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.
2018-09-21 | 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 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:The experiment was conducted using four 11-year-old potted grapevines of V. vinifera L. cv. Cabernet Sauvignon grafted on SO4 (Selection Oppenheim No. 4) grown in a phytotron. Vines were trained on a Guyot trellising system and each vine carried 4-10 clusters of grapes. The experiment started approximately 1 week before veraison, when berry softening started, and continued to fruit maturity. The two temperature regimes consisted of a high day (06.00–20.00 h) temperature (max.35C) and a control (max. 25C). Under both conditions, the night-time (20.00–06.00 h) temperature was 20C. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Kentaro Mori. The equivalent experiment is VV9 at PLEXdb
2011-08-26 | GSE31675 | GEO
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 transcriptome 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 from berry skins and DNase treated. 18 mRNA seq libraries were prepared, starting from total RNA (1 µg), using TruSeq RNA sample preparation kit (Illumina), according to manufacturers’ instructions. Libraries were quantified through qRT-PCR, as recommended by the protocol, and single-end sequenced for 100 bases on an Illumina Genome Analyzer (GAIIx).
2020-07-06 | E-MTAB-8758 | biostudies-arrayexpress
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:The experiment was conducted using four 11-year-old potted grapevines of V. vinifera L. cv. Cabernet Sauvignon grafted on SO4 (Selection Oppenheim No. 4) grown in a phytotron. Vines were trained on a Guyot trellising system and each vine carried 4-10 clusters of grapes. The experiment started approximately 1 week before veraison, when berry softening started, and continued to fruit maturity. The two temperature regimes consisted of a high day (06.00–20.00 h) temperature (max.35C) and a control (max. 25C). Under both conditions, the night-time (20.00–06.00 h) temperature was 20C. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Kentaro Mori. The equivalent experiment is VV9 at PLEXdb developmental stage: 2 weeks - temperature: High (2-replications); developmental stage: 2 weeks - temperature: Control(2-replications); developmental stage: 4 weeks - temperature: High (2-replications); developmental stage: 4 weeks - temperature: Control(2-replications); developmental stage: 6 weeks - temperature: High (2-replications); developmental stage: 6 weeks - temperature: Control(2-replications)
2011-08-25 | E-GEOD-31675 | 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.
2010-09-24 | GSE20511 | GEO