Unknown,Transcriptomics,Genomics,Proteomics

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Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening

ABSTRACT: 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.

ORGANISM(S): Vitis vinifera

SUBMITTER: Ana Fortes

PROVIDER: E-GEOD-28779 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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

Project description:In the production of seedless table grapes, it is conventional to use plant growth regulators including gibberellins. Little is known about the differences in aroma volatiles between seedless-treated grapes and nontreated (seeded) grapes. Therefore, in this study, the aroma volatile profiles of seedless-treated and nontreated ‘Shine Muscat’ grape berries during ripening were compared using gas chromatography-mass spectrometry. Measurements of volatiles during ripening showed 202 peaks in the seedless-treated and nontreated whole grape berries. According to two-way analysis of variance, the number of volatiles with differences between seedless-treated and nontreated berries and/or between ripening stages was 123, whereas those with no differences between treatments and between ripening stages was 79. Two-way hierarchical clustering analysis for the 123 volatiles showed that seedless-treated berries at the early ripening stages were separated from the other berries, and the seedless-treated and nontreated berries at the post-ripening stage were classified into the same cluster. At the early ripening stage, more lipoxygenase-pathway volatiles were produced in the seedless-treated berries than in the non-treated ones. Linalool compounds increased in both seedless-treated and nontreated berries with ripening. Gene expression profile comparisons using principal component analysis of RNA-sequencing data showed that the seedless-treated berries ripened earlier than the nontreated berries at the early ripening stage. The number of differentially expressed genes in the seedless-treated berries decreased during ripening. Using weighted gene co-expression network analyses, 12 modules and 24 modules were detected in berry skin and flesh, respectively. The correlation analysis revealed that 33 volatiles correlated with four modules in the skin and 50 volatiles correlated with nine modules in the flesh. Most of the volatiles correlated with these modules were those that showed significant differences between treatments and/or ripening stages by two-way analysis of variance. The differences in the aroma volatile profiles between seedless-treated and nontreated berries decreased as harvest was delayed, suggesting that delaying the harvest may make it possible to bring the aroma of seedless-treated ‘Shine Muscat’ berries closer to the original aroma of the seeded berries.

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 polyaminesM-BM-4 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 GrapeGenM-BM-. 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 M-bM-^@M-^\metabolismM-bM-^@M-^], M-bM-^@M-^\regulation overviewM-bM-^@M-^], M-bM-^@M-^\signalingM-bM-^@M-^], M-bM-^@M-^\cellular processM-bM-^@M-^], M-bM-^@M-^\transport overviewM-bM-^@M-^], M-bM-^@M-^\response to stimulus, stressM-bM-^@M-^], M-bM-^@M-^\diverse/miscellaneous functionsM-bM-^@M-^], M-bM-^@M-^\xenoprotein, transposable elementM-bM-^@M-^], M-bM-^@M-^\developmentM-bM-^@M-^] and M-bM-^@M-^\unknownM-bM-^@M-^]. 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 terpenesM-BM-4 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. 1 time point in 2010 season at EL 38. 3 biological replicates. 2 treatments

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.

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Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening

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