Ontology highlight
ABSTRACT:
PROVIDER: PRJNA889166 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21855917.fastq.gz | Fastqsanger.gz | |||
| SRR21855918.fastq.gz | Fastqsanger.gz | |||
| SRR21855919.fastq.gz | Fastqsanger.gz | |||
| SRR21855920.fastq.gz | Fastqsanger.gz | |||
| SRR21855921.fastq.gz | Fastqsanger.gz |
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Project description:Drought stress dramatically affects the growth and development of grapevine (Vitis vinifera) in many areas of the world, and identifying the mechanisms responsible for drought stress responses is therefore of great interest. The transcription factor, VlbZIP30 has been reported to enhance drought resistance in grapevine, however, the regulatory mechanisms mediated by VlbZIP30 remain poorly understood. Here, we performed chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses to identify the direct VlbZIP30 target genes at a genome-wide scale. The ChIP-seq analysis determined that VlbZIP30 binds to DNA sequences containing an ACGTG core motif, termed a G-box. By combining the ChIP-seq and RNA-seq results, we identified 48 VlbZIP30-induced target genes, related mainly to the gene ontology (GO) terms: nucleic acid-templated transcription, plant hormone and abiotic stimulus. Through ChIP-qPCR analysis, we confirmed that VlbZIP30 binds directly to the promoters of four of the target genes (VvNAC26, VvDHN1, VvGRAS17 and VvVQ6) containing a G-box motif. In addition, overexpression of VlbZIP30 led to less H2O2 accumulation compared with the wild type under drought conditions in both Arabidopsis thaliana and grapevine, indicating a role for VlbZIP30 in reactive oxygen species (ROS) scavenging. In summary, we report that VlbZIP30 promotes the activity of ROS scavenging by directly regulating the expression of downstream target genes, thereby conferring drought resistance. We also reveal that VlbZIP30 directly regulates the expression of a number of target genes (such as VvDHN1, VvGRAS17 and VvVQ6) to improve plant drought resistance.
2020-10-01 | GSE158852 | GEO
Project description:Experimental research on the effects of abiotic stress over grapevine has mainly focused on water shortage. The adaptation of plants to stress is a complex response triggered by cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues. Gene expression upon acute (heat and light) and steady (drought) individual stresses and field conditions were compared in two grapevine (Vitis vinifera L.) varieties, Trincadeira (TR) and Touriga Nacional (TN).
2017-01-01 | GSE57669 | GEO
Project description:The growth and fruit quality of grapevine are widely affected by abnormal climatic conditions such as extreme temperature. But how grapevine responds to cold stress is still largely unknown. Here we found that VaMyb14, a member of R2R3 Myb transcription factor family, was up-regulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardiness wild Vitis species. Overexpression VaMyb14 in Arabidopsis increased antioxidant enzyme activity, especially POD activity, than that of the wild type and decreased the MDA content. A series of ABA metabolism and signal transduction genes in transgenic Arabidopsiswere were up-regulated in microarry results, including several nsLTPs, PP2Cs, RD29B, COR78 and other structural genes, suggesting that VaMyb14 not only affect the ABA signaling pathways, but also activates the CBF-COR independent nsLTP genes. Collectively, these results illustrate that Vitis Myb14 could represent a node of convergence regulating grapevine stress responses, including improve defence induced phytoalexin resveratrol against necrotrophic as well as drought and/or cold stress tolerance, highlighting Myb14 as a potential gene resource in future grapevine breeding.
