Transcripts and metabolites of grape ripening and aroma development
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE35172 | GEO | 2012/10/30
SECONDARY ACCESSION(S): PRJNA150807
REPOSITORIES: GEO
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Project description:Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening in berries as well as how aroma is developed are aspects not fully understood. In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, AragonM-CM-*s, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and to mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set: primary metabolism, M-bM-^@M-^\secondary metabolismM-bM-^@M-^], cellular metabolismM-bM-^@M-^], developmentM-bM-^@M-^], M-bM-^@M-^\cellular processM-bM-^@M-^], M-bM-^@M-^\diverse functionsM-bM-^@M-^], M-bM-^@M-^\regulation overviewM-bM-^@M-^], response to stimulus, stressM-bM-^@M-^], M-bM-^@M-^\signalingM-bM-^@M-^], M-bM-^@M-^\transport overviewM-bM-^@M-^], and M-bM-^@M-^\xenoprotein, transposable elementM-bM-^@M-^] besides 32.24% genes of M-bM-^@M-^\unknownM-bM-^@M-^] function. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/ MS and headspace GC-EI-MS platforms. Molecular and metabolic markers of grape ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at the transcriptional level. 2 time points in 2008 season. 3 biological replicates. 3 cultivars
2012-10-30 | E-GEOD-35172 | biostudies-arrayexpress
Project description:Background Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variantion. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses. Results Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through veraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5862 unigenes indicates the activation of common pathways in between years despite the irregular development of Trincadeira grapes. These unigenes were assigned in the functional categories of “metabolism, development”, “cellular process”, “diverse functions”, “regulation overview”, “response to stimulus, stress”, “signaling”, “transport overview”, “xenoprotein, transposable element” and “unknown”. Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism in grape ripening. This information was integrated with transcriptional profiling obtained using genome array and qRT-PCR for five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Conclusions Altogether the results provide new information regarding the network of events leading to grape ripening as well as highlight features that may be cultivar specific namely in what concerns the role of carbohydrates and growth regulators´ metabolism as well as epigenetic factors and signaling pathways. 4 time points in 2007 season. 3 time points in 2008 season. 3 biological replicates.
2011-09-29 | E-GEOD-28779 | biostudies-arrayexpress
Project description:Background Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variantion. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses. Results Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through veraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5862 unigenes indicates the activation of common pathways in between years despite the irregular development of Trincadeira grapes. These unigenes were assigned in the functional categories of “metabolism, development”, “cellular process”, “diverse functions”, “regulation overview”, “response to stimulus, stress”, “signaling”, “transport overview”, “xenoprotein, transposable element” and “unknown”. Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism in grape ripening. This information was integrated with transcriptional profiling obtained using genome array and qRT-PCR for five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Conclusions Altogether the results provide new information regarding the network of events leading to grape ripening as well as highlight features that may be cultivar specific namely in what concerns the role of carbohydrates and growth regulators´ metabolism as well as epigenetic factors and signaling pathways.
2011-09-30 | GSE28779 | GEO
Project description:Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to ripening of nonclimacteric fruits is not fully understood. In particular the role of polyamines´ catabolism has been little explored. Ripening of Trincadeira grapes submitted to mock and guazatine treatments, a potent inhibitor of polyamine oxidase activity, was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of one time point (EL 38) corresponding to harvest stage was compared between mock and guazatine treatments using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18711 unique sequences. A total of 2113 probesets (1877 unigenes) were significantly differentially expressed (1.5 fold) between these samples. These unigenes were assigned to the functional categories of “metabolism”, “regulation overview”, “signaling”, “cellular process”, “transport overview”, “response to stimulus, stress”, “diverse/miscellaneous functions”, “xenoprotein, transposable element”, “development” and “unknown”. Quantitative RT-PCR validated microarrays results being carried out for seven selected genes and three developmental stages (EL 35, EL 36 and EL 38). Functional enrichment analysis revealed that genes involved in amino acid, carbohydrate and water transport were more up-regulated in mock treated samples which may suggest that the strong dehydrated phenotype obtained in guazatine treated samples may be due to impaired transport mechanisms. In addition, genes involved in terpenes´ metabolism were differentially expressed between guazatine and mock treated samples. Altogether, the results support an important role of polyamine catabolism in normal grape ripening namely in aroma development and cell expansion.
