Gene expression associated with compatible viral diseases in berry
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE31660 | GEO | 2011/08/26
SECONDARY ACCESSION(S): PRJNA145409
REPOSITORIES: GEO
Similar Datasets
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: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: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.
2018-09-21 | GSE98923 | GEO
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.
2010-09-24 | GSE20511 | GEO
Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies. A total of 12 samples were analyzed representing three berry developmental stages (two after the onset of ripening, one during green growth). At each stage, heat stress was applied at day and night. Controls and treated berry samples were drawn in triplicates (two in duplicates) at day and at night on the microvine dwarf (Dwarf Rapid Cycling and Continous Flowering; DRCF) gibberellin-insensitive (GAI) mutant.
2014-01-08 | E-GEOD-53409 | 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: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:The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. The shift to the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of neighboring genes and global regulation based on codon preference. A total of 54 grapevine samples, covering most of the Grape organs at different stages, were collected. Three biological replicates were taken for each sample, resulting in a total of 162 observations. The collected plant organs were: bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berry, seed, rachis, anther, carpel, petal, pollen, and seedling.
2012-09-10 | E-GEOD-36128 | 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 °Brix. 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 °Brix. Results: There were approximatedly 18,000 transcripts whose abundance changed with °Brix 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 °Brix levels revealed that there were significantly higher abundances of transcripts changing with °Brix 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.
2014-11-01 | GSE55302 | GEO