Transcriptome investigations supports the role of rootstock-scion interaction in grapevine berry quality
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer IIx
ORGANISM(S): Vitis vinifera
SUBMITTER: Paolo Bagnaresi
PROVIDER: E-MTAB-8758 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study aimed at investigating the effect in Grapevine of two different rootstocks (1103 Paulsen - P - and Mgt 101-14 - M) in comparison with not grafted plants - F - on the miRNome of berry skin in Pinot noir (clone Entav 115), to explore the influence of rootstock-scion interaction on grape quality. 7-year old grapevine plants were grown in 70-liters, in an open field arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized and were abundantly irrigated. Berry samples (15 per plant, 3 plants per replicate), were collected at two different developmental stage: veraison (1) and maturation (2), and dissected to separate skin tissues. Total RNA was extracted and DNase treated, small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina®), following all manufacturers' instructions. Eighteen bar-coded small RNA libraries were constructed starting from 1 µg of total RNAs.
2020-09-30 | E-MTAB-8756 | biostudies-arrayexpress
Project description:Heat stress is a serious and widespread threat to the quality and yield of many crops, including grape (Vitis vinifera), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves from grape cultivated in four distinct temperature regimes. The phosphorylation or acetylation of a total of 1,011 phosphoproteins with 1,828 phosphosites, and 96 acetylproteins with 148 acetylsites, changed when plants were grown at 35°C, 40°C and 45°C in comparison with the proteome profiles of plants grown at 25°C. The greatest number of changes were observed at higher temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the responses to high temperatures. This is congruent with previous observations that alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat shock proteins were more associated with modifications in phosphorylation than in acetylation. Nineteen proteins were identified with changes in both phosphorylation and acetylation, consistent with crosstalk between these post-translational modifications.
2019-11-13 | PXD014090 | Pride
Project description:Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes. Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries. Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales. A total of 54 samples were hybridized. Three different circadian time course series consisted on six time point each. Series corresponded to pericarp of Verdejo grapevine cultivar and berry flesh and skin in separate of Tempranillo cultivar. Three biological replicates were analyzed for each series.
2014-03-28 | E-GEOD-52167 | biostudies-arrayexpress
Project description:White grape (Vitis vinifera cv. Furmint) berry samples subjected to natural noble rot were collected in a vineyard in Mád, Hungary (Tokaj wine region). Raw data include grapevine and Botrytis cinerea sequence reads.
2021-11-25 | E-MTAB-11205 | biostudies-arrayexpress
Project description:Background: The composition of grapevine berry at harvest is a major determinant of wine quality. Optimal oenological maturity of berries is characterized by a high sugar/acidity ratio, high anthocyanin content in the skin, and low astringency. However, harvest time is still mostly determined empirically, based on crude biochemical composition and berry tasting. In this context, it is interesting to identify genes that are expressed/repressed specifically at the late stages of ripening and which may be used as indicators of maturity. Results: Whole bunches and berries sorted by density were collected in vineyard on Chardonnay (white cultivar) grapevines for two consecutive years at three stages of ripening (7-days before harvest (TH-7),harvest (TH), and 10-days after harvest (TH+10)). Microvinification and sensory analysis indicate that the quality of the wines made from the whole bunches collected at TH-7, TH and TH+10 differed, TH providing the highest quality wines. In parallel, gene expression was studied with Qiagen/Operon microarrays using two types of samples, i.e. whole bunches and berries sorted by density. Only 12 genes were consistently up- or down-regulated in whole bunches and density sorted berries for the two years studied in Chardonnay. 52 genes were differentially expressed between the TH-7 and TH samples. In order to determine whether these genes followed a similar pattern of expression during the late stagesof berry ripening in a red cultivar, nine genes were selected for RT-PCR analysis with Cabernet Sauvignon grown under two different temperature regimes affecting the precocity of ripening. The expression profiles and their relationship to ripening were confirmed in Cabernet Sauvignon for seven genes, encoding a carotenoid cleavage dioxygenase, a galactinol synthase, a late embryogenesis abundant protein, a dirigent-like protein, a histidine kinase receptor, avalencene synthase and a putative S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase. Conclusions: This set of up- and down-regulated genes characterize the late stages of berry ripening in the two cultivars studied, and are indirectly linked to wine quality. They might be used directly or indirectly to design immunological, biochemical or molecular tools aimed at the determination of optimal ripening in these cultivars.
