Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress

Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.)

Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus olitorius. Variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety Corchorus olitorius var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy.

Arbuscular mycorrhizal fungi enhanced resistance to low-temperature weak-light stress in snapdragon (Antirrhinum majus L.) through physiological and transcriptomic responses

Introduction

Low temperature (LT) and weak light (WL) seriously affects the yield and quality of snapdragon in winter greenhouse. Arbuscular mycorrhizal fungi (AMF) exert positive role in regulating growth and enhancing abiotic stress tolerance in plants. Nevertheless, the molecular mechanisms by AMF improve the LT combined with WL (LTWL) tolerance in snapdragon remain mostly unknown.

Methods

We compared the differences in root configuration, osmoregulatory substances, enzymatic and non-enzymatic antioxidant enzyme defense systems and transcriptome between AMF-inoculated and control groups under LT, WL, low light, and LTWL conditions.

Results

Our analysis showed that inoculation with AMF effectively alleviated the inhibition caused by LTWL stress on snapdragon root development, and significantly enhanced the contents of soluble sugars, soluble proteins, proline, thereby maintaining the osmotic adjustment of snapdragon. In addition, AMF alleviated reactive oxygen species damage by elevating the contents of AsA, and GSH, and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR), and glutathione reductase (GR). RNA-seq analysis revealed that AMF regulated the expression of genes related to photosynthesis (photosystem I related proteins, photosystem II related proteins, chlorophyll a/b binding protein), active oxygen metabolism (POD, Fe-SOD, and iron/ascorbate family oxidoreductase), plant hormone synthesis (ARF5 and ARF16) and stress-related transcription factors gene (bHLH112, WRKY72, MYB86, WRKY53, WRKY6, and WRKY26) under LTWL stress.

Discussion

We concluded that mycorrhizal snapdragon promotes root development and LTWL tolerance by accumulation of osmoregulatory substances, activation of enzymatic and non-enzymatic antioxidant defense systems, and induction expression of transcription factor genes and auxin synthesis related genes. This study provides a theoretical basis for AMF in promoting the production of greenhouse plants in winter.

Hybrid Vitis Cultivars with American or Asian Ancestries Show Higher Tolerance towards Grapevine Trunk Diseases

Grape production worldwide is increasingly threatened by grapevine trunk diseases (GTDs). No grapevine cultivar is known to be entirely resistant to GTDs, but susceptibility varies greatly. To quantify these differences, four Hungarian grape germplasm collections containing 305 different cultivars were surveyed to determine the ratios of GTDs based on symptom expression and the proportion of plant loss within all GTD symptoms. The cultivars of monophyletic Vitis vinifera L. origin were amongst the most sensitive ones, and their sensitivity was significantly (p < 0.01) higher than that of the interspecific (hybrid) cultivars assessed, which are defined by the presence of Vitis species other than V. vinifera (e.g., V. labrusca L., V. rupestris Scheele, and V. amurensis Rupr.) in their pedigree. We conclude that the ancestral diversity of grapes confers a higher degree of resilience against GTDs.

Transcriptome Profiling during Sequential Stages of Cryopreservation in Banana (Musa AAA cv Borjahaji) Shoot Meristem

Cryopreservation approaches have been implemented in gene banks as a strategy to back up plant genetic resource collections that are vegetatively propagated. Different strategies have been employed to effectively cryopreserve plant tissue. There is little information on the cellular processes and molecular adjustments that confer resilience to the multiple stresses imposed during a cryoprotocol. In the present work, the cryobionomics of banana (Musa sp.), a non-model species, was investigated through the transcriptomic approach using RNA-Seq. Proliferating meristems of in vitro explants (Musa AAA cv 'Borjahaji') were cryopreserved using the droplet-vitrification technique. Transcriptome profiling analysis of eight cDNA libraries including the bio-replicates for T0 (stock cultures (control tissue), T1 (high sucrose pre-cultured), T2 (vitrification solution-treated) and T3 (liquid nitrogen-treated) meristem tissues was carried out. The raw reads obtained were mapped with a Musa acuminata reference genome sequence. A total of 70 differentially expressed genes (DEGs) comprising 34 upregulated and 36 downregulated were identified in all three phases as compared to control (T0). Among the significant DEGs (>log FC 2.0), during sequential steps, 79 in T1, 3 in T2 and the 4 in T3 were upregulated and 122 in T1, 5 in T2 and 9 in T3 were downregulated. Gene ontology (GO) enrichment analysis showed that these significant DEGs were involved in the upregulation of biological process (BP-170), cellular component (CC-10) and molecular function (MF-94) and downregulation of biological process (BP-61), cellular component (CC-3) and molecular function (MF-56). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were involved in the biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, MAPK signaling, EIN 3-lke 1 protein, 3-ketoacy-CoA synthase 6-like, and fatty acid elongation during cryopreservation. For the first time, a comprehensive transcript profiling during four stages of cryopreservation in banana were carried out, which will pave the way for devising an effective cryopreservation protocol.

Transcriptomics Reveals the Effect of Short-Term Freezing on the Signal Transduction and Metabolism of Grapevine

Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of dormant cv. Cabernet Sauvignon exposed to several low-temperature conditions to identify differentially expressed genes and determine their function based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)enrichment analyses. Our results indicated that exposure to subzero low temperatures resulted in damage to plant cell membranes and extravasation of intracellular electrolytes, and that this damage increased with decreasing temperature or increasing duration. The number of differential genes increased as the duration of stress increased, but most of the common differentially expressed genes reached their highest expression at 6 h of stress, indicating that 6 h may be a turning point for vines to tolerate extreme low temperatures. Several pathways play key roles in the response of Cabernet Sauvignon to low-temperature injury, namely: (1) the role of calcium/calmodulin-mediated signaling; (2) carbohydrate metabolism, including the hydrolysis of cell wall pectin and cellulose, decomposition of sucrose, synthesis of raffinose, and inhibition of glycolytic processes; (3) the synthesis of unsaturated fatty acids and metabolism of linolenic acid; and (4) the synthesis of secondary metabolites, especially flavonoids. In addition, pathogenesis-related protein may also play a role in plant cold resistance, but the mechanism is not yet clear. This study reveals possible pathways for the freezing response and leads to new insights into the molecular basis of the tolerance to low temperature in grapevine.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation

Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.

Emerging Roles of Plant DNA-Binding With One Finger Transcription Factors in Various Hormone and Stress Signaling Pathways

Coordinated transcriptional regulation of stress-responsive genes orchestrated by a complex network of transcription factors (TFs) and the reprogramming of metabolism ensure a plant's continued growth and survival under adverse environmental conditions (e.g., abiotic stress). DNA-binding with one finger (Dof) proteins, a group of plant-specific TF, were identified as one of several key components of the transcriptional regulatory network involved in abiotic stress responses. In many plant species, Dofs are often activated in response to a wide range of adverse environmental conditions. Dofs play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Moreover, Dofs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid, jasmonate, SA and redox signaling in response to many abiotic stresses. Taken together, we highlight a unique role of Dofs in hormone and stress signaling that integrates plant response to adverse environmental conditions with different aspects of plant growth and development.