2018-06-01 | GSE112389 | GEO
Project description:Since the roots of grapevine rootstocks have a direct contact with drying soil and has an important role in abiotic stimuli, any plasticity on the architecture of the rootstocks would enable grapevine varieties to a better respond to drought stress. However, genomics evidences behind the physiological responses of rootstocks under prolonged drought stress are poorly documented in the literature. In the current study, eight widely used hybrid grapevine rootstocks in viticulture were firstly grafted with sultana seedless and subjected to drought stress to test their physiological and biochemical responses. The results of experiment indicated that the roots of V.rupestris X V.berlandieri (110 R, 1103P, 140 Ru) rootstocks possessed much higher water content as well as non-structural carbohydrate and nitrogen concentrations compared to V.riparia X V.berlandieri (SO4, 5BB, 420A, 8B) and V.vinifera X V.berlandieri (41B) hybrids under drought. V.rupestris X V.berlandieri hybrids were also performed much higher root elongation performance under drought compared to other rootstock hybrids. Three rootstock varieties (110R, 5BB and 41B) having different pedigrees and root architectural responses to drought were also investigated at transcriptome level to find out gene regulation network behind differential physiological responses to drought. Transcriptome analysis revealed 2795, 1196 and 1612 differentially expressed transcripts for the roots of 110R, 5BB and 41B, respectively. The highest expression increases in 110R compared to other rootstocks were recorded for the transcripts functional in carbohydrate (SWEET14, CWINV) and nitrate/peptide (NRT1/ PTR FAMILY) transportation as well as osmoregulation (dehydrins, osmotins, LEAs and proline-glycine rich proteins) during drought. Higher induction of these genes in the roots of tolerant 110R genotype indicated importance of efficient uptake of carbohydrate and nitrogen source released from canopy under drought and preservation of water with osmotic regulation on the root elongation and drought tolerance of grapevines. Expression increases in several other pathogenesis related proteins, regulation of cell wall modification enzymes and activity of several secondary metabolites have been also associated to altered root architecture and drought tolerance in the grapevine rootstocks for the first time with the current study.
2016-10-25 | GSE89075 | GEO
Project description:Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought tolerant) or 125AA (drought sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100 % veraison. The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signalling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA concerning genes related to jasmonate, phenylpropanoid metabolism and PR-proteins. The data also suggests a link between jasmonate and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and jasmonate are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties.
2015-03-19 | GSE66391 | GEO
Project description:Grafting is a well-established practice for grapevine to facilitate propagation of productive and tolerant cultivars against several stress factors. It is also considered to be a suitable method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. So far, controlling only effect of rootstock over scion was investigated and root-to-shoot transcriptomic alterations were fallowed on the scions or graft interfaces. The objective of this study was to investigate transcriptomic and physiological influence of scion on the rootstock under drought stress. Therefore, drought tolerant 110R rootstock were firstly grafted with sultana seedless and tested under drought stress with its non-grafted counterpart. The results of treatment indicated that grafted 110R performed the highest root elongation under drought. We carried out a microarray based transcriptome analysis on the roots of grafted and non-grafted 110R to explain this drought derived interaction through scion-to-rootstock. The highest expression increase under drought was recorded for sugar (SWEET) and nitrate or di/tri-peptide (NRT1/ PTR FAMILY) transporter proteins. Expression level of these genes was more highly increased in grafted 110R than its non-grafted counterpart. This situation indicated their potential role in drought tolerance and scion/rootstock harmony. Overexpression of these transporters attributed to increased amount of released nutrient and nitrogen source from abscised leaves of sultana seedless under drought. Remobilization of these rich sources was suggested to chance transcriptomic response of rootstocks and enabled much better growth in grafted 110R. Other transcripts annotated to cell wall modification enzymes (chitinases), osmoregulator proteins (dehydrins, proline-glycine rich proteins) and secondary metabolites (stilbene synthase) were also more highly induced in grafted 110R. This is the first report indicating transcriptomic influence of scion on the grapevine rootstocks and representing the genes responsible in scion/rootstock harmony and drought tolerance.
