Transcriptomic study of biological networks involving grapevine berry development
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE77218 | GEO | 2016/01/27
SECONDARY ACCESSION(S): PRJNA309765
REPOSITORIES: GEO
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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
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2023-05-31 | GSE205428 | 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: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:To investigate global genome expression changes during fruit developmemt, We then performed genome-wide expression analyses on the fruit peel at 120 and 150 DAF with RNA-seq approach.A total of 865 genes were identified as differentially expressed, among which 494 genes were up-regulated and 371 genes were down-regulated in the fruits harvested at 150 DAF compared with in those harvested at 120 DAF.In general, data obtained from RNA-seq showed that the genes involved in photosynthesis and tetrapyrrole synthesis were significantly repressed at 150 DAF; in contrast, the genes involved in secondary metabolism including the biosynthesis of wax, terpenoids and phenylpropanoid were significantly induced at 150 DAF. Total four sample pools (two independent biological replicates of fruits peel from 120 DAF and 150 DAF)
2016-05-13 | E-GEOD-68865 | 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 | 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: Not available
| S-EPMC3706941 | biostudies-literature
Project description:To investigate global genome expression changes during fruit developmemt, We then performed genome-wide expression analyses on the fruit peel at 120 and 150 DAF with RNA-seq approach.A total of 865 genes were identified as differentially expressed, among which 494 genes were up-regulated and 371 genes were down-regulated in the fruits harvested at 150 DAF compared with in those harvested at 120 DAF.In general, data obtained from RNA-seq showed that the genes involved in photosynthesis and tetrapyrrole synthesis were significantly repressed at 150 DAF; in contrast, the genes involved in secondary metabolism including the biosynthesis of wax, terpenoids and phenylpropanoid were significantly induced at 150 DAF.
2016-05-13 | GSE68865 | GEO
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar ‘Summer Black’ and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed.
2013-10-05 | GSE24531 | GEO