Insight into Carbohydrate Metabolism and Signaling in Grapevine Buds during Dormancy Progression

Perennial fruit crops enter dormancy to ensure bud tissue survival during winter. However, a faster phenological advancement caused by global warming exposes bud tissue to a higher risk of spring frost damage. Tissue dehydration and soluble sugars accumulation are connected to freezing tolerance, but non-structural carbohydrates also act as metabolic substrates and signaling molecules. A deepened understanding of sugar metabolism in the context of winter freezing resistance is required to gain insight into adaptive possibilities to cope with climate changes. In this study, the soluble sugar content was measured in a cold-tolerant grapevine hybrid throughout the winter season. Moreover, the expression of drought-responsive hexose transporters VvHT1 and VvHT5, raffinose synthase VvRS and grapevine ABA-, Stress- and Ripening protein VvMSA was analyzed. The general increase in sugars in December and January suggests that they can participate in protecting bud tissues against low temperatures. The modulation of VvHT5, VvINV and VvRS appeared consistent with the availability of the different sugar species; challenging results were obtained for VvHT1 and VvMSA, suggesting interesting hypotheses about their role in the sugar-hormone crosstalk. The multifaceted role of sugars on the intricate phenomenon, which is the response of dormant buds to changing temperature, is discussed.

VviRafS5 Is a Raffinose Synthase Involved in Cold Acclimation in Grapevine Woody Tissues

The accumulation of raffinose family oligosaccharides (RFOs) is a hallmark of plant response to different abiotic stresses, including cold. The synthesis of galactinol, by galactinol synthases (GolS), and raffinose, by raffinose synthases (RafS), are fundamental for stress-induced accumulation of RFOs, but the role of these enzymes in the cold response of grapevine (Vitis vinifera L.) woody tissues is still unclear. To address this gap in the literature, 1-year-lignified grapevine canes were incubated at 4°C for 7 and 14 days and tissues were analyzed for sugar content and gene expression. Results showed that, in parallel to starch breakdown, there was an increase in soluble sugars, including sucrose, glucose, fructose, raffinose, and stachyose. Remarkably, abscisic acid (ABA) levels increased during cold acclimation, which correlated with the increased expression of the key ABA-synthesis genes VviNCED2 and VviNCED3. Expression analysis of the VviGolS and VviRafS family allowed the identification of VviRafS5 as a key player in grapevine cold response. The overexpression of VviRafS5 in Saccharomyces cerevisiae allowed the biochemical characterization of the encoded protein as a raffinose synthase with a size of ~87 kDa. In grapevine cultured cells, VviRafS5 was upregulated by cold and ABA but not by heat and salt stresses. Our results suggest that ABA accumulation in woody tissues during cold acclimation upregulates VivRafS5 leading to raffinose synthesis.

Grafting Watermelon Onto Pumpkin Increases Chilling Tolerance by Up Regulating Arginine Decarboxylase to Increase Putrescine Biosynthesis

Low temperature is a major environmental factor that severely impairs plant growth and productivity. Watermelon (Citrullus lanatus) is a chilling-sensitive crop. Grafting of watermelon onto pumpkin rootstock is an effective technique to increase the chilling tolerance of watermelon when exposure to short-time chilling stress. However, the mechanism by which pumpkin rootstock increases chilling tolerance remains poorly understood. Under 10°C/5°C (day/night) chilling stress treatment, pumpkin-grafted watermelon seedlings showed higher chilling tolerance than self-grafted watermelon plants with significantly reduced lipid peroxidation and chilling injury (CI) index. Physiological analysis revealed that pumpkin rootstock grafting led to the notable accumulation of putrescine in watermelon seedlings under chilling conditions. Pre-treat foliar with 1 mM D-arginine (inhibitor of arginine decarboxylase, ADC) increased the electrolyte leakage (EL) of pumpkin-grafted watermelon leaves under chilling stress. This result can be ascribed to the decrease in transcript levels of ADC, ornithine decarboxylase, spermidine synthase, and polyamine oxidase genes involved in the synthesis and metabolism of polyamines. Transcriptome analysis showed that pumpkin rootstock improved chilling tolerance in watermelon seedlings by regulating differential gene expression under chilling stress. Pumpkin-grafted seedling reduced the number and expression level of differential genes in watermelon scion under chilling stress. It specifically increased the up-regulated expression of ADC (Cla97C11G210580), a key gene in the polyamine metabolism pathway, and ultimately promoted the accumulation of putrescine. In conclusion, pumpkin rootstock grafting increased the chilling tolerance of watermelon through transcription adjustments, up regulating the expression level of ADC, and promoting the synthesis of putrescine, which ultimately improved the chilling tolerance of pumpkin-grafted watermelon plants.

GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response

Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

Transcriptomic analysis of grapevine Dof transcription factor gene family in response to cold stress and functional analyses of the VaDof17d gene

Dof genes enhance cold tolerance in grapevine and VaDof17d is tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides. DNA-binding with one finger (Dof) proteins comprise a large family that plays important roles in the regulation of abiotic stresses. No in-depth analysis of Dof genes has been performed in the grapevine. In this study, we analyzed a total of 25 putative Dof genes in grapevine at genomic and transcriptomic levels, compiled expression profiles of 11 selected VaDof genes under cold stress and studied the potential function of the VaDof17d gene in grapevine calli. The 25 Dof proteins can be classified into four phylogenetic groups. RNA-seq and qRT-PCR results demonstrated that a total of 11 VaDof genes responded to cold stress. Comparative mRNA sequencing of 35S::VaDof17d grape calli showed that VaDof17d was tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides (RFOs), as observed by the up-regulation of galactinol synthase (GolS) and raffinose synthase genes. We found that the Dof17d-ED (CRISPR/Cas9-mediated mutagenesis of Dof17d-ED) mutant had low cold tolerance with a decreased RFOs level during cold stress. These results formed the fundamental knowledge for further analysis of the biological roles of Dof genes in the grapevine's adaption to cold stresses.

VvBAP1, a Grape C2 Domain Protein, Plays a Positive Regulatory Role Under Heat Stress

Temperature is considered one of the critical factors directly influencing grapevine during the three primary growth and development stages: sprout, flowering, and fruit-coloring, which is strongly correlated to the yield and quality of the grape. The grapevine is frequently exposed to high-temperature conditions that are detrimental to growth. However, the mechanisms of the heat stress response and adaptation in grapevine are not adequately studied. The Arabidopsis copine gene AtBON1 encodes a highly conserved protein containing two C2 domains at the amino terminus, participation in cell death regulation and defense responses. Previously, we showed that a BON1 association protein from the grapevine, VvBAP1, plays a positive role in cold tolerance. Similarly, the involvement of VvBAP1 in the resistance to heat stress was also found in the present study. The results indicated VvBAP1 was significantly induced by high temperature, and the elevated expression of VvBAP1 was significantly higher in the resistant cultivars than the sensitive cultivars under heat stress. Seed germination and phenotypic analysis results indicated that overexpression of VvBAP1 improved Arabidopsis thermoresistance. Compared with the wild type, the chlorophyll content and net photosynthetic rate in VvBAP1 overexpressing Arabidopsis plants were markedly increased under heat stress. At high temperatures, overexpression of VvBAP1 also enhanced antioxidant enzyme activity as well as their corresponding gene transcription levels, to reduce the accumulation of reactive oxygen species and lipid peroxidation. Besides, the transcriptional activities of HSP70, HSP101, HSFA2, and HSFB1 in VvBAP1 overexpressing Arabidopsis plants were significantly up-regulated compare to the wild type. In summary, we propose that VvBAP1 may play a potential important role in enhanced grapevine thermoresistance, primarily through the enhancement of antioxidant enzyme activity and promoted heat stress response genes expression.