2011-11-08 | E-MTAB-481 | biostudies-arrayexpress
Project description:Background: Grapevine berry, a nonclimacteric fruit, goes through three developmental stages, the last one called the ripening stage, when the berry changes color and dramatically increases in sugar. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the latter stages of ripening between 22 and 37 M-BM-0Brix. Grapevine berry, a nonclimacteric fruit, goes through three developmental stages, the last one called the ripening stage, when the berry changes color and dramatically increases in sugar. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the latter stages of ripening between 22 and 37 M-BM-0Brix. Results: There were approximatedly 18,000 transcripts whose abundance changed with M-BM-0Brix level and tissue type. There were very broad changes in many gene ontology (GO) categories involving metabolism, signaling and abiotic stress. GO categories reflecting tissue differences were overrepresentation in photoysynthesis, isoprenoid metabolism and pigment biosynthesis. A more detailed analysis of the interaction of the skin and pulp with M-BM-0Brix levels revealed that there were significantly higher abundances of transcripts changing with M-BM-0Brix level in the skin that were involved in ethylene signaling, isoprenoid and fatty acid metabolism. Many of these transcripts were peaking around the optimal fruit stage for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF Superfamily of transcription factors changed during these developmental stages. The transcript abundance of a unique clade of ERF6-type transcription factors had the largest changes and clustered with other genes involved in ethylene, senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcript abundance of other important transcription factors (i.e. SPL, RIN, etc.) involved in the regulation of fruit ripening was also higher in the skin. Conclusions: A detailed analysis of the transcriptomic response of grapevine berries revealed that these berries went through massive changes in chemical signaling and metabolism in both the pulp and skin, particularly in the skin. The ethylene signaling pathway of this nonclimacteric fruit was significantly stimulated in the late stages of ripening when the production of transcripts for important flavor and aroma compounds were at their highest. Ethylene transcription factors known to play a role in leaf senescence also appear to play a role in fruit senescence. Ethylene may play a bigger role than previously thought in this non-climacteric fruit. Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berries were harvested from J. Lohr Vineyards & Wines, Paso Robles, CA, USA. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of berries in the latter stages of ripening between 22 and 37 M-BM-0Brix (2008 vintage).
2014-11-01 | E-GEOD-55302 | biostudies-arrayexpress
Project description:Grapevine is a commercially important fruit crop that provides berries for direct consumption, juice pressing, drying (raisins), and fermentation to produce wine. The economic value of the crop has encouraged many researchers to study the physiological and molecular basis of berry development, particularly processes that affect wine quality. Post-harvest withering of grapevine berries is used in the production of dessert and fortified wines to alter must quality characteristics and to increase the concentration of simple sugars. Vitis vinifera cv Corvina berries were sampled during the 2006 growing season at four developmental time points and three additional time points during the 91-day post-harvest withering process. The four developmental time points were 59, 71, 98 and 112 days after fruit set, corresponding to pre-veraison, veraison, early ripening and late ripening, and the three withering time points (WI, WII and WIII) were 35, 56 and 91 days after harvest. Three biological replicates were taken at each time point resulting in a total of 21 samples.
2010-09-24 | E-GEOD-20511 | biostudies-arrayexpress
Project description:Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. Results: Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during one growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries. Conclusions: Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems. Vitis vinifera cultivar Corvina clone 48 berries were harvested from different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions. Berries were harvested at three different developmental stages: véraison, mid-ripening and harvest; each sample was collected in three biological replicates, to cover the whole vineyard variability. The same sampling procedure had been repeated over three consecutive vintages (2006, 2007 and 2008).
2013-04-11 | E-GEOD-41633 | 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
Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
2020-01-22 | PXD000319 | Pride