, maintaining carbon accumulation, and thereby enhancing drought tolerance. Seven StPIP1 transformed potato (Solanum tuberosum L.) lines (namely T1, T2…T7) were compared with non-transgenic control plant at molecule and whole-plant levels. The relative expression of StPIP1 gene was found in leaves, stems and roots, with the most abundant expression being in the roots. The transgenic lines T6 and T7 had the highest StPIP1 expression, averaging 7.2 times that of the control and the greatest differences occurred 48 h after mannitol osmotic stress treatment. Using an evaluation index to quantifying the degree of drought tolerance, we found that the StPIP1 transgenic lines T6 and T7 had the highest drought tolerance, averaging 8.5 times that of the control. Measured at 30 days in drought stress treatment, the control plant decreased net photosynthetic rate by 33 and 56%, respectively, under moderate and severe stresses; also decreased stomatal conductance by 39 and 65%; and lowered transpiration rate by 49 and 69%, compared to the no-stress treatment, whereas the transgenic lines T6 and T7 maintained a relatively stable level with slight decreases in these properties. The constitutive overexpression of StPIP1 in potato improved plant water use efficiency and increased nonstructural carbohydrate concentration, which helped alleviate carbon starvation and minimized the loss of biomass and tuber yield due to drought stress. We conclude that the expression of StPIPs improves overall water relations in the plant and helps maintain photosynthesis and stomatal conductance; these help minimize carbon starvation and enhance the whole plant tolerance to drought stress.

Sucrose non-ferment 1 related protein kinase 2 (SnRK2) genes could mediate the stress responses in potato (Solanum tuberosum L.).

BACKGROUND: The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinase 2 (SnRK2) subfamily has been conducted in potato (Solanum tuberosum L.). RESULTS: In this study, eight StSnRK2 genes (StSnRK2.1- StSnRK2.8) were identified in the genome of the potato (Solanum tuberosum L.) cultivar 'Longshu 3', with similar characteristics to SnRK2 from other plant species in gene structure, motif distribution and secondary structures. The C-terminal regions were highly divergent among StSnRK2s, while they all carried the similar Ser/Thr protein kinase domain. The fluorescence of GFP fused with StSnRK2.1, StSnRK2.2, StSnRK2.6, StSnRK2.7 and StSnRK2.8 was detected in the nucleus and cytoplasm of onion epidermal cells with StSnRK2.3 and StSnRK2.4 mainly associated to the nucleus while StSnRK2.5 to subcellular organelles. Expression level analysis by qRT-PCR showed that StSnRK2.1, 2.2, 2.5 and 2.6 were more than 1 fold higher in the root than in the leaf, tuber and stem tissues. The expressions of StSnRK2.3, 2.7, and 2.8 were at least 1.5 folds higher in the leaf and stem than in the root, but lower in the tuber. The expression of StSnRK2.4 was also significantly (P < 0.05) higher in leaf, stem, and tuber than in the root. From the perspective of the relative expressions of StSnRK2 genes in potato, ABA treatment had a different effect from NaCl and PEG treatments. CONCLUSION: In the present study, we identified and characterized eight SnRK2s in the potato genome. The eight StSnRK2s exhibit similar gene structure and secondary structures in potato to the SnRK2s found in other plant species. The relative expression of eight genes varied among various tissues (roots, leaves, tubers, and stems) and abiotic stresses (ABA, NaCl and PEG-6000) with the prolongation of treatments. This study provides valuable information for the future functional dissection of potato SnRK2 genes in stress signal transduction, plant growth and development.

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L.

Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenylpropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of miRNA and mRNA expression profiles in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.

Functional diversification of the potato R2R3 MYB anthocyanin activators AN1, MYBA1, and MYB113 and their interaction with basic helix-loop-helix cofactors.

In potato (Solanum tuberosum L.), R2R3 MYBs are involved in the regulation of anthocyanin biosynthesis. We examined sequences of these MYBs in cultivated potatoes, which are more complex than diploid potato due to ploidy and heterozygosity. We found amino acid variants in the C-terminus of the MYB StAN1, termed R0, R1, and R3, due to the presence of a repeated 10-amino acid motif. These variant MYBs showed some expression in both white and pigmented tubers. We found several new alleles or gene family members of R2R3 MYBs,StMYBA1 and StMYB113, which were also expressed in white potato tubers. From functional analysis in tobacco, we showed that the presence of a C-terminal 10-amino acid motif is optimal for activating anthocyanin accumulation. Engineering a motif back into a MYB lacking this sequence enhanced its activating ability. Versions of StMYBA1 and StMYB113 can also activate anthocyanin accumulation in tobacco leaves, with the exception of StMYB113-3, which has a partial R2R3 domain. We isolated five family members of potato StbHLH1, and one StJAF13, to test their ability to interact with MYB variants. The results showed that two alleles of StbHLH1 from white skin and red skin are non-functional, while three other StbHLH1s have different co-regulating abilities, and need to be activated by StJAF13. Combined with expression analysis in potato tuber, results suggest that StbHLH1 and StJAF13a re key co-regulators of anthocyanin biosynthesis, while the transcripts of MYB variants StAN1,StMYBA1, and StMYB113 are well expressed, even in the absence of pigmentation.

[Control of continuous potato monoculture barrier via biological soil disinfestation method in Yellow River irrigation areas of central Gansu Province, Northwest China].

The potential of biological soil disinfestation (BSD) in control of continuous potato monoculture barrier was investigated in present study. BSD involves the induction of soil reduction conditions through incorporation of easily decomposed organic materials into soil, flooding the soil by irrigation, and covering the soil surface with plastic film. Control (CK) was left without cover and organic amendment as well as flooding. Field experiment was conducted for testing the effect of BSD approach on the control of continuous potato monoculture barrier, especially on tube yield, plant growth and development, suppression of soil-borne pathogen, and soil microbial community and enzyme activities. Compared with CK, BSD treatment significantly increased tuber yield by 16.1% and plant biomass by 30.8%, respectively. Meanwhile, the incidence of diseased plant and the ratio of diseased tuber in BSD treatment also significantly decreased by 68.0% and 46.7% as compared to those in CK, respectively. BSD treatment significantly increased the content of chlorophyll and branch numbers per main stem of potato plants, improved the morphological characteristics of potato root system. In the course of BSD before potato sowing, soil pH value and bacteria/fungi significantly increased, but populations of fungi and Fusarium sp. significantly decreased compared with CK. There were no significant changes in populations of bacteria and actinomycetes between CK and BSD treatments. During potato growing stage, the populations of both soil fungi and Fusarium sp. were lower in BSD treatment than those of CK. With the advance of potato growth, the population of Fusarium sp. in BSD treatment gradually increased compared with CK. There were no significant changes in soil enzyme activities in the course of BSD before potato sowing and the whole of potato growing stage. It was concluded that BSD has the potential to control continuous potato monoculture barrier and may be an important element in a sustainable and effective management strategy for potato soil-borne diseases.