ABA signaling pathway genes and function during abiotic stress and berry ripening in Vitis vinifera

Abscisic acid (ABA) plays important roles in plant development and tolerance to abiotic stresses. Limited information is available regarding ABA signaling pathway genes in grape. In this study, 9 VvPYR/PYLs, 85 VvPP2Cs, 7 VvABIs, 7 VvSnRK2s, and 8 VvABFs were identified in the grape genome. Duplication analysis indicated that whole genome duplication might contribute to the expansion of these gene families. The comprehensive transcriptome analysis in various organs/tissues implied that most of these genes were tissue-specific, and few were environment-specific genes. Exogenous ABA treatment reduced the grape maturation period. VvPP2C59, VvPP2C60, VvPP2C66, and VvABF8 were all involved in tolerance to cold, heat, and drought stresses, revealing their crucial roles in regulating environmental stress responses. This work provides detailed information of ABA signaling pathway genes and new insights regarding their expression patterns during grape development and abiotic stress treatment.

Comparative transcriptome analysis provides insight into regulation pathways and temporal and spatial expression characteristics of grapevine (Vitis vinifera) dormant buds in different nodes

BACKGROUND

Bud dormancy is a strategic mechanism plants developed as an adaptation to unfavorable environments. The grapevine (Vitis vinifera) is one of the most ancient fruit vine species and vines are planted all over the world due to their great economic benefits. To better understand the molecular mechanisms underlying bud dormancy between adjacent months, the transcriptomes of 'Rosario Bianco' grape buds of 6 months and three nodes were analyzed using RNA-sequencing technology and pair-wise comparison. From November to April of the following year, pairwise comparisons were conducted between adjacent months.

RESULTS

A total of 11,647 differentially expressed genes (DEGs) were obtained from five comparisons. According to the results of cluster analysis of the DEG profiles and the climatic status of the sampling period, the 6 months were divided into three key processes (November to January, January to March, and March to April). Pair-wise comparisons of DEG profiles of adjacent months and three main dormancy processes showed that the whole grapevine bud dormancy period was mainly regulated by the antioxidant system, secondary metabolism, cell cycle and division, cell wall metabolism, and carbohydrates metabolism. Additionally, several DEGs, such as VvGA2OX6 and VvSS3, showed temporally and spatially differential expression patterns, which normalized to a similar trend during or before April.

CONCLUSION

Considering these results, the molecular mechanisms underlying bud dormancy in the grapevine can be hypothesized, which lays the foundation for further research.

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture

Cultivated grapevines, Vitis vinifera subsp. sativa, are thought to have been domesticated from wild populations of Vitis vinifera subsp. sylvestris in Central Asia. V. vinifera subsp. sativa is one of the most economically important fruit crops worldwide. Since cultivated grapevines are susceptible to multiple biotic and abiotic soil factors, they also need to be grafted on resistant rootstocks that are mostly developed though hybridization between American wild grapevine species (V. berlandieri, V. riparia, and V. rupestris). Therefore, wild grapevine species are essential genetic materials for viticulture to face biotic and abiotic stresses in both cultivar and rootstock parts. Actually, viticulture faces several environmental constraints that are further intensified by climate change. Recently, several reports on biotic and abiotic stresses-response in wild grapevines revealed accessions tolerant to different constraints. The emergence of advanced techniques such as omics technologies, marker-assisted selection (MAS), and functional analysis tools allowed a more detailed characterization of resistance mechanisms in these wild grapevines and suggest a number of species (V. rotundifolia, V. rupestris, V. riparia, V. berlandieri and V. amurensis) have untapped potential for new resistance traits including disease resistance loci and key tolerance genes. The present review reports on the importance of different biotechnological tools in exploring and examining wild grapevines tolerance mechanisms that can be employed to promote elite cultivated grapevines under climate change conditions.

Transcriptomic Profiling of Acute Cold Stress-Induced Disease Resistance (SIDR) Genes and Pathways in the Grapevine Powdery Mildew Pathosystem

Temperatures from 2 to 8°C transiently induce quantitative resistance to powdery mildew in several host species (cold stress-induced disease resistance [SIDR]). Although cold SIDR events occur in vineyards worldwide an average of 14 to 21 times after budbreak of grapevine and can significantly delay grapevine powdery mildew (Erysiphe necator) epidemics, its molecular basis was poorly understood. We characterized the biology underlying the Vitis vinifera cold SIDR phenotype-which peaks at 24 h post-cold (hpc) treatment and results in a 22 to 28% reduction in spore penetration success-through highly replicated (n = 8 to 10) RNA sequencing experiments. This phenotype was accompanied by a sweeping transcriptional downregulation of photosynthesis-associated pathways whereas starch and sugar metabolism pathways remained largely unaffected, suggesting a transient imbalance in host metabolism and a suboptimal target for pathogen establishment. Twenty-six cold-responsive genes peaked in their differential expression at the 24-hpc time point. Finally, a subset of genes associated with nutrient and amino acid transport accounted for four of the eight most downregulated transcripts, including two nodulin 1A gene precursors, a nodulin MtN21 precursor, and a Dynein light chain 1 motor protein precursor. Reduced transport could exacerbate localized nutrient sinks that would again be transiently suboptimal for pathogen growth. This study links the transient cold SIDR phenotype to underlying transcriptional changes and provides an experimental framework and library of candidate genes to further explore cold SIDR in several systems, with an ultimate goal of identifying novel breeding or management targets for reduced disease.

Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine

Background

Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.).

Result

Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses.

Conclusion

Our study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.

The ethylene response factor VaERF092 from Amur grape regulates the transcription factor VaWRKY33, improving cold tolerance

Cold stress is a major limiting factor in grape (Vitis) productivity. In this study, we characterized a cold-responsive ethylene response factor (ERF) transcription factor, VaERF092, from Amur grape (Vitis amurensis). VaERF092 expression was induced by both low temperatures and the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC), but was suppressed by treatment with the ethylene inhibitor aminoethoxyvinylglycine (AVG) under cold conditions. Ectopic expression of VaERF092 in Arabidopsis thaliana enhanced cold tolerance. Co-expression network analysis of V. vinifera genes indicated that WRKY33 might be a downstream target of VaERF092. This hypothesis was supported by the fact that VaWRKY33 was expressed temporally after VaERF092 expression and could also be induced by cold and ACC, and inhibited by AVG. Yeast one-hybrid, transient β-glucuronidase (GUS) and dual-luciferase reporter assays provided evidence for an interaction between VaERF092 and a GCC-box element in the VaWRKY33 promoter. In addition, heterologous overexpression of VaWRKY33 in A. thaliana resulted in enhanced cold tolerance. VaERF092- and VaWRKY33 overexpressing grape calli showed lower low-temperature exothermic values than the empty vector (EV) calli, indicating enhanced tolerance to cold. Together, these results indicated that VaERF092 regulates VaWRKY33 through binding to its promoter GCC-box, leading to enhanced cold stress tolerance.

