Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening
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ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE36234 | GEO | 2012/03/05
SECONDARY ACCESSION(S): PRJNA153147
REPOSITORIES: GEO
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Project description:Background: Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning. Results: We profiled the transcriptome of Vitis vinifera cv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m2 leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed. Conclusion: Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process. Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three cluster thinned vines (50% of cluster removed) at beginning of véraison (BV), end of véraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.
2012-03-05 | E-GEOD-36234 | 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: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: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 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:Grapevine cluster compactness is a multi-componential trait of agronomical interest; it greatly influences the vineyard management and the visual aspect of table grape. Clusters with greater compactness are more susceptible to disease. The compactness can be break down in a patchwork of agronomical traits, each having agronomical importance that includes parameters related to inflorescence and cluster architecture (cluster length and width, length of pedicels, etc.), fruitfulness (number of berries, number of seeds) and berry (size, shape, volume...). Through visual evaluation of a collection of 730 clones from the cultivar Tempranillo and 501 clones from Garnacha Tinta we identified and fully phenotyped distinct clones which transcriptomes were compared at key developmental stages in order to identify the genes playing a role in mechanisms involved in cluster compactness such as the ones determining number of berries, cluster length or berry size. Key genes involved in this process were identified. The findings lead us to hypothesize that berry size and/or number at ripening are greatly influenced by the rate of cell replication in flowers during the first stages after pollination. A total of 57 samples were hybridized. Comparison G1 was performed between clones showing differences in the cluster compactness and in the total number of berries per cluster and berries size (compact: clone 1134. loose: clone 0368). Comparison G2 was performed between two compact clones (Garnacha Tinta 147 and 1134) significantly differing for cluster length and number of nodes (branches) of the rachis. Comparison G3 was performed with two loose clones (Garnacha Tinta 681 and 1154) differing in the number of nodes of the rachis (p<0.01). Comparisons G4 and T were performed between clones showing differences in the cluster compactness and in the total number of berries per cluster (compact: clones 0906 and 0126. loose: clones 1154 and 1041).
2015-08-31 | E-GEOD-67708 | biostudies-arrayexpress
Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison. Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three defoliated vines at pre-bloom (PB, JD 147,6 basal leaves and relative laterals removed from each shoot) and three defoliated vines at veraison (V, JD 211,6 basal leaves and relative laterals removed from each shoot) at beginning of veraison (BV), end of veraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.
2013-03-08 | E-GEOD-40487 | biostudies-arrayexpress
Project description:Grapevine cluster compactness is a multi-componential trait of agronomical interest; it greatly influences the vineyard management and the visual aspect of table grape. Clusters with greater compactness are more susceptible to disease. The compactness can be break down in a patchwork of agronomical traits, each having agronomical importance that includes parameters related to inflorescence and cluster architecture (cluster length and width, length of pedicels, etc.), fruitfulness (number of berries, number of seeds) and berry (size, shape, volume...). Through visual evaluation of a collection of 730 clones from the cultivar Tempranillo and 501 clones from Garnacha Tinta we identified and fully phenotyped distinct clones which transcriptomes were compared at key developmental stages in order to identify the genes playing a role in mechanisms involved in cluster compactness such as the ones determining number of berries, cluster length or berry size. Key genes involved in this process were identified. The findings lead us to hypothesize that berry size and/or number at ripening are greatly influenced by the rate of cell replication in flowers during the first stages after pollination.
2015-08-31 | GSE67708 | GEO
Project description:Among environmental factors, temperature is the one that poses serious threats to viticulture in the present and future scenarios of global climate change. In this work, we evaluated the effects on berry ripening of two thermal regimes, imposed from veraison to harvest. Potted vines were grown in two air-conditioned greenhouses with High Temperature (HT) and Low Temperature (LT) regimes characterized by 26 and 21°C as average and 42 and 35°C as maximum air daily temperature, respectively. We conducted analyses of the main berry compositional parameters, berry skin flavonoids and berry skin transcriptome on HT and LT berries sampled during ripening. The two thermal conditions strongly differentiated the berries. HT regime increased sugar accumulation at the beginning of ripening, but not at harvest, when HT treatment contributed to a slight total acidity reduction and pH increase. Conversely, growing temperatures greatly impacted on anthocyanin and flavonol concentrations, which resulted as strongly reduced, while no effects were found on skin tannins accumulation. Berry transcriptome was analyzed with several approaches in order to identify genes with different expression profile in berries ripened under HT or LT conditions. The analysis of whole transcriptome showed that the main differences emerging from this approach appeared to be more due to a shift in the ripening process, rather than to a strong rearrangement at transcriptional level, revealing that the LT temperature regime could delay berry ripening, at least in the early stages. Moreover, the results of the in-depth screening of genes differentially expressed in HT and LT did not highlight differences in the expression of transcripts involved in the biosynthesis of flavonoids (with the exception of PAL and STS) despite the enzymatic activities of PALs and UFGT being significantly higher in LT than HT. This suggests only a partial correlation between molecular and biochemical data in our conditions and the putative existence of post-transcriptional and post-translational mechanisms playing significant roles in the regulation of flavonoid metabolic pathways and in particular of anthocyanins.
2017-06-14 | GSE92864 | GEO
Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison.
2013-03-08 | GSE40487 | GEO