Heat stress effects on gene expression in the grape berry. Comparison of pre- and post-véraison berries and microarray versus mRNA-seq datasets.
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE33222 | GEO | 2018/11/22
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of the present work was the quantitative profiling of small RNAs involved in berry development and responding to heat stress and the identification of chromosome location and putative gene targets.
2018-11-22 | GSE33349 | GEO
Project description:The vacuole occupies a large portion of plant cell volume, it is especially true to fruit tissues. Berry flesh cell vacuole serves as storage organelle for water, sugars, acids, secondary metabolites and others, which largely determining berry quality (Fontes et al., 2011a, b; Shiratake and Martinoia, 2007, Conde et al., 2006). However, the molecular basis of these compartmentation processes is still poorly understood. As in many species, the major bottle neck to study these aspects in grapevine is to obtain highly purified vacuoles with a good yield (Fontes et al., 2010). Up to date, several vacuole or tonoplast proteome researches were applied on a few plants mainly on Arabidopsis thaliana, vacuoles or tonoplast were derived from mesophyll cells (Carter et al., 2004, Endler et al., 2006, Schulze, et al., 2012) or cell culture (Jaquinod et al 2006, Shimaoka et al 2004), cauliflower buds (Schmidt et al., 2007) and sugar beet taproots (Jung et al., 2015). Though the grape berry protoplasts and intact vacuoles were successfully isolated from Cabernet Sauvignon berry suspension-cultured cells (Fontes et al., 2010), the vacuoles isolated from grape berry or different development and ripening stages of grape berry mesocarp tissues were not achieved.
2019-11-12 | PXD010556 | Pride
Project description:Studying the effect of varying durations (1, 7 and 14 days) of locally applied heat stress on grape berries at three developmental stages (middle green, veraison and middle ripening). Among various environmental factors, temperature is a major regulator affecting plant growth, development and fruit composition. Reproductive development of grapevine and berry composition, are both highly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries tolerance to high temperatures (HS) are poorly understood. Although recent data addressed the consequences on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat stress. In the context of climate change, this work focused on microclimate effect is of particular interest to better understand the consequences of leaf removal (a common viticultural practice) on berry development. HS (+ 8°C) was locally applied to clusters from Cabernet Sauvignon fruiting cuttings at three different developmental stages (middle green, véraison and middle ripening). Samples were collected 1, 7 and 14 days after treatment and used for metabolic and transcriptomic analyses. The results showed dramatic and specific biochemical and transcriptomic changes in heat exposed berries, depending on the developmental stage and the stress duration. When applied at the herbaceous stage, HS delayed the onset of véraison. Heating also strongly altered the berry concentration of amino acids and organic acids (e.g. PHE, GABA, and malate) and decreased the anthocyanin content at maturity. These physiological alterations could be partly explained by the deep remodelling of transcriptome in heated berries. More than 7000 genes were deregulated in at least one of the nine experimental conditions. The most affected processes belong to the categories “stress responses”, “protein metabolism” and “secondary metabolisms”, highlighting the intrinsic capacity of grape berries to perceive heat stress and to build adaptive responses. Additionally, important changes in processes related to “transport”, “hormone” and “transcription” might contribute to the postponing of véraison. Finally, opposite effects depending on heating duration were observed for genes encoding enzymes of the general phenylpropanoid pathway, suggesting that the HS-induced decrease in anthocyanin content may result from a combination of transcript abundance and product degradation.
2017-03-08 | GSE86551 | GEO
Project description:Grapevine (Vitis vinifera L) is considered one of the most environmentally sensitive crops and is characterized by broad phenotypic plasticity, offering important advantages such as the large range of different wines that can be produced from the same cultivar, and the adaptation of existing cultivars to diverse growing regions. The uniqueness of berry quality traits reflects complex interactions between the grapevine plant and the combination of natural factors and human cultural practices, defined as terroir, which leads to the expression of wine typicity. Despite the scientific and commercial importance of genotype interactions with growing conditions, few studies have characterized the genes and metabolites directly involved in this phenomenon. Here we used two large-scale analytical approaches to explore the metabolomic and transcriptomic basis of the broad phenotypic plasticity of Garganega, a white berry variety grown at four sites characterized by different pedoclimatic conditions (altitudes, soil texture and composition). These conditions determine berry ripening dynamics in terms of sugar accumulation and the abundance of phenolic compounds. Multivariate analysis unraveled a highly plastic metabolomic response to different environments, especially the accumulation of hydroxycinnamic and hydroxybenzoic acids and flavonols. Principal component analysis revealed that the four sites strongly affected the berry transcriptome allowing the identification of environmentally-modulated genes and the plasticity of commonly-modulated transcripts at different sites. Many genes that control transcription, translation, transport and carbohydrate metabolism showed different expression depending on the environmental conditions, indicating a key role in the observed transcriptomic plasticity of Garganega berries. Interestingly, genes representing the phenylpropanoid/flavonoid pathway showed plastic responses to the environment mirroring the accumulation of the corresponding metabolites. The comparison of Garganega and Corvina berries showed that the metabolism of phenolic compounds is more plastic in ripening Garganega berries under different pedoclimatic conditions.