2017-12-31 | GSE89185 | GEO
Project description:Background: Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant’s response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that respond to dehydration in three different grapevine species differing in their drought tolerance. Results: Transcriptomic analyses of the leaves of Cabernet Sauvignon, Riparia Gloire, and Ramsey were evaluated at different times during a 24-h controlled dehydration. ANOVA revealed that 11,000 transcripts changed significantly with respect to the genotype x treatment interaction term and 6,000 transcripts changed significantly according to the genotype x treatment x time interaction term indicating massive differential changes in gene expression over time. Standard analyses determined substantial effects on the transcript abundance of genes involved in the metabolism and signaling of two known plant stress hormones, ABA and ethylene. ABA and ethylene signaling maps were constructed and revealed specific changes in transcript abundance that were associated with the known drought tolerance of the genotypes including genes such as VviABI5, VviABF2, VviACS2, and VviWRKY22. Weighted-gene coexpression network analysis (WGCNA) confirmed these results. In particular, WGCNA identified 30 different modules, some of which had highly enriched gene ontology categories for photosynthesis, phenylpropanoid metabolism, ABA and ethylene signaling. The ABA signaling transcription factors, VviABI5 and VviABF2, were highly connected hubs in two modules, one having overrepresentation in gaseous transport and the other in ethylene signaling. VviABI5 was distinctly correlated with an early response and high expression for the drought tolerant Ramsey and with little response from the drought sensitive Riparia Gloire. These ABA signaling transcription factors were highly connected to VviSNRK1 and other gene hubs associated with sugar, ethylene and ABA signaling. The ABA and ethylene signaling hubs were highly connected, supporting the hypothesis that there is substantial cross-talk between the two hormone pathways. This study identifies solid gene candidates for future investigations of drought tolerance in grapevine.
2016-03-05 | GSE78920 | GEO
Project description:The growth and fruit quality of grapevine are widely affected by abnormal climatic conditions such as water deficit. But how grapevine responds to drought stress is still largely unknown. Here we found that VaNAC26, a member of NAC transcription factor family, was up-regulated dramatically during cold, drought and salinity treatments in Vitis amurensis, a cold and drought-hardiness wild Vitis species. Ectopic overexpression of VaNAC26 enhanced the drought and salt tolerances in transgenic Arabidopsis. Higher activities of antioxidant enzymes and the lower concentration of H2O2 and O2- were found in VaNAC26-OE lines than in wild type plants under drought stress. These results indicate that the reactive oxygen species (ROS) scavenging was enhanced by VaNAC26 in transgenic lines. Microarray based transcriptome analysis reveals that genes related to jasmonic acid (JA) synthesis and signaling were up-regulated in VaNAC26-OE lines under both normal and drought conditions. VaNAC26 showed a specific binding ability on NACRS motif, which was broadly existent in the promoter regions of up-regulated genes in transgenic lines. Endogenous JA content was found increased obviously in VaNAC26-OE-2/3 lines. Our data suggests that VaNAC26 responds to abiotic stresses and may enhance the drought tolerance by transcriptional regulation of JA synthesis in Arabidopsis.
2015-08-14 | GSE72050 | GEO
Project description:Drought has become an increasingly important constraint on grapevine sustainability due to global climate change. Vitis riparia, the only grapevine native to the upper Midwest region of the United States, is widely used in scion and rootstock breeding; however, it is not considered drought tolerant. In this study, RNA-Seq data were generated from grapevine root/shoot under WD and well-watered (control (C)) conditions to compare root signaling and shoot responses to water deficit.
2018-12-15 | GSE109065 | GEO
Project description:Cassava is a drought–resistant food crop in tropical and subtropical regions. Although cassava is a relatively drought-tolerant species, the development and yields are greatly affected by the adverse drought conditions. Information about molecular breeding will obtain by studying genetic regulatory mechanism. In this study, we demonstrate the drought-tolerant mechanisms in leaves of both cassava varieties(Xinxuan048 and KU50) by using RNA-Seq technique. 1,880 and 2,066 differentially expressed genes(DEGs) were induced by drought stress in leaves of KU50 and Xinxuan048, respectively. DEGs in the response to drought stress involve in many regulated pathways. ROS- and ABA-associated signaling pathways and photosynthesis-associated regulation are mainly elucidated. In addition, alternative splicing and ingle nucleotide polymorphism also involve in drought-stress responses in both cassava varieties, showing their important roles in response to drought stress in leaves. This study not only increases the understanding of physiological and molecular mechanisms to the drought response in cassava, but also lays a solid foundation on the breeding of drought-resistant varieties using molecular methods.
2018-07-01 | GSE98537 | GEO