Vitis vinifera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA382369 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G3E) on the berry transcriptome [RNA-seq]
2020-04-03 | E-GEOD-97960 | ExpressionAtlas
Project description:Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G3E) on the berry transcriptome [RNA-seq]
| PRJNA383486 | ENA
Project description:The plasticity of the grapevine berry transcriptome
| PRJNA177819 | ENA
Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies. A total of 12 samples were analyzed representing three berry developmental stages (two after the onset of ripening, one during green growth). At each stage, heat stress was applied at day and night. Controls and treated berry samples were drawn in triplicates (two in duplicates) at day and at night on the microvine dwarf (Dwarf Rapid Cycling and Continous Flowering; DRCF) gibberellin-insensitive (GAI) mutant.
2014-01-08 | E-GEOD-53409 | biostudies-arrayexpress
Project description:Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.
2021-08-27 | GSE164586 | GEO
Project description:Grapevine cluster compactness is a multi-componential trait of agronomical interest; it greatly influences the vineyard management and the visual aspect of table grape. Clusters with greater compactness are more susceptible to disease. The compactness can be break down in a patchwork of agronomical traits, each having agronomical importance that includes parameters related to inflorescence and cluster architecture (cluster length and width, length of pedicels, etc.), fruitfulness (number of berries, number of seeds) and berry (size, shape, volume...). Through visual evaluation of a collection of 730 clones from the cultivar Tempranillo and 501 clones from Garnacha Tinta we identified and fully phenotyped distinct clones which transcriptomes were compared at key developmental stages in order to identify the genes playing a role in mechanisms involved in cluster compactness such as the ones determining number of berries, cluster length or berry size. Key genes involved in this process were identified. The findings lead us to hypothesize that berry size and/or number at ripening are greatly influenced by the rate of cell replication in flowers during the first stages after pollination.
2015-08-31 | GSE67708 | GEO
Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies.
2014-01-08 | GSE53409 | GEO
Project description:Transcriptomic study of biological networks involving grapevine berry development
| PRJNA309765 | ENA
Project description:A dissection of Genotype x Environment interactions in grapevine berry using a multi-layered -omics approach Grapevine, the most widely-cultivated perennial fruit crop, is also considered a very environmentally sensitive crop. It is characterized by remarkable phenotypic plasticity which in turn is believed to effectively buffer environmental extremes especially through transcriptomic and epigenomic reprogramming. Thus, the final phenotype (P) of a given vine is the result of the close interaction between its genetic composition (G) and the environment (E). Here we analyzed Genotype x Environment (GxE) interactions in two grapevine varieties by characterizing their transcriptome plasticity when cultivated in different environments. Specifically, two genotypes (Sangiovese and Cabernet Sauvignon) were cultivated in three different locations in Italy (Bolgheri -littoral Tuscany-, Montalcino – Appennine Tuscany- and Romagna -foothill area-), trained in an almost identical manner, and sampled at four developmental stages over two grapevine growing seasons, 2011 and 2012, for a total of 144 samples that were analyzed by hybridization to a whole-genome microarray and by Reduced Representation Bisulfite Sequencing (RRBS-seq). In order to study the relationships among differential gene expression profiles and environmental cues, we have developed a new statistical data mining tool based on data reduction approaches which allowed a dissection of the transcriptomic data into stage-specific, cultivar-related and GxE important clusters of gene expression. This deep inspection of inner relationships between the different dataset variables allowed the identification of several candidate genes that could represent putative markers of berry quality traits in grapevine GxE interactions. Moreover, the methods used to establish our model provide a framework for the analysis of transcriptome plasticity in other crops as they respond to diverse environments.
2018-04-09 | GSE98762 | GEO
Project description:Grapevine leaf and berry mycobiome
| PRJNA851958 | ENA