Drought Exacerbates Botryosphaeria Dieback Symptoms in Grapevines and Confounds Host-based Molecular Markers of Infection by Neofusicoccum parvum

Neofusicoccum parvum, causal fungus of the grapevine trunk disease Botryosphaeria dieback, attacks the wood of Vitis vinifera. Because lesions are internal, using putative host-based markers of infection from leaves for diagnosis is a nondestructive option. However, their specificity under drought stress is unknown. Potted 'Cabernet-Sauvignon' were inoculated with N. parvum in the greenhouse after wounding (IW), and with wounded and nonwounded noninoculated controls. At 2 weeks postinoculation (WPI), half of the plants were severely stressed (SS), receiving 30% water volume of the well-watered (WW) plants. Larger lesions at 12 WPI among IW-SS plants, compared with all other treatments, revealed an interactive effect of inoculation and drought on lesion length. Expression of eight putative marker genes was analyzed in leaves by qPCR at the onset of drought stress, and at 8 and 12 WPI. One marker showed consistent over-expression at 8 WPI in IW plants, regardless of water treatment, suggesting specificity to infection. By 12 WPI, higher expression of seven genes in all SS plants (across inoculation treatments) revealed specificity to drought. Cross-reactivity of markers to drought, therefore, limits their utility for disease diagnosis in the field, where drought induced by climate and deficit irrigation is common.

On a Cold Night: Transcriptomics of Grapevine Flower Unveils Signal Transduction and Impacted Metabolism

Low temperature is a critical environmental factor limiting plant productivity, especially in northern vineyards. To clarify the impact of this stress on grapevine flower, we used the Vitis array based on Roche-NimbleGen technology to investigate the gene expression of flowers submitted to a cold night. Our objectives were to identify modifications in the transcript levels after stress and during recovery. Consequently, our results confirmed some mechanisms known in grapes or other plants in response to cold stress, notably, (1) the pivotal role of calcium/calmodulin-mediated signaling; (2) the over-expression of sugar transporters and some genes involved in plant defense (especially in carbon metabolism), and (3) the down-regulation of genes encoding galactinol synthase (GOLS), pectate lyases, or polygalacturonases. We also identified some mechanisms not yet known to be involved in the response to cold stress, i.e., (1) the up-regulation of genes encoding G-type lectin S-receptor-like serine threonine-protein kinase, pathogen recognition receptor (PRR5), or heat-shock factors among others; (2) the down-regulation of Myeloblastosis (MYB)-related transcription factors and the Constans-like zinc finger family; and (3) the down-regulation of some genes encoding Pathogen-Related (PR)-proteins. Taken together, our results revealed interesting features and potentially valuable traits associated with stress responses in the grapevine flower. From a long-term perspective, our study provides useful starting points for future investigation.

Microtubule dynamics modulate sensing during cold acclimation in grapevine suspension cells

Cold acclimation is of practical relevance, since it can avoid cold-induced damage in various crops. To efficiently activate cold acclimation requires that the chilling stress is perceived and processed efficiently. In the current work, we use a transgenic cell line of V. rupestris expressing a GFP-labelled tubulin to follow the effect of cold acclimation and the relation between microtubules and the expression of the transcription factor Cold Box Factor 4 (CBF4) as molecular readout for adaptive responses to cold stress. We find that chilling induced cold tolerance correlated with increased CBF4 expression. We show that cold acclimation can be achieved through stabilisation of microtubules by taxol, as well as through transient elimination of microtubules by pronamide in the absence of cold stress. Furthermore, results from inhibitor studies indicate that transcriptional activation of CBF4 appears to be under control of calcium influx. We screened a population of the ancestor of V. sylvestris and could identify different clades with strong induction of CBF4, indicative of genetic variation in cold adaptability that can be used for breeding. We summarize our findings into a working model where microtubule dynamics controls the sensitivity of cold induced calcium influx mediating the induction of CBF4 culminating in cold hardening.

Metabolomic and transcriptomic changes underlying cold and anaerobic stresses after storage of table grapes

The currently accepted paradigm is that fruits and vegetables should be consumed fresh and that their quality deteriorates during storage; however, there are indications that some metabolic properties can, in fact, be improved. We examined the effects of low temperature and high-CO₂ conditions on table grapes, Vitis vinifera L. cv. 'Superior Seedless'. Berries were sampled at harvest (T0) and after low-temperature storage for 6 weeks under either normal atmosphere conditions (TC) or under an O₂ level of 5 kPa and elevated CO₂ levels of 5, 10 or 15 kPa (T5, T10, T15). Accumulation of 10 stilbenes, including E-ε-viniferin, E-miyabenol C and piceatannol, significantly increased under TC treatment as compared to T0 or T15. Sensory analysis demonstrated that elevated CO₂ elicited dose-dependent off-flavor accumulation. These changes were accompanied by an accumulation of 12 volatile metabolites, e.g., ethyl acetate and diacetyl, that imparted disagreeable flavors to fresh fruit. Transcriptome analysis revealed enrichment of genes involved in pyruvate metabolism and the phenylpropanoid pathway. One of the transcription factors induced at low temperature but not under high CO₂ was VvMYB14, which regulates stilbene biosynthesis. Our findings reveal the potential to alter the levels of targeted metabolites in stored produce through understanding the effects of postharvest treatments.

Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation

Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures. However, the accumulation of metabolites during cold acclimation (CA) in V. amurensis remains largely unknown. In this study, plantlets of V. amurensis and V. vinifera cv. Muscat of Hamburg were treated at 4 °C for 24 and 72 h, and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry. Most of the identified metabolites, including carbohydrates, amino acids, and organic acids, accumulated in the two types of grape after CA. Galactinol, raffinose, fructose, mannose, glycine, and ascorbate were continuously induced by cold in V. amurensis, but not in Muscat of Hamburg. Twelve metabolites, including isoleucine, valine, proline, 2-oxoglutarate, and putrescine, increased in V. amurensis during CA. More galactinol, ascorbate, 2-oxoglutarate, and putrescine, accumulated in V. amurensis, but not in Muscat of Hamburg, during CA, which may be responsible for the excellent cold tolerance in V. amurensis. The expression levels of the genes encoding β-amylase (BAMY), galactinol synthase (GolS), and raffinose synthase (RafS) were evaluated by quantitative reverse transcription-PCR. The expression BAMY (VIT_02s0012 g00170) and RafS (VIT_05s0077 g00840) were primarily responsible for the accumulation of maltose and raffinose, respectively. The accumulation of galactinol was attributed to different members of GolS in the two grapes. In conclusion, these results show the inherent differences in metabolites between V. amurensis and V. vinifera under CA.

