Gene expression analysis in grape berries at veraison (SIB_06)
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE7752 | GEO | 2018/11/22
REPOSITORIES: GEO
Similar Datasets
Project description:A bunch of grapes at veraison is comprised of berries at different stages of development ranging from hard green to soft ripe red. Veraison represents an important transition stage in the ripening process where key genes may be switched on or off. Single berries at various stages of development from hard green to ripe red were collected at a single time point from a single bunch of grapes going through veraison. Gene expression patterns were obtained from single berries representing different developmental stages. Keywords: Developmental series
2018-11-22 | GSE7394 | 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. Experiment Overall Design: Individual grape berries were selected at 4 developmental stages along ripening initiation for RNA extraction and hybridization to Affymetrix Vitis Genome GeneChips. One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS). Individual berries representing each stage were collected from either the distal or the proximal position of one cluster one each of two plants used for experiments.
2008-10-20 | E-GEOD-11406 | biostudies-arrayexpress
Project description:Blueberry is one of the most desirable and nutritious fruits. During fruit development, the blueberry’s organoleptic properties and phytonutrient composition are ever-changing [1]. Blueberry fruit development is typically described in five phases: pads, cups, green, pink, and blue (ripe) [2]. The former two phases are referred to as the initial “expansion”. During expansion, young fruit is generally hard, dark green and distinguishable by size [3]. The latter three phases are referred to as maturation. Green fruit are hard and fully rounded green berries; pink berries are partially pigmented; blue (ripe) berries are fully colored and soft. Fruit maturation has attracted considerable research attention, and typically, the characteristics fruit softening, coloring, and sweetening are assessed [4].
2019-05-13 | PXD011815 | Pride
Project description:The role of photosynthesis in fruits still challenges scientists. This is especially true in the case of mature grape berries of red varieties lined by an anthocyanin-enriched exocarp (skin) almost impermeable to gases. Although chlorophylls are degraded and replaced by carotenoids in several fruits, available evidence suggests that they may persist in red grapes at maturity. In the present study, chloroplasts were isolated from the skin of red grape berries (cv. Vinhão) to measure chlorophyll levels and the organelle proteome. The results showed that chloroplasts (and chlorophylls) are maintained in ripe berries masked by anthocyanin accumulation and that the proteome of chloroplasts from green and mature berries is distinct. Several proteins of the light reactions significantly accumulated in chloroplasts at the mature stage, including those of light-harvesting complexes of photosystems I (PSI) and II (PSII), redox chain, and ATP synthase, while chloroplasts at the green stage accumulated more proteins involved in the Calvin cycle and the biosynthesis of amino acids, including precursors of secondary metabolism. Taken together, results suggest that although chloroplasts are more involved in biosynthetic reactions in green berries, at the mature stage, they may provide ATP for energy-demanding processes such as anthocyanin biosynthesis or even O2 to feed the respiratory demand of inner tissues.
2022-10-25 | PXD037346 | 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:Berries were sample at three developmental stages (green, veraison and ripe) and flash frozen in the field in liquid nitrogen. The frozen tissue was subsequently ground in liquid nitrogen and stored at 80°C. At least three independent berry samples were collected (with n≥50 berries per sample) at three time points: at pre-véraison/green stage (Eichhorn-Lorenz (E-L) system stage 31), at véraison (E-L stage 34) and at ripe/harvest stage (E-L stage 38)
2012-12-31 | GSE34634 | GEO
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:The experiment was aimed at describing similarities and differences between grapevine flesh and skin ripening at the transcriptome level. Transcriptional profiles throughout flesh and skin ripening were followed in three biological replicas during two consecutive growing seasons in a table grape cultivar ‘Muscat Hamburg’. Berries were weekly picked off bunches (one bunch per vine from each selected vine) from june to august. For each sampling, berries were classified in five ripening stages based on monitoring developmental stages instead of a simple chronological sampling. They corresponded to pre-véraison (P), 50% véraison (V1), 100% véraison (V2), ripe 1 (R1), and ripe 2 R2). P samples were harvested as green, hard berries of at least 15 mm in size, according to touch-assessed hardiness. Véraison berries with half or full coloured skin surface corresponded to V1 and V2 samples. After véraison, ripening berries were classified according to their floatability in solutions with different NaCl densities, as an indication of the internal sugar concentration. At this stage berries were sampled with densities between 110-130 g NaCl/L for R1 and between 130-150 g NaCl/L for R2, which corresponded to commercially ripen table grape berries. On each of the five samples, frozen berries were dissected and RNA from flesh and skin was obtained and processed for Grapegen Genechip microarray hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Pablo Carbonell-Bejerano. The equivalent experiment is VV33 at PLEXdb.]
2012-09-27 | GSE41206 | GEO
Project description:Berries were sample at three developmental stages (green, veraison and ripe) and flash frozen in the field in liquid nitrogen. The frozen tissue was subsequently ground in liquid nitrogen and stored at 80°C. At least three independent berry samples were collected (with n≥50 berries per sample) at three time points: at pre-véraison/green stage (Eichhorn-Lorenz (E-L) system stage 31), at véraison (E-L stage 34) and at ripe/harvest stage (E-L stage 38) Ground tissues for each developmental stage were pooled. Replicates: Separate RNA extractions were performed on aliquots of the ground tissue from each developmental stage, labeled and hybiridized to the microarrays
2012-12-31 | E-GEOD-34634 | 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