2013-09-30 | GSE44823 | GEO
Project description:Blanc Du bois grapes are gaining popularity in the South eastern US due to its distinctive flavor and disease tolerance characteristics. Berry composition at harvest is a major contributing factor of wine quality. Blanc Du bois grapes are harvested from EL-38 and EL-39 stages depending on the style of wine desired or harvested early to avoid rain nearing harvest. In the current study, gel-free proteome analysis was applied to investigate changes in enzymes, primary and secondary metabolism proteins during ripening and late ripe stage. Grape berries from EL-33, EL-34, EL-36, EL-38 and EL-39 were collected based on brix, acidity and density. Protein extracts from different berry stages were resolved by electrophoresis. Proteins were extracted from the gel as a single band, detained and subjected to proteolysis with sequencing grade trypsin. Trypsin digested peptides from different berry protein extracts were separated on a nano LC and the eluent was sprayed onto to a LTQ Orbitrap Velos mass spectrometer. The raw files were analyzed using Proteome Discoverer with Sequest and Mascot search nodes using Vitis species FASTA database (70,263 entries) and the data were further validated by Scaffold software. A total of 1091, 1131, 1078, 1042 and 1066 proteins were detected in EL-33, EL-34, EL-36, EL-38 and EL-39 of berries respectively. Statistical ANOVA analysis revealed 927 proteins present across the stages that are involved in various biochemical and metabolic pathways. Seventeen proteins including dihydroflavonol reductase, sucrose phosphate synthase, PR proteins increased more than three-fold between ripe and late ripe berry stages. Other proteins that increased during ripe and late ripe stage berries were alcohol dehydrogenase 1, anthocyanidin reductase, phospho-2-dehydro-3-deoxyheptonate aldolase, fatty acid hydroperoxide lyase, cinnamyl alcohol dehydrogenase, -isopiperitenol (-)-carveol and SAM-methyltransferases.
2018-04-09 | PXD004157 | Pride
Project description:Vitis vinifera berries are sensitive towards infection by the necrothopic pathogen Botrytis cinerea leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with the infection has not been previously performed in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, pepper- corn size fruits (EL 29) were infected in-field and green berries (EL 33) and veraison berries (EL 35) were collected for microarray analysis complemented with metabolic profiling using GC-EI-TOF/MS and headspace GC-EI-MS platforms. The results provide evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defense such as trans-resveratrol and gallic acid. The response is mainly activated in green berries with the putative involvement of jasmonic acid, ethylene, polyamines and auxins whereas salicylic acid does not seem to be involved. At veraison, however, genes encoding protein kinases, MYB and WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase and phenylalanine ammonia-lyase are no longer up-regulated or even down-regulated suggesting that the basal defense response is not active with the onset of ripening. This non-sustained defense response has not been previously reported for necrotrophic, biotrophic, or hemibiotrophic pathogens, and highlights the importance of conducting studies in fruits and not solely in vegetative tissues. Furthermore, this study provided with metabolic biomarkers of infection namely azelaic acid, arabitol and gluconic acid that can be used to monitor infection early in the vineyard. 2 time points in 2011 season at EL 33 and EL 35. 3 biological replicates. Grapes Infected with Botrytis cinerea and control with phosphate buffer
2014-03-31 | E-GEOD-52586 | biostudies-arrayexpress
Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.
2015-10-12 | E-GEOD-67932 | biostudies-arrayexpress
Project description:Grape berries undergo considerable physical and biochemical changes during the ripening process. Ripening is characterized by a number of changes, including the degradation of chlorophyll, an increase in berry deformability, a rapid increase in the level of hexoses in the berry vacuole, an increase in berry volume, the catabolism of organic acids, the development of skin colour, and the formation of compounds that influence flavour, aroma, and therefore, wine quality. The aim of this work is to identify differentially expressed genes during grape ripening by microarray and real-time PCR techniques. Using a custom array of new generation, we analysed the expression of 6000 grape genes from pre-veraison to full maturity, in Vitis vinifera cultivar Muscat of Hamburg, in two different years (2006 and 2007). Five time points per year and two biological replicates per stadium were considered. To reduced intra-plant and inter-plant biological variability, for each ripening stadium we collected around hundred berries from several bunch grapes of five plants of V. vinifera cv Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.Muscat of Hamburg. We will use the real-time PCR technique to validate microarray data.
2010-11-09 | E-MEXP-2451 | biostudies-arrayexpress
Project description: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.
2014-09-09 | E-GEOD-54636 | biostudies-arrayexpress
Project description:Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma.
2015-10-12 | GSE67932 | GEO