Genome-wide identification and characterization of the 14-3-3 family in Vitis vinifera L. during berry development and cold- and heat-stress response

Background

The 14–3-3 family of ubiquitous proteins in eukaryotes plays important roles in the regulation of various plant biological processes. However, less information is known about this family in grape fruit.

Results

To investigate the characteristics and functions of 14–3-3 in grape, a total of 11 14–3-3 proteins were identified. Phylogenetic analysis of 14–3-3 proteins in grape (VviGRFs) with homologous proteins in Arabidopsis showed that these proteins were classified into two groups, namely, epsilon and non-epsilon groups. Epsilon group members commonly contained more introns and motifs than non-epsilon group, and some intron positions were found to be conserved between Vitis and Arabidopsis 14–3-3 genes. RNA-seq and qRT-PCR results indicated that VviGRF genes may be involved in the regulation of grape development and berry ripening. Moreover, six VviGRFs exhibited significantly up- or down-regulated expression in response to cold and heat stresses, thereby revealing their potential roles in the regulation of abiotic stress responses.

Conclusions

This work provides fundamental knowledge for further studies about the biological roles of VviGRFs in grape development and abiotic stress response. The present result will also be beneficial for understanding their molecular mechanisms and improving grape agricultural traits in the future.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4955-8) contains supplementary material, which is available to authorized users.

The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides

Grapevine (Vitis vinifera L.) is a widely cultivated fruit crop whose growth and productivity are greatly affected by low temperatures. On the other hand, wild Vitis species represent valuable genetic resources of natural stress tolerance. We have isolated and characterized a MYB-like gene encoding a putative GARP-type transcription factor from Amur grape (V. amurensis) designated as VaAQUILO. AQUILO (AQ) is induced by cold in both V. amurensis and V. vinifera, and its overexpression results in significantly improved tolerance to cold both in transgenic Arabidopsis and in Amur grape calli. In Arabidopsis, the ectopic expression of VaAQ increased antioxidant enzyme activities and up-regulated reactive oxygen species- (ROS) scavenging-related genes. Comparative mRNA sequencing profiling of 35S:VaAQ Arabidopsis plants suggests that this transcription factor is related to phosphate homeostasis like their Arabidopsis closest homologues: AtHRS1 and AtHHO2. However, when a cold stress is imposed, AQ is tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides (RFOs), as observed by the up-regulation of galactinol synthase (GoLS) and raffinose synthase genes. Gene co-expression network (GCN) and cis-regulatory element (CRE) analyses in grapevine indicated AQ as potentially regulating VvGoLS genes. Increased RFO content was confirmed in both transgenic Arabidopsis and Amur grape calli overexpressing VaAQ. Taken together, our results imply that AQ improves cold tolerance through promoting the accumulation of osmoprotectants.

Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story

Seed plants are sessile organisms that have developed a plethora of strategies for sensing, avoiding, and responding to stress. Several proteins, including the glycine-rich protein (GRP) superfamily, are involved in cellular stress responses and signaling. GRPs are characterized by high glycine content and the presence of conserved segments including glycine-containing structural motifs composed of repetitive amino acid residues. The general structure of this superfamily facilitates division of GRPs into five main subclasses. Although the participation of GRPs in plant stress response has been indicated in numerous model and non-model plant species, relatively little is known about the key physiological processes and molecular mechanisms in which those proteins are engaged. Class I, II, and IV members are known to be involved in hormone signaling, stress acclimation, and floral development, and are crucial for regulation of plant cells growth. GRPs of class IV [RNA-binding proteins (RBPs)] are involved in alternative splicing or regulation of transcription and stomatal movement, seed, pollen, and stamen development; their accumulation is regulated by the circadian clock. Owing to the fact that the overexpression of GRPs can confer tolerance to stress (e.g., some are involved in cold acclimation and may improve growth at low temperatures), these proteins could play a promising role in agriculture through plant genetic engineering. Consequently, isolation, cloning, characterization, and functional validation of novel GRPs expressed in response to the diverse stress conditions are expected to be growing areas of research in the coming years. According to our knowledge, this is the first comprehensive review on participation of plant GRPs in the response to diverse stress stimuli.

Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)

Low-temperature stresses limit the sustainability and productivity of grapevines when early spring frosts damage young grapevine leaves. Spring conditions often expose grapevines to low, but not damaging, chilling temperatures and these temperatures have been shown to increase freeze resistance in other model systems. In this study, we examined whole-transcriptome gene expression patterns of young leaf tissue from cuttings of five different grapevine cultivars, exposed to chill and freeze shock, in order to understand the underlying transcriptional landscape associated with cold stress response. No visible damage was observed when grapevine leaves were exposed to chilling temperatures while freeze temperatures resulted in variable damage in all cultivars. Significant differences in gene expression were observed between warm control conditions and all types of cold stress. Exposure to chill stress (4 °C) versus freezing stress (-3 °C) resulted in very different patterns of gene expression and enriched pathway responses. Genes from the ethylene signaling, ABA signaling, the AP2/ERF, WRKY, and NAC transcription factor families, and starch/sucrose/galactose pathways were among the most commonly observed to be differentially regulated. Preconditioning leaves to chill temperatures prior to freezing temperatures resulted in slight buffering of gene expression responses, suggesting that differences between chill and freeze shock perception complicates identification of candidate genes for cold resistance in grapevine. Overall, the transcriptional landscape contrasts observed between low temperature and freezing stresses demonstrate very different activation of candidate pathways impacting grapevine cold response.

Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera

Ubiquitin-conjugating (UBC) E2 enzyme plays crucial roles in plant growth and development. Limited information can describe the function of UBC enzyme E2 in grapes. A total of 43 UBC enzyme E2 genes with conserved UBC domain were identified in grapes. These genes were divided into five groups based on phylogenetic tree with tomatoes. Sequence analyses indicated that VvUBCs in the same group possessed similar gene structures and conserved motifs. Gene distribution in chromosomes was uneven, and gene duplication existed in 36 VvUBCs. Transcriptome and qRT-PCR analysis indicated that most VvUBCs are involved in ripening and post-harvest stage, and feature functional roles in grape organs. According to the transcriptome and qRT-PCR results, seven and six VvUBCs in grape responded to cold and heat stress, respectively, whereas no remarkable VvUBCs change was noted under salt or water-deficit stress. This study provides new insights to physiological and developmental roles of these enzymes and regulation mechanism of E2 genes in grapes.

Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress

Spring frost is a major limiting abiotic stress for the cultivation of almonds [Prunus dulcis (Mill.)] in Mediterranean areas or the Middle East. Spring frost, in particular, damages almond fully open flowers, resulting to significant reduction in yield. Little is known about the genetic factors expressed after frost stress in Prunus spp. as well as in almond fully open flowers. Here, we provide the molecular signature of pistils of fully open flowers from a frost-tolerant almond genotype. The level of frost tolerance in this genotype was determined for all three flowering stages and was confirmed by comparing it to two other cultivars using several physiological analyses. Afterwards, comprehensive expression profiling of genes expressed in fully open flowers was performed after being exposed to frost temperatures (during post-thaw period). Clean reads, 27,104,070 and 32,730,772, were obtained for non-frost-treated and frost-treated (FT) libraries, respectively. A total of 62.24 Mb was assembled, generating 50,896 unigenes and 66,906 transcripts. Therefore, 863 upregulated genes and 555 downregulated genes were identified in the FT library. Functional annotation showed that most of the upregulated genes were related to various biological processes involved in responding to abiotic stress. For the first time, a highly expressed cold-shock protein was identified in the reproductive organ of fruit trees. The expression of six genes was validated by RT-PCR. As the first comprehensive analysis of open flowers in a frost-tolerant almond genotype, this study represents a key step toward the molecular breeding of fruit tree species for frost tolerance.

An efficient method for transgenic callus induction from Vitis amurensis petiole

Transformation is the main platform for genetic improvement and gene function studies in plants. However, the established somatic embryo transformation system for grapevines is time-consuming and has low efficiency, which limits its utilization in functional genomics research. Vitis amurensis is a wild Vitis species with remarkable cold tolerance. The lack of an efficient genetic transformation system for it has significantly hindered the functional identification of cold stress related genes in the species. Herein, an efficient method was established to produce transformed calli of V. amurensis. Segments of petioles from micropropagated plantlets of V. amurensis exhibited better capacity to differentiate calli than leaf-discs and stem segments, and thus was chosen as target tissue for Agrobacterium-mediated transformation. Both neomycin phosphotransferase II (NPTII) and enhanced green fluorescent protein (eGFP) genes were used for simultaneous selection of transgenic calli based on kanamycin resistance and eGFP fluorescence. Several parameters affecting the transformation efficiency were optimized including the concentration of kanamycin, Agrobacterium stains, bacterial densities, infection treatments and co-cultivation time. The transgenic callus lines were verified by checking the integration of NPTII gene into calli genomes, the expression of eGFP gene and the fluorescence of eGFP. Up to 20% of the petiole segments produced transformed calli after 2 months of cultivation. This efficient transformation system will facilitate the functional analysis of agronomic characteristics and related genes not only in V. amurensis but also in other grapevine species.

Transcriptome Analysis of Differentially Expressed Genes Induced by Low and High Potassium Levels Provides Insight into Fruit Sugar Metabolism of Pear

Potassium (K) deficiency is a common abiotic stress that can inhibit the growth of fruit and thus reduce crop yields. Little research has been conducted on pear transcriptional changes under low and high K conditions. Here, we performed an experiment with 7-year-old pot-grown "Huangguan" pear trees treated with low, Control or high K levels (0, 0.4, or 0.8 g·K2O/kg soil, respectively) during fruit enlargement and mature stages. We identified 36,444 transcripts from leaves and fruit using transcriptome sequencing technology. From 105 days after full blooming (DAB) to 129 DAB, the number of differentially expressed genes (DEGs) in leaves and fruit in response to low K increased, while in response to high K, the number of DEGs in leaves and fruit decreased. We selected 17 of these DEGs for qRT-PCR analysis to confirm the RNA sequencing results. Based on GO enrichment and KEGG pathway analysis, we found that low-K treatment significantly reduced K nutrient and carbohydrate metabolism of the leaves and fruit compared with the Control treatment. During the fruit development stages, AKT1 (gene39320) played an important role on K+ transport of the leaves and fruit response to K stress. At maturity, sucrose and acid metabolic pathways were inhibited by low K. The up-regulation of the expression of three SDH and two S6PDH genes involved in sorbitol metabolism was induced by low K, promoting the fructose accumulation. Simultaneously, higher expression was found for genes encoding amylase under low K, promoting the decomposition of the starch and leading the glucose accumulation. High K could enhance leaf photosynthesis, and improve the distribution of the nutrient and carbohydrate from leaf to fruit. Sugar components of the leaves and fruit under low K were regulated by the expression of genes encoding 8 types of hormone signals and reactive oxygen species (ROS). Our data revealed the gene expression patterns of leaves and fruit in response to different K levels during the middle and late stages of fruit development as well as the molecular mechanism of improvement of fruit sugar levels by K and provided a scientific basis for improving fruit quality with supplemental K fertilizers.

Natural products against Alzheimer's disease: Pharmaco-therapeutics and biotechnological interventions

Alzheimer's disease (AD) is a severe, chronic and progressive neurodegenerative disease associated with memory and cognition impairment ultimately leading to death. It is the commonest reason of dementia in elderly populations mostly affecting beyond the age of 65. The pathogenesis is indicated by accumulation of the amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFT) in brain tissues and hyperphosphorylation of tau protein in neurons. The main cause is considered to be the formation of reactive oxygen species (ROS) due to oxidative stress. The current treatment provides only symptomatic relief by offering temporary palliative therapy which declines the rate of cognitive impairment associated with AD. Inhibition of the enzyme acetylcholinesterase (AChE) is considered as one of the major therapeutic strategies offering only symptomatic relief and moderate disease-modifying effect. Other non-cholinergic therapeutic approaches include antioxidant and vitamin therapy, stem cell therapy, hormonal therapy, use of antihypertensive or lipid-lowering medications and selective phosphodiesterase (PDE) inhibitors, inhibition of β-secretase and γ-secretase and Aβ aggregation, inhibition of tau hyperphosphorylation and intracellular NFT, use of nonsteroidal anti-inflammatory drugs (NSAIDs), transition metal chelators, insulin resistance drugs, etanercept, brain-derived neurotrophic factor (BDNF) etc. Medicinal plants have been reported for possible anti-AD activity in a number of preclinical and clinical trials. Ethnobotany, being popular in China and in the Far East and possibly less emphasized in Europe, plays a substantial role in the discovery of anti-AD agents from botanicals. Chinese Material Medica (CMM) involving Chinese medicinal plants has been used traditionally in China in the treatment of AD. Ayurveda has already provided numerous lead compounds in drug discovery and many of these are also undergoing clinical investigations. A number of medicinal plants either in their crude forms or as isolated compounds have exhibited to reduce the pathological features associated with AD. In this present review, an attempt has been made to elucidate the molecular mode of action of various plant extracts, phytochemicals and traditional herbal formulations investigated against AD as reported in various preclinical and clinical tests. Herbal synergism often found in polyherbal formulations were found effective to combat disease heterogeneity as found in complex pathogenesis of AD. Finally a note has been added to describe biotechnological improvement, genetic and genomic resources and mathematical and statistical techniques for empirical model building associated with anti-AD plant secondary metabolites and their source botanicals.

