Plasticity of the ripening process among berry classes
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE49569 | GEO | 2013/08/07
SECONDARY ACCESSION(S): PRJNA214316
REPOSITORIES: GEO
Similar Datasets
Project description:Investigation of gene expression differences between three tissues of developmentally different berry classes before, at the onset of ripening, and at maturity The berry classes analyzed in these studies were at prevéraison stage, at midvéraison and 5 week postmidvéraison. A 63-array study on gene expression variability among developmentally berry classes (PV, GS, PS, RS, GSH, PSH, RSH) sampled at three developmental stages (prevéraison for PV, midvéraison for GS, PS, and RS and maturityfor GSH, PSH, and RSH ) in skin, seed, and pulp tissues. Each data point was performed in triplicate
2013-08-07 | E-GEOD-49569 | 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:Study of Frontenac and Marquette Grape berry ripening profile using Transcriptomics
2022-04-18 | GSE130055 | GEO
Project description:Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.
2018-09-21 | GSE98923 | GEO
Project description:Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.
2018-10-15 | GSE113224 | GEO
Project description:Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.
2018-10-15 | GSE113223 | GEO
Project description:This microarray experiment provides data which shows of the effects on gene expression from the artificial application of certain hormones on their own or in combination on ripening berries from the Adelaide Hills Various hormones have been implicated as having an effect on the grape berry ripening process. Their application prior to ripening may change the gene expression profile at veraison. The identification of the genes which are expressed at different levels due to the various hormone treatments may give insight to key gene expression changes in the ripening process. Keywords: Hormone treatment-Development
2018-11-22 | GSE7758 | 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: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:This SuperSeries is composed of the SubSeries listed below. The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.
2016-05-22 | GSE76000 | GEO