Vitis vinifera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA325007 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3650990.fastq.gz | Fastqsanger.gz | |||
| SRR3651000.fastq.gz | Fastqsanger.gz | |||
| SRR3650991.fastq.gz | Fastqsanger.gz | |||
| SRR3651001.fastq.gz | Fastqsanger.gz | |||
| SRR3650992.fastq.gz | Fastqsanger.gz |
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Project description:Long distance transfers on genetic material (mRNA, miRNA, Protein, etc.) and metabolites (Hormone) between rootstock and scion is also well documented in the homo-grafting hybrids, but the process in distant-grafting is not reported where rootstock and scion belonging to different Familly. We repeatedly grafted the Vitis vinifera scion onto the Schisandra chinensis stock and got 20 interfamily vegetative hybrids ― Vitis vinifera / Schisandra chinensis (Vs) that could grow normally over 25 years. We found the phonotype leaf, internode, fruit of Vs upper the graft union transformed to intermediate stage between V. vinifera and S. chinensis, and the new traits was inherited by vegetative propagation. To expose the reason, using the simultaneous self-rooted Vitis vinifera (Vv) as control, differences of transcriptomics, miRNAs, degradome between Vv and Vs were analyzed by high-throughput sequencing, and the metabolome by liquid Chromatograph Mass Spectrometer (LC-MS). The results showed that a total of 2113 differentially expressed genes (DEGs), GO annotation and KEGG pathway enrichment analysis found that DEGs function mainly included oxidation-reduction process, metabolic process, etc. 79 differentially expressed miRNAs (DEMs) contains 27 known miRNAs and 52 novel miRNAs were identificated, the main functions of DEMs were defense response, biosynthetic process, etc. The target gene detected by degradome sequencing were mainly regulation of transcription & DNA-templated, auxin-activated signaling pathway, etc. And the degradation group detected 840 target genes corresponding to 252 miRNAs, of which 12 DEMs and the corresponding target gene expression levels were mostly negatively correlated. Meanwhile, 1188 differentially metabolic compounds were identified, the most common of which were sputum metabolism, arginine and proline metabolism, and ABC transporters. Especially the metabolites schizandrin was significantly down regulated and gomisin was up regulated in Vs that were main medicinal ingredients in Schisandra. KEGG pathway enrichment analysis of differential metabolites found more than 30 differential metabolic pathways of Vv-Vs. Our data demonstrate the impact of interfamily graft on the genetic materials and metabolites for the scion and the traits can stable inherited by vegetative propagation, providing an important reference and basis for future breeding through select target gene type rootstocks.
2022-11-30 | GSE130209 | 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: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:In order to investigate the putative roles of the VvPLCP genes in grapevine resistance, the leaves-specific expression patterns of VvPLCPs were analyzed according to transcriptome data in two cultivars including V. vinifera cv. ‘Zitian Seedless’ and Vitis rootstocks ‘Kober 5BB’ when infected with P. viticola
2021-08-22 | GSE182149 | GEO
Project description:Study of gene expression during Plasmopara viticola infection in the resistant Vitis vinifera cultivar 'Regent'. The oomycete fungus Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is responsible for grapevine downy mildew disease. Most of the cultivated grapevines are sensitive to this pathogen, thus requiring intensive fungicide treatments. The molecular basis of resistance to this pathogen is poorly understood. We have carried out a cDNA microarray transcriptome analysis to identify grapevine genes associated with resistance traits. Early transcriptional changes associated with downy mildew infection in the resistant Vitis vinifera cultivar ‘Regent’, when compared to the susceptible cultivar ‘Trincadeira’, were analyzed. Transcript levels were measured at three time-points: 0, 6 and 12 hours post inoculation (hpi). Our data indicate that resistance in V. vinifera ‘Regent’ is induced after infection. This study provides the identification of several candidate genes that may be related to ‘Regent’ defense mechanisms, allowing a better understanding of this cultivar's resistance traits.
2012-04-06 | GSE28439 | GEO
Project description:itis vinifera cv. Tannat is largely cultivated in Uruguay for the production of high quality red wines. Its most notable characteristic is an elevated content of polyphenolic compounds, which provide an intense purple color and remarkable antioxidant properties to the wine. To characterize the genetic components encoding this important phenotypic characteristic, the genome of the Uruguayan Tannat clone UY11 was sequenced to 134X coverage using the Illumina technology and assembled with a mixed approach of de novo assembly and iterative mapping on the PN40024 reference genome. An approach based on both reference-guided annotation and de novo transcript assembly of RNA-Seq data allowed the definition of 3,673 genes not previously annotated in PN40024 that we consider novel, and the discovery of 2,228 genes not shared with the grapevine reference genome that we consider private to Tannat. Expression analysis showed that private genes contributed substantially (more than 50%) to the overall expression of enzymes involved in phenol and polyphenol biosynthesis indicating that the dispensable portion of the grapevine genome contains many private genes which are likely to contribute to the peculiar phenotypic characteristics of this grapevine variety.
2014-01-09 | E-MTAB-4278 | biostudies-arrayexpress
Project description:Study of gene expression during Plasmopara viticola infection in the resistant Vitis vinifera cultivar 'Regent'. The oomycete fungus Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is responsible for grapevine downy mildew disease. Most of the cultivated grapevines are sensitive to this pathogen, thus requiring intensive fungicide treatments. The molecular basis of resistance to this pathogen is poorly understood. We have carried out a cDNA microarray transcriptome analysis to identify grapevine genes associated with resistance traits. Early transcriptional changes associated with downy mildew infection in the resistant Vitis vinifera cultivar M-bM-^@M-^XRegentM-bM-^@M-^Y, when compared to the susceptible cultivar M-bM-^@M-^XTrincadeiraM-bM-^@M-^Y, were analyzed. Transcript levels were measured at three time-points: 0, 6 and 12 hours post inoculation (hpi). Our data indicate that resistance in V. vinifera M-bM-^@M-^XRegentM-bM-^@M-^Y is induced after infection. This study provides the identification of several candidate genes that may be related to M-bM-^@M-^XRegentM-bM-^@M-^Y defense mechanisms, allowing a better understanding of this cultivar's resistance traits. 3 time points: 0, 6 and 12 hours post inoculation by P. viticola. Two cultivars: control (Trinacedira) and test (Regent). Two biological replicates were performed at 0 hpi, and 3 biological replicates at 6 and 12hpi. At 12hpi, three technical replicates also were performed.
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Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164583 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164582 | GEO