Cluster thinning effect on Cabernet Sauvignon berry ripening
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA412324 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6080250.fastq.gz | Fastqsanger.gz | |||
| SRR6080260.fastq.gz | Fastqsanger.gz | |||
| SRR6080270.fastq.gz | Fastqsanger.gz | |||
| SRR6080280.fastq.gz | Fastqsanger.gz | |||
| SRR6080290.fastq.gz | Fastqsanger.gz |
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Project description:The impact of yield on fruit and wine quality has been studied extensively; vine response to increased yield is well known, but responsible mechanisms – including the regulation of pathways responsible for color, aroma and mouthfeel – have not been characterized at the level of genetic regulation. To examine the impact of crop load on transcriptomic and metabolomic changes during grape berry maturation vines from two cluster thinning treatments (50% or 75% of clusters removed following fruit set) were compared to control vines (no cluster thinning). Treatments were applied to mature Cabernet Sauvignon grapevines over three consecutive vintages. Agronomic parameters, including yield per vine and the yield to pruning weight ratio, as well as fruit and wine composition, were determined at harvest. Fruit transcriptomic and metabolomic changes were measured in berry samples collected from each treatment at 7 to 10 day intervals from fruit set to harvest. The patterns of berry development by weight, sugar accumulation, and malic acid degradation indicated that vines responded differentially to crop load reduction by accelerating berry maturation progress. RNA-Seq analysis, and untargeted GC-MS and UHPLC-QTOF-MS -based metabolomic approaches were used. The indication of the acceleration of maturation transcriptional programs and of metabolite accumulation in the treated vines was suggested by multivariate analyses. To identify the transcriptional key triggers of this response we applied a two-regression step statistical approach which identified genes modulated over development dependent on the crop load. Comparing vintages we were able to estimate the environmental influence on the crop load treatments among years. The application of this multifaceted approach allowed the construction of robust models describing the impact of crop load on the genetic regulation of grape maturation.
2023-04-28 | GSE104316 | GEO
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: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
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:Background: The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety ‘Norton’, with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways. Results: A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3´-O-hydroxylase (F3´H), flavonoid-3´,5´-hydroxylase (F3´5´H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3´-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin. Conclusions: This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3´H, F3´5´H, LDOX, UFGT, ANR LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles of Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties.
2010-10-08 | GSE24561 | GEO
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.
2011-08-26 | GSE31660 | GEO
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: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:Background: The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety âNortonâ, with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways. Results: A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3´-O-hydroxylase (F3´H), flavonoid-3´,5´-hydroxylase (F3´5´H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3´-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin. Conclusions: This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3´H, F3´5´H, LDOX, UFGT, ANR LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles of Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties. At each of six developmental stages, three biological replicates of berry samples were collected, each consists of ten randomly selected vines, a total of 18 samples were proccessed for analysis
2010-10-08 | E-GEOD-24561 | biostudies-arrayexpress
Project description:The goal of this project aims to decipher the molecular effects of high temperature on developing Cabernet Sauvignon berries. Using grapevine fruiting cuttings, control and heat-treated berries were sampled to conduct transcriptomic, proteomic and metabolomic analysis.
2020-01-29 | PXD014693 | Pride