Comparative Physiological, Metabolomic, and Transcriptomic Analyses Reveal Developmental Stage-Dependent Effects of Cluster Bagging on Phenolic Metabolism in Cabernet Sauvignon Grape Berries
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ABSTRACT:
PROVIDER: PRJNA533137 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8916050.fastq.gz | Fastqsanger.gz | |||
| SRR8916060.fastq.gz | Fastqsanger.gz | |||
| SRR8916070.fastq.gz | Fastqsanger.gz | |||
| SRR8916080.fastq.gz | Fastqsanger.gz | |||
| SRR8916051.fastq.gz | Fastqsanger.gz |
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Project description:Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.
2019-11-25 | GSE129916 | GEO
Project description:To obtain an interpretation from the view of transcriptome on distinct metabolite accumulation between ecologically different regions in China, next-generation sequencing technology was performed on E-L 31, 35 and 38 stages of Cabernet Sauvignon grape berries from Changli (CL, eastern) and Gaotai (GT, western). The transcript abundance of epoxycarotenoid dioxygenase and xanthoxin dehydrogenase required for ABA biosynthesis was significantly higher in the GT berries at E-L 35 and 38 stages compared with the CL berries, which may explain the relatively short maturation period of berries in the western region. Some genes required for carbohydrate metabolism, such as hexose transporter, L-idonate dehydrogenase and phosphoenolpyruvate carboxylase, were significantly up-regulated in the CL berries in relative to the GT berries, which positively correlated with the sugar and organic acid accumulations. Pathway enrichment analysis of differentially expressed genes revealed that the CL berries had higher levels of phenylpropanoid biosynthesis at E-L 38 stage than the GT berries, which may relate to the quick fading of the GT wines because of weak co-pigmentation. cDNA libraries generated from three developmental stages (E-L 31, 35 and 38) of Cabernet Sauvignon grape berries from Changli (CL, eastern) and Gaotai (GT, western) in China were sequenced using Illumina HiSeq 2000.
2014-11-21 | E-GEOD-63512 | biostudies-arrayexpress
Project description:Primary and secondary metabolism in grape berries is under the control of complex interactions among environmental conditions, genotypes, and management practices. To obtain an interpretation from the view of transcriptome on distinct metabolite accumulation between ecologically different regions in China, next-generation sequencing technology was performed on E-L 31, 35, and 38 stages of Cabernet Sauvignon grape berries from Changli (CL, eastern) and Gaotai (GT, western). The transcript abundance of epoxycarotenoid dioxygenase and xanthoxin dehydrogenase required for ABA biosynthesis was significantly higher in the GT berries at E-L 35 and 38 stages compared with the CL berries, which may explain the relatively short maturation period of berries in the western region. Some genes required for carbohydrate metabolism, such as hexose transporter, L-idonate dehydrogenase, and phosphoenolpyruvate carboxylase, were significantly up-regulated in the CL berries in relation to the GT berries, which positively correlated with the sugar and organic acid accumulations. Pathway enrichment analysis of differentially expressed genes revealed that the CL berries had higher levels of phenylpropanoid biosynthesis at E-L 38 stage than the GT berries, which may relate to the quick fading of the GT wines because of weak co-pigmentation. This observation lays a foundation for further study concerning the molecular basis for environmental effects on berry quality formation.
2014-11-21 | GSE63512 | GEO
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
Project description:Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.
2020-09-02 | GSE157347 | GEO
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:Studying the effect of varying durations (1, 7 and 14 days) of locally applied heat stress on grape berries at three developmental stages (middle green, veraison and middle ripening). Among various environmental factors, temperature is a major regulator affecting plant growth, development and fruit composition. Reproductive development of grapevine and berry composition, are both highly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries tolerance to high temperatures (HS) are poorly understood. Although recent data addressed the consequences on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat stress. In the context of climate change, this work focused on microclimate effect is of particular interest to better understand the consequences of leaf removal (a common viticultural practice) on berry development. HS (+ 8°C) was locally applied to clusters from Cabernet Sauvignon fruiting cuttings at three different developmental stages (middle green, véraison and middle ripening). Samples were collected 1, 7 and 14 days after treatment and used for metabolic and transcriptomic analyses. The results showed dramatic and specific biochemical and transcriptomic changes in heat exposed berries, depending on the developmental stage and the stress duration. When applied at the herbaceous stage, HS delayed the onset of véraison. Heating also strongly altered the berry concentration of amino acids and organic acids (e.g. PHE, GABA, and malate) and decreased the anthocyanin content at maturity. These physiological alterations could be partly explained by the deep remodelling of transcriptome in heated berries. More than 7000 genes were deregulated in at least one of the nine experimental conditions. The most affected processes belong to the categories “stress responses”, “protein metabolism” and “secondary metabolisms”, highlighting the intrinsic capacity of grape berries to perceive heat stress and to build adaptive responses. Additionally, important changes in processes related to “transport”, “hormone” and “transcription” might contribute to the postponing of véraison. Finally, opposite effects depending on heating duration were observed for genes encoding enzymes of the general phenylpropanoid pathway, suggesting that the HS-induced decrease in anthocyanin content may result from a combination of transcript abundance and product degradation.
2017-03-08 | GSE86551 | GEO
Project description:We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster. Keywords: time course (berry development series)
2008-07-15 | GSE11406 | GEO
Project description:The experiment was conducted using grapevines of Cabernet Sauvignon grown in a field. At veraison, the clusters in the vines were sprayed with a 400 mgl-1(+)-abscisic acid (ABA) solution. The ABA treated berries and non-treated berries (control) were harvested at 14 and 28 days after veraison and peeled. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Kazuya Koyama. The equivalent experiment is VV16 at PLEXdb.
2011-08-27 | GSE31664 | GEO
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