Grape berry response to heatwaves in a climate change scenario: a physiological, transcriptional, and metabolic overview
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ABSTRACT:
PROVIDER: PRJNA851974 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19793100.fastq.gz | Fastqsanger.gz | |||
| SRR19793101.fastq.gz | Fastqsanger.gz | |||
| SRR19793102.fastq.gz | Fastqsanger.gz | |||
| SRR19793103.fastq.gz | Fastqsanger.gz | |||
| SRR19793104.fastq.gz | Fastqsanger.gz |
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Project description:Grapevines cv Sauvignon Blanc were subjected to different stress regimes by simulating the most common extreme weather events occurring within the current climate change scenario. During spring, just before bud break, the vines were either flooded or kept under normal conditions. Both vines were then split in two groups and put in differnt tunnels, either undergoing a simulated heatwave or not. Berry samples were collected from the four groups of plants (control, only flooded, only heatwave, flooded + heatwave) at different timepoints before, during and after the stress. Transcriptomic analyses were carried out on these samples along with some metabolomic assessments to characterize the response to stress in the different samples and the effect of the combined stresses.
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Project description:The vacuole occupies a large portion of plant cell volume, it is especially true to fruit tissues. Berry flesh cell vacuole serves as storage organelle for water, sugars, acids, secondary metabolites and others, which largely determining berry quality (Fontes et al., 2011a, b; Shiratake and Martinoia, 2007, Conde et al., 2006). However, the molecular basis of these compartmentation processes is still poorly understood. As in many species, the major bottle neck to study these aspects in grapevine is to obtain highly purified vacuoles with a good yield (Fontes et al., 2010). Up to date, several vacuole or tonoplast proteome researches were applied on a few plants mainly on Arabidopsis thaliana, vacuoles or tonoplast were derived from mesophyll cells (Carter et al., 2004, Endler et al., 2006, Schulze, et al., 2012) or cell culture (Jaquinod et al 2006, Shimaoka et al 2004), cauliflower buds (Schmidt et al., 2007) and sugar beet taproots (Jung et al., 2015). Though the grape berry protoplasts and intact vacuoles were successfully isolated from Cabernet Sauvignon berry suspension-cultured cells (Fontes et al., 2010), the vacuoles isolated from grape berry or different development and ripening stages of grape berry mesocarp tissues were not achieved.
2019-11-12 | PXD010556 | Pride
Project description:Wheat is one of the most significant crops in terms of human consumption in the world. In a climate change scenario, extreme weather event such as heatwaves will be more frequent especially during the grain-filling (GF) stage and could affect grain weight and quality of crops. Molecular mechanisms underlying the response to short heat stress (HS) have been widely reported for the hexaploid wheat (Triticum aestivum) but the regulatory heat stress mechanisms in tetraploid durum wheat (Triticum turgidum ssp. durum) remain partially understood. In this work, we performed a transcriptomic analysis of durum wheat grains to HS during early GF to identify key HS response genes and their predicted regulatory networks under glasshouse conditions.
2021-10-26 | GSE186472 | GEO
Project description:Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenarios.
| S-EPMC9788187 | biostudies-literature
Project description:We conducted transcript profiling and metabolome profiling induced by UV irradiation in grape berry skin. Transcriptome analysis was carried out with genome-wide microarray and two hundred thirty eight genes were more than 5-fold up-regulated by UV irradiation. The enrichment analysis showed GO terms including stilbene synthase (STS) gene. Moreover, the principal component analysis (PCA) of metabolome analysis showed a compound, identified resveratrol, accumulated in grape berry skin specifically. Our result clearly shows that UV irradiation induced only accumulation of resveratrol and its analogues but did not induce accumulation of the other phenolic compounds.
2014-12-01 | GSE59436 | 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 ‘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.
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Project description:To gain a comprehensive understanding of non-histone methylation during grape berry ripening. A 4D-label free quantitative proteomics approach was used to study the non-histone methylation of lysine during grape berry development and ripening. The ‘Kyoho’ grape berries at EL 31, EL 33, EL 35 and EL 37 were collected from six trees with equal vigor were selected in spring 2022 at the vineyard of the Henan University of Science and Technology, Luoyang, Henan, China (34.66° N, 112.37° E).
2024-05-31 | PXD042527 |
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:This microarray experiment provides data which shows of the effects on gene expression from the artificial application of certain hormones on their own or in combination on ripening berries from the Adelaide Hills Various hormones have been implicated as having an effect on the grape berry ripening process. Their application prior to ripening may change the gene expression profile at veraison. The identification of the genes which are expressed at different levels due to the various hormone treatments may give insight to key gene expression changes in the ripening process. Keywords: Hormone treatment-Development
2018-11-22 | GSE7758 | GEO