Comparative transcriptome profiling of chilling stress responsiveness in grafted watermelon seedlings

Rootstock grafting may improve the resistance of watermelon plants to low temperatures. However, information regarding the molecular responses of rootstock grafted plants to chilling stress is limited. To elucidate the molecular mechanisms of chilling tolerance in grafted plants, the transcriptomic responses of grafted watermelon under chilling stress were analyzed using RNA-seq analysis. Sequencing data were used for digital gene expression (DGE) analysis to characterize the transcriptomic responses in grafted watermelon seedlings. A total of 702 differentially-expressed genes (DEGs) were found in rootstock grafted (RG) watermelon relative to self-grafted (SG) watermelon; among these genes, 522 genes were up-regulated and 180 were down-regulated. Additionally, 164 and 953 genes were found to specifically expressed in RG and SG seedlings under chilling stress, respectively. Functional annotations revealed that up-regulated DEGs are involved in protein processing, plant-pathogen interaction and the spliceosome, whereas down-regulated DEGs are associated with photosynthesis. Moreover, 13 DEGs were randomly selected for quantitative real time PCR (qRT-PCR) analysis. The expression profiles of these 13 DEGs were consistent with those detected by the DGE analysis, supporting the reliability of the DGE data. This work provides additional insight into the molecular basis of grafted watermelon responses to chilling stress.

Transcriptomic comparison between two Vitis vinifera L. varieties (Trincadeira and Touriga Nacional) in abiotic stress conditions

BACKGROUND

Predicted climate changes announce an increase of extreme environmental conditions including drought and excessive heat and light in classical viticultural regions. Thus, understanding how grapevine responds to these conditions and how different genotypes can adapt, is crucial for informed decisions on accurate viticultural actions. Global transcriptome analyses are useful for this purpose as the response to these abiotic stresses involves the interplay of complex and diverse cascades of physiological, cellular and molecular events. The main goal of the present work was to evaluate the response to diverse imposed abiotic stresses at the transcriptome level and to compare the response of two grapevine varieties with contrasting physiological trends, Trincadeira (TR) and Touriga Nacional (TN).

RESULTS

Leaf transcriptomic response upon heat, high light and drought treatments in growth room controlled conditions, as well as full irrigation and non-irrigation treatments in the field, was compared in TR and TN using GrapeGene GeneChips®. Breakdown of metabolism in response to all treatments was evidenced by the functional annotation of down-regulated genes. However, circa 30 % of the detected stress-responsive genes are still annotated as «Unknown» function. Selected differentially expressed genes from the GrapeGene GeneChip® were analysed by RT-qPCR in leaves of growth room plants under the combination of individual stresses and of field plants, in both varieties. The transcriptomic results correlated better with those obtained after each individual stress than with the results of plants from field conditions.

CONCLUSIONS

From the transcriptomic comparison between the two Portuguese grapevine varieties Trincadeira and Touriga Nacional under abiotic stress main conclusions can be drawn: 1. A different level of tolerance to stress is evidenced by a lower transcriptome reprogramming in TN than in TR. Interestingly, this lack of response in TN associates with its higher adaptation to extreme conditions including environmental conditions in a changing climate; 2. A complex interplay between stress transcriptional cascades is evidenced by antagonistic and, in lower frequency, synergistic effects on gene expression when several stresses are imposed together; 3. The grapevine responses to stress under controlled conditions are not fully extrapolated to the complex vineyard scenario and should be cautiously considered for agronomic management decision purposes.

Ethylene positively regulates cold tolerance in grapevine by modulating the expression of ETHYLENE RESPONSE FACTOR 057

Ethylene (ET) is a gaseous plant hormone that plays essential roles in biotic and abiotic stress responses in plants. However, the role of ET in cold tolerance varies in different species. This study revealed that low temperature promotes the release of ET in grapevine. The treatment of exogenous 1-aminocyclopropane-1-carboxylate increased the cold tolerance of grapevine. By contrast, the application of the ET biosynthesis inhibitor aminoethoxyvinylglycine reduced the cold tolerance of grapevine. This finding suggested that ET positively affected cold stress responses in grapevine. The expression of VaERF057, an ET signaling downstream gene, was strongly induced by low temperature. The overexpression of VaERF057 also enhanced the cold tolerance of Arabidopsis. Under cold treatment, malondialdehyde content was lower and superoxide dismutase, peroxidase, and catalase activities were higher in transgenic lines than in wild-type plants. RNA-Seq results showed that 32 stress-related genes, such as CBF1-3, were upregulated in VaERF057-overexpressing transgenic line. Yeast one-hybrid results further demonstrated that VaERF057 specifically binds to GCC-box and DRE motifs. Thus, VaERF057 may directly regulate the expression of its target stress-responsive genes by interacting with a GCC-box or a DRE element. Our work confirmed that ET positively regulates cold tolerance in grapevine by modulating the expression of VaERF057.

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.

Expression of Vitis amurensis NAC26 in Arabidopsis enhances drought tolerance by modulating jasmonic acid synthesis

The growth and fruit quality of grapevines are widely affected by abnormal climatic conditions such as water deficits, but many of the precise mechanisms by which grapevines respond to drought stress are still largely unknown. Here, we report that VaNAC26, a member of the NAC transcription factor family, was upregulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardy wild Vitis species. Heterologous overexpression of VaNAC26 enhanced drought and salt tolerance in transgenic Arabidopsis. Higher activities of antioxidant enzymes and lower concentrations of H2O2 and O2 (-) were found in VaNAC26-OE lines than in wild type plants under drought stress. These results indicated that scavenging by reactive oxygen species (ROS) was enhanced by VaNAC26 in transgenic lines. Microarray-based transcriptome analysis revealed that genes related to jasmonic acid (JA) synthesis and signaling were upregulated in VaNAC26-OE lines under both normal and drought conditions. VaNAC26 showed a specific binding ability on the NAC recognition sequence (NACRS) motif, which broadly exists in the promoter regions of upregulated genes in transgenic lines. Endogenous JA content significantly increased in the VaNAC26-OE lines 2 and 3. Our data suggest that VaNAC26 responds to abiotic stresses and may enhance drought tolerance by transcriptional regulation of JA synthesis in Arabidopsis.

Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress

Cowpea (V. unguiculata L. Walp.) is an important tropical grain legume. Asparagus bean (V. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea, which is considered one of the top ten Asian vegetables. It can be adapted to a wide range of environmental stimuli such as drought and heat. Nevertheless, it is an extremely cold-sensitive tropical species. Improvement of chilling tolerance in asparagus bean may significantly increase its production and prolong its supply. However, gene regulation and signaling pathways related to cold response in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in response to chilling stress in two asparagus bean cultivars—“Dubai bean” and “Ningjiang-3”, which are tolerant and sensitive to chilling, respectively—were investigated. More than 1.8 million clean reads were obtained from each sample. After de novo assembly, 88,869 unigenes were finally generated with a mean length of 635 bp. Of these unigenes, 41,925 (47.18%) had functional annotations when aligned to public protein databases. Further, we identified 3,510 differentially expressed genes (DEGs) in Dubai bean, including 2,103 up-regulated genes and 1,407 down-regulated genes. While in Ningjiang-3, we found 2,868 DEGs, 1,786 of which were increasing and the others were decreasing. 1,744 DEGs were commonly regulated in two cultivars, suggesting that some genes play fundamental roles in asparagus bean during cold stress. Functional classification of the DEGs in two cultivars using Mercator pipeline indicated that RNA, protein, signaling, stress and hormone metabolism were five major groups. In RNA group, analysis of TFs in DREB subfamily showed that ICE1-CBF3-COR cold responsive cascade may also exist in asparagus bean. Our study is the first to provide the transcriptome sequence resource for asparagus bean, which will accelerate breeding cold resistant asparagus bean varieties through genetic engineering, and advance our knowledge of the genes involved in the complex regulatory networks of this plant under cold stress.

Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis

VaPAT1 functions as a stress-inducible GRAS gene and enhanced cold, drought and salt tolerance in transgenic Arabidopsis via modulation of the expression of a series of stress-related genes. The plant-specific GRAS transcription factor family regulates diverse processes involved in plant growth, development and stress responses. In this study, VaPAT1, a GRAS gene from Vitis amurensis was isolated and functionally characterized. Sequence alignment and phylogenetic analysis showed that VaPAT1 has a high sequence identity to CmsGRAS and OsCIGR1, which belong to PAT1 branch of GRAS family and function in stress resistance. The transcription of VaPAT1 was markedly induced by stress-related phytohormone abscisic acid (ABA) and various abiotic stress treatments such as cold, drought and high salinity, however, it was repressed by exogenous gibberellic acid (GA) application. Overexpression of VaPAT1 increased the cold, drought and high salinity tolerance in transgenic Arabidopsis. When compared with wild type (WT) seedlings, the VaPAT1-overexpression lines accumulated higher levels of proline and soluble sugar under these stress treatments. Moreover, stress-related genes such as AtSIZ1, AtCBF1, AtATR1/MYB34, AtMYC2, AtCOR15A, AtRD29A and AtRD29B showed higher expression levels in VaPAT1 transgenic lines than in WT Arabidopsis under normal growth conditions. Together, our results indicated that VaPAT1 functions as a positive transcriptional regulator involved in grapevine abiotic stress responses.

Identification and expression analysis of heat shock transcription factors in the wild Chinese grapevine (Vitis pseudoreticulata)

Heat shock transcription factors (Hsfs) are known to play pivotal roles in the adaptation of plants to heat stress and other stress stimuli. While grapevine (Vitis vinifera L.) is one of the most important fruit crops worldwide, little is known about the Hsf family in Vitis spp. Here, we identified nineteen putative Hsf genes (VviHsfs) in Vitis spp based on the 12 × grape genome (V. vinifera L.). Phylogenetic analysis revealed three classes of grape Hsf genes (classes A, B, and C). Additional comparisons between grape and Arabidopsis thaliana demonstrated that several VviHsfs genes occurred in corresponding syntenic blocks of Arabidopsis. Moreover, we examined the expression profiles of the homologs of the VviHsfs genes (VpHsfs) in the wild Chinese Vitis pseudoreticulata accession Baihe-35-1, which is tolerant to various environmental stresses. Among the nineteen VpHsfs, ten VpHsfs displayed lower transcript levels under non-stress conditions and marked up-regulation during heat stress treatment; several VpHsfs also displayed altered expression levels in response to cold, salt, and hormone treatments, suggesting their versatile roles in response to stress stimuli. In addition, eight VpHsf-GFP fusion proteins showed differential subcellular localization in V. pseudoreticulata mesophyll protoplasts. Taken together, our data may provide an important reference for further studies of Hsf genes in Vitis spp.

Hormonal control of cold stress responses in plants

Cold stress responses in plants are highly sophisticated events that alter the biochemical composition of cells for protection from damage caused by low temperatures. In addition, cold stress has a profound impact on plant morphologies, causing growth repression and reduced yields. Complex signalling cascades are utilised to induce changes in cold-responsive gene expression that enable plants to withstand chilling or even freezing temperatures. These cascades are governed by the activity of plant hormones, and recent research has provided a better understanding of how cold stress responses are integrated with developmental pathways that modulate growth and initiate other events that increase cold tolerance. Information on the hormonal control of cold stress signalling is summarised to highlight the significant progress that has been made and indicate gaps that still exist in our understanding.

Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome Profiling

Table grapes (Vitis vinifera cv. Cardinal) are highly perishable and their quality deteriorates during postharvest storage at low temperature mainly because of sensitivity to fungal decay and senescence of rachis. The application of a 3-day CO2 treatment (20 kPa CO2 + 20 kPa O2 + 60 kPa N2) at 0°C reduced total decay and retained fruit quality in early and late-harvested table grapes during postharvest storage. In order to study the transcriptional responsiveness of table grapes to low temperature and high CO2 levels in the first stage of storage and how the maturity stage affect these changes, we have performed a comparative large-scale transcriptional analysis using the custom-made GrapeGen GeneChip®. In the first stage of storage, low temperature led to a significantly intense change in grape skin transcriptome irrespective of fruit maturity, although there were different changes within each stage. In the case of CO2 treated samples, in comparison to fruit at time zero, only slight differences were observed. Functional enrichment analysis revealed that major modifications in the transcriptome profile of early- and late-harvested grapes stored at 0°C are linked to biotic and abiotic stress-responsive terms. However, in both cases there is a specific reprogramming of the transcriptome during the first stage of storage at 0°C in order to withstand the cold stress. Thus, genes involved in gluconeogenesis, photosynthesis, mRNA translation and lipid transport were up-regulated in the case of early-harvested grapes, and genes related to protein folding stability and intracellular membrane trafficking in late-harvested grapes. The beneficial effect of high CO2 treatment maintaining table grape quality seems to be an active process requiring the induction of several transcription factors and kinases in early-harvested grapes, and the activation of processes associated to the maintenance of energy in late-harvested grapes.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Gene Expression Analysis of Pak Choi in Response to Vernalization

Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.

Arabidopsis BNT1, an atypical TIR-NBS-LRR gene, acting as a regulator of the hormonal response to stress

During their life cycle, plants have to cope with fluctuating environmental conditions. The perception of the stressful environmental conditions induces a specific stress hormone signature specifying a proper response with an efficient fitness. By reverse genetics, we isolated and characterized a novel mutation in Arabidopsis, associated with environmental stress responses, that affects the At5g11250/BURNOUT1 (BNT1) gene which encode a Toll/Interleukin1 receptor-nucleotide binding site leucine-rich repeat (TIR-NBS-LRR) protein. The knock-out bnt1 mutants displayed, in the absence of stress conditions, a multitude of growth and development defects, suchas severe dwarfism, early senescence and flower sterility, similar to those observed in vitro in wild type plants upon different biotic and/or abiotic stresses. The disruption of BNT1 causes also a drastic increase of the jasmonic, salicylic and abscisic acids as well as ethylene levels. Which was consistent with the expression pattern observed in bnt1 showing an over representation of genes involved in the hormonal response to stress? Therefore, a defect in BNT1 forced the plant to engage in an exhausting general stress response, which produced frail, weakened and poorly adapted plants expressing "burnout" syndromes. Furthermore, by in vitro phenocopying experiments, physiological, chemical and molecular analyses, we propose that BNT1 could represent a molecular link between stress perception and specific hormonal signature.