Expression profiling in grapevine berry during development and withering processes
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ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE20511 | GEO | 2010/09/24
SECONDARY ACCESSION(S): PRJNA125229
REPOSITORIES: GEO
Similar Datasets
Project description:Grapevine is a commercially important fruit crop that provides berries for direct consumption, juice pressing, drying (raisins), and fermentation to produce wine. The economic value of the crop has encouraged many researchers to study the physiological and molecular basis of berry development, particularly processes that affect wine quality. Post-harvest withering of grapevine berries is used in the production of dessert and fortified wines to alter must quality characteristics and to increase the concentration of simple sugars. Vitis vinifera cv Corvina berries were sampled during the 2006 growing season at four developmental time points and three additional time points during the 91-day post-harvest withering process. The four developmental time points were 59, 71, 98 and 112 days after fruit set, corresponding to pre-veraison, veraison, early ripening and late ripening, and the three withering time points (WI, WII and WIII) were 35, 56 and 91 days after harvest. Three biological replicates were taken at each time point resulting in a total of 21 samples.
2010-09-24 | E-GEOD-20511 | biostudies-arrayexpress
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.
2011-11-08 | E-MTAB-481 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar M-bM-^@M-^XSummer BlackM-bM-^@M-^Y and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.
2013-10-05 | E-GEOD-24531 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar ‘Summer Black’ and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed.
2013-10-05 | GSE24531 | GEO
Project description:Purpose: Microarray technologies provide a unique opportunity to deeply investigate the molecular mechanisms involved in plant-pathogen interaction. Botrytis cinerea, is the agent of grapevine grey mould, but in yet uncharacterized environmental conditions, a latent infection can occur determining favourable metabolic and physico-chemical berry modifications which possibly contribute to the typical aromas of “passito” wines (“noble rot”). The present project aims at the identification of the grapevine responses to B. cinerea during fungal colonization in the latent form, in comparison with control berries. Methods: A total of 150 untreated berries were sampled as time 0 of the experiment. Moreover, 300 healthy berries have been artificially inoculated one by one with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing an early stage (T1) and a late stage (T2) of noble rot pourri plein. Control samples (300 berries) have been inoculated with water and sampled at the same time of infected berries. The microarray experiments on T0 and healthy or infected samples in biological triplicate resulted in 15 samples to be analyzed (Agilent-048771 4x44K Grape all custom microarray chip; Agilent Technologies, Santa Clara, CA, USA). Conclusions: This work identified important molecular mechanisms involved in Botrytis cinerea colonization of grapevine berries during the noble rot infection.
2019-07-26 | GSE116740 | GEO
Project description:The postharvest dehydration of grape berries allows theaccumulation of sugars and other solutesand promotes the synthesis of aroma compounds unique to high-quality raisin wines such as thepassito wines made in Italy. These dynamic changes are dependent on environmental parameters such as temperature and relative humidity,as well asendogenous factors such as berry morphology and genotype, but the contribution of each variable isnot well understood.Here wecompared berries subjected to natural or accelerated dehydration, the latterdriven by forced airflow.We followed the evolution of transcript andmetaboliteprofiles and found that accelerated dehydration clearly dampened the natural transcriptomic and metabolomic programs of postharvest berries. We found that slow dehydration over a prolonged duration isnecessary to inducegene expression and metabolite accumulation associated with the final quality traits of dehydrated berries. The accumulation of key metabolites (particularly stilbenoids)during postharvest dehydration isinhibited by rapid dehydration conditions that shorten the berry life time.
2020-09-10 | GSE138021 | GEO
Project description:Grapevine (Vitis vinifera L) is considered one of the most environmentally sensitive crops and is characterized by broad phenotypic plasticity, offering important advantages such as the large range of different wines that can be produced from the same cultivar, and the adaptation of existing cultivars to diverse growing regions. The uniqueness of berry quality traits reflects complex interactions between the grapevine plant and the combination of natural factors and human cultural practices, defined as terroir, which leads to the expression of wine typicity. Despite the scientific and commercial importance of genotype interactions with growing conditions, few studies have characterized the genes and metabolites directly involved in this phenomenon. Here we used two large-scale analytical approaches to explore the metabolomic and transcriptomic basis of the broad phenotypic plasticity of Garganega, a white berry variety grown at four sites characterized by different pedoclimatic conditions (altitudes, soil texture and composition). These conditions determine berry ripening dynamics in terms of sugar accumulation and the abundance of phenolic compounds. Multivariate analysis unraveled a highly plastic metabolomic response to different environments, especially the accumulation of hydroxycinnamic and hydroxybenzoic acids and flavonols. Principal component analysis revealed that the four sites strongly affected the berry transcriptome allowing the identification of environmentally-modulated genes and the plasticity of commonly-modulated transcripts at different sites. Many genes that control transcription, translation, transport and carbohydrate metabolism showed different expression depending on the environmental conditions, indicating a key role in the observed transcriptomic plasticity of Garganega berries. Interestingly, genes representing the phenylpropanoid/flavonoid pathway showed plastic responses to the environment mirroring the accumulation of the corresponding metabolites. The comparison of Garganega and Corvina berries showed that the metabolism of phenolic compounds is more plastic in ripening Garganega berries under different pedoclimatic conditions.
2016-07-13 | GSE75565 | GEO
Project description:Global gene expression analysis of grapevine cv. Pinot Noir berries during development and ripening. Time-course comparison of samples collected at three developmental stages (stages 33, 34 and 36 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) during three seasons (2003, 2005 and 2006).
2008-01-16 | E-MEXP-1282 | 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:itis vinifera cv. Tannat is largely cultivated in Uruguay for the production of high quality red wines. Its most notable characteristic is an elevated content of polyphenolic compounds, which provide an intense purple color and remarkable antioxidant properties to the wine. To characterize the genetic components encoding this important phenotypic characteristic, the genome of the Uruguayan Tannat clone UY11 was sequenced to 134X coverage using the Illumina technology and assembled with a mixed approach of de novo assembly and iterative mapping on the PN40024 reference genome. An approach based on both reference-guided annotation and de novo transcript assembly of RNA-Seq data allowed the definition of 3,673 genes not previously annotated in PN40024 that we consider novel, and the discovery of 2,228 genes not shared with the grapevine reference genome that we consider private to Tannat. Expression analysis showed that private genes contributed substantially (more than 50%) to the overall expression of enzymes involved in phenol and polyphenol biosynthesis indicating that the dispensable portion of the grapevine genome contains many private genes which are likely to contribute to the peculiar phenotypic characteristics of this grapevine variety.
2014-01-09 | E-MTAB-4278 | biostudies-arrayexpress