2016-07-13 | GSE75565 | GEO
Project description:Grapevine is a popular fruit crop worldwide with essential economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. To better understand this dynamic process, we applied mass spectrometry based platforms to analysis the metabolome and proteome of grape berries at 12 developmental stages covering the whole developmental process of grape berries. Primary metabolites involved in central carbon metabolism such as sugars, organic acids and amino acids metabolism together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the metabolomic and proteomic data revealed growing trajectories with minor difference indicating that grape berry development is a sequential process resulting in changes in all examined processes. The incorporation of the metabolomic and proteomic results allowed us to schematize representative metabolome and proteome candidates on sugar, glycolysis, TCA cycle, amino acid, phenylpropanoid, flavonoid biosynthetic pathways. The overview of the metabolism dynamics on both protein and metabolite level unveiled the metabolism switch and adjustments during grape berry development.
2018-10-18 | PXD003769 | Pride
Project description:To understand the fruit changes and mechanisms involved in the compatible grapevine-virus interaction, we analyzed the berry transcriptome in two stages of development (veraison and ripening) in the red wine cultivar Cabernet Sauvignon infected with Grapevine leaf-roll-associated virus-3 (GLRaV-3). Analysis of global gene expression patterns indicate incomplete berry maturation in infected berries as compared to uninfected fruit suggesting viral infection interrupts the normal berry maturation process. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Andrea Vega. The equivalent experiment is VV28 at PLEXdb.
2011-08-26 | GSE31660 | GEO
Project description:Study of Frontenac and Marquette Grape berry ripening profile using Transcriptomics
2022-04-18 | GSE130055 | GEO
Project description:To understand the fruit changes and mechanisms involved in the compatible grapevine-virus interaction, we analyzed the berry transcriptome in two stages of development (veraison and ripening) in the red wine cultivar Cabernet Sauvignon infected with Grapevine leaf-roll-associated virus-3 (GLRaV-3). Analysis of global gene expression patterns indicate incomplete berry maturation in infected berries as compared to uninfected fruit suggesting viral infection interrupts the normal berry maturation process. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Andrea Vega. The equivalent experiment is VV28 at PLEXdb. GLRaV-3 virus-infected, developmental stage: Veraison(3-replications); GLRaV-3 virus-infected, developmental stage: Ripening(3-replications); Virus-free, developmental stage: Veraison(4-replications); Virus-free, developmental stage: Ripening(4-replications)
2011-08-25 | E-GEOD-31660 | 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:The application of sensors in viticulture is a fast and efficient method to monitor grapevine vegetative, yield, and quality parameters and determine spatial intra-vineyard variability. Molecular analysis at the gene expression level can further contribute to the understanding of the observed variability by elucidating how pathways contributing to different grape quality traits behave in zones diverging on any of these parameters. The intra-vineyard variability of a Cabernet Sauvignon vineyard was evaluated through a Normalized Difference Vegetation Index (NDVI) map calculated from a multispectral image and detailed ground-truthing (e.g., vegetative, yield, and berry ripening compositional parameters). The relationships between NDVI and ground measurements were explored by correlation analysis. Moreover, berries were investigated by microarray gene expression analysis performed at five time points from fruit set to full ripening. Comparison between the transcriptomes of samples taken from locations with the highest and lowest NDVI values identified 968 differentially expressed genes. Spatial variability maps of the expression level of key berry ripening genes showed consistent patterns aligned with the vineyard vigor map. These insights indicate that berries from different vigor zones present distinct molecular maturation programs and suggest that transcriptome analysis may be a valuable tool for the management of vineyard variability.
2024-02-27 | GSE254304 | GEO