Vitis vinifera cultivar:Merlot
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA394039 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5829260_1.fastq.gz | Fastqsanger.gz | |||
| SRR5829260_2.fastq.gz | Fastqsanger.gz | |||
| SRR5829280_1.fastq.gz | Fastqsanger.gz | |||
| SRR5829280_2.fastq.gz | Fastqsanger.gz | |||
| SRR5829261_1.fastq.gz | Fastqsanger.gz |
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Project description:Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.
2020-05-22 | GSE132262 | GEO
Project description:We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster. Keywords: time course (berry development series)
2008-07-15 | GSE11406 | GEO
Project description:We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster. Experiment Overall Design: Individual grape berries were selected at 4 developmental stages along ripening initiation for RNA extraction and hybridization to Affymetrix Vitis Genome GeneChips. One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS). Individual berries representing each stage were collected from either the distal or the proximal position of one cluster one each of two plants used for experiments.
2008-10-20 | E-GEOD-11406 | biostudies-arrayexpress
Project description:Seedless varieties are of particular importance to the table-grape and raisin industries. Gibberellin (GA) application is widely used in the early stages of seedless berry development to increase berry size and economic value. However, the underlying mechanism of GA induction of berry enlargement is not well understood. Here, RNA-sequencing analysis of âCentennial Seedlessâ (Vitis vinifera L.) berries treated with GA3 12 days after flowering is reported.
2014-12-05 | E-MTAB-4247 | biostudies-arrayexpress
Project description:Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
2010-11-09 | E-MEXP-2451 | biostudies-arrayexpress
Project description:We report the berry pericarp transcriptomic profiles of 5 red Vitis vinifera varieties: Sangiovese, Barbera, Negro amaro, Refosco and Primitivo at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89)
2015-01-19 | GSE62744 | GEO
Project description:We report the berry pericarp transcriptomic profiles of 5 white Vitis vinifera varieties: Vermentino, Garganega, Glera, Moscato bianco and Passerina at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89)
2017-06-28 | GSE62745 | GEO
Project description:Protein expression from berry skin of four different red grape biotypes was compared at a proteome-wide level by bottom-up shotgun proteomics, label free quantification and MaxQuant-assisted computational analysis. Red grapes were from a purebred Vitis vinifera (Aglianico cv.), a V. vinifera (local Sciascinoso cv.) grafted onto an American rootstock, an interspecific hybrid (V. vinifera × V. labrusca, Isabel) and an uncharacterized red grape with some hybrid lineage, as demonstrated by the presence of relatively high amounts of anthocyanidin 3,5-O-diglucosides. The aim was assessing the differences among red grape biotypes at a protein expression levels, also addressing the possible effect of the grafting on the phenotypic expression of some key metabolic enzymes in grape berries.
2022-02-22 | PXD025784 | Pride
Project description:Vitis vinifera endogenous small RNAs Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
2010-04-29 | E-GEOD-18405 | biostudies-arrayexpress
Project description:We report the berry pericarp transcriptomic profiles of 5 red Vitis vinifera varieties: Sangiovese, Barbera, Negro amaro, Refosco and Primitivo at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89) mRNA profiles of 5 red grapevine varieties at 4 growth stages were generated by deep sequencing, in triplicate, using Illumina Hiseq 1000.
2015-01-19 | E-GEOD-62744 | biostudies-arrayexpress