Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Effect of solar ultraviolet radiation on grape berry skin transcriptome

ABSTRACT: UV radiation (UV) alters secondary metabolism in the skin of Vitis vinifera L. berries, which may affect on the final composition of both, grapes and wines. We compared berry skin transcriptome and phenolic composition between Tempranillo berries grown in the presence or absence of solar UV in a mid-altitude Tempranillo vineyard. By analysing two different ripening degrees, expression of 121 genes was significantly altered. Functional enrichment identified that, principally, secondary metabolism-related transcripts were induced by UV, including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes induction. Concurrently, flavonol accumulation was the most evident impact of UV on the berry skin phenolic composition. Monoterpenoid biosynthetic transcripts were also up-regulated by UV, whereas induction of stilbenoid biosynthetic transcripts and stilbenes accumulation was probably induced by the joint action of UV and other condition under the UV-blocking filter, likely higher temperature. Among regulatory genes, VvMYBF1, VvMYB24 and three bHLH transcription factors were up-regulated by UV. Homologs to Arabidopsis UVR8-dependent UV-B-induced genes were also induced, including VvHY5-1, VvHY5-2 and VvRUP UV-B signalling genes. This suggests that the UV-B-specific signalling pathway is activated in the skin of grapes grown at low-medium altitudes. The biosynthesis and accumulation of UV-absorbing compounds that are appreciated for winemaking were almost specifically triggered, which indicates that viticultural practices increasing solar UV incidence may improve grape features important to wine production. A total of 12 samples were hybridized. Grape skin RNA from berries ripening under a UV-transmitting filter (FUV+) and a UV-blocking filter (FUV-) was compared. Berry skin of two different ripening stages was analysed on each UV treatment. All samples were harvested simultaneously and a NaCl series was used to select the ripening degree in a non-invasive way. Three biological replicates were analyzed for each sample.

ORGANISM(S): Vitis vinifera

SUBMITTER: Pablo Carbonell-Bejerano

PROVIDER: E-GEOD-54636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses.

Carbonell-Bejerano Pablo P Diago Maria-Paz MP Martínez-Abaigar Javier J Martínez-Zapater José M JM Tardáguila Javier J Núñez-Olivera Encarnación E

BMC plant biology 20140709

<h4>Background</h4>Ultraviolet (UV) radiation modulates secondary metabolism in the skin of Vitis vinifera L. berries, which affects the final composition of both grapes and wines. The expression of several phenylpropanoid biosynthesis-related genes is regulated by UV radiation in grape berries. However, the complete portion of transcriptome and ripening processes influenced by solar UV radiation in grapes remains unknown.<h4>Results</h4>Whole genome arrays were used to identify the berry skin t ...[more]

PMID: 25012688

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Project description:Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes. Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries. Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales. A total of 54 samples were hybridized. Three different circadian time course series consisted on six time point each. Series corresponded to pericarp of Verdejo grapevine cultivar and berry flesh and skin in separate of Tempranillo cultivar. Three biological replicates were analyzed for each series.

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-3Â´-O-hydroxylase (F3Â´H), flavonoid-3Â´,5Â´-hydroxylase (F3Â´5Â´H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3Â´-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 F3Â´H, F3Â´5Â´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

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).

Project description:Among environmental factors, temperature is the one that poses serious threats to viticulture in the present and future scenarios of global climate change. In this work, we evaluated the effects on berry ripening of two thermal regimes, imposed from veraison to harvest. Potted vines were grown in two air-conditioned greenhouses with High Temperature (HT) and Low Temperature (LT) regimes characterized by 26 and 21°C as average and 42 and 35°C as maximum air daily temperature, respectively. We conducted analyses of the main berry compositional parameters, berry skin flavonoids and berry skin transcriptome on HT and LT berries sampled during ripening. The two thermal conditions strongly differentiated the berries. HT regime increased sugar accumulation at the beginning of ripening, but not at harvest, when HT treatment contributed to a slight total acidity reduction and pH increase. Conversely, growing temperatures greatly impacted on anthocyanin and flavonol concentrations, which resulted as strongly reduced, while no effects were found on skin tannins accumulation. Berry transcriptome was analyzed with several approaches in order to identify genes with different expression profile in berries ripened under HT or LT conditions. The analysis of whole transcriptome showed that the main differences emerging from this approach appeared to be more due to a shift in the ripening process, rather than to a strong rearrangement at transcriptional level, revealing that the LT temperature regime could delay berry ripening, at least in the early stages. Moreover, the results of the in-depth screening of genes differentially expressed in HT and LT did not highlight differences in the expression of transcripts involved in the biosynthesis of flavonoids (with the exception of PAL and STS) despite the enzymatic activities of PALs and UFGT being significantly higher in LT than HT. This suggests only a partial correlation between molecular and biochemical data in our conditions and the putative existence of post-transcriptional and post-translational mechanisms playing significant roles in the regulation of flavonoid metabolic pathways and in particular of anthocyanins.

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.

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.

Dataset Information

Effect of solar ultraviolet radiation on grape berry skin transcriptome

Publications

Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses.

Similar Datasets

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