E-GEOD-97960
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-97960 | ExpressionAtlas | 2020-04-03
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-97960-analysis-methods.tsv | Tabular | |||
| E-GEOD-97960-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-97960-coexpressions.tsv.gz | Tabular | |||
| E-GEOD-97960-configuration.xml | Xml | |||
| E-GEOD-97960-factors.xml | Xml |
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2015-11-19 | E-GEOD-62744 | ExpressionAtlas
Project description:Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. Results: Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during one growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries. Conclusions: Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems.
2013-04-11 | GSE41633 | GEO
Project description:Transcriptome investigations supports the role of rootstock-scion interaction in grapevine berry quality
2020-07-20 | E-MTAB-8758 | ExpressionAtlas
Project description:Changes in the performance of genotypes in different environments are defined as genotype 3 environment (G3E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G3E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G3E-related. The G3E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G3E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.
2018-04-09 | GSE97578 | GEO
Project description:Changes in the performance of genotypes in different environments are defined as genotype 3 environment (G3E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G3E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G3E-related. The G3E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G3E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.
2018-04-09 | GSE97960 | GEO
Project description:This study aimed at investigating the effect in Grapevine of two different rootstocks (1103 Paulsen - P - and Mgt 101-14 - M) in comparison with not grafted plants - F - on the transcriptome of berry skin in Pinot noir (clone Entav 115), to explore the influence of rootstock-scion interaction on grape quality. 7-year old grapevine plants were grown in 70-liters, in an open field arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized and were abundantly irrigated. Berry samples (15 per plant, 3 plants per replicate), were collected at two different developmental stage: veraison (1) and maturation (2), and dissected to separate skin tissues. Total RNA was extracted from berry skins and DNase treated. 18 mRNA seq libraries were prepared, starting from total RNA (1 µg), using TruSeq RNA sample preparation kit (Illumina), according to manufacturers’ instructions. Libraries were quantified through qRT-PCR, as recommended by the protocol, and single-end sequenced for 100 bases on an Illumina Genome Analyzer (GAIIx).
2020-07-06 | E-MTAB-8758 | biostudies-arrayexpress
Project description:Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. Results: Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during one growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries. Conclusions: Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems. Vitis vinifera cultivar Corvina clone 48 berries were harvested from different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions. Berries were harvested at three different developmental stages: véraison, mid-ripening and harvest; each sample was collected in three biological replicates, to cover the whole vineyard variability. The same sampling procedure had been repeated over three consecutive vintages (2006, 2007 and 2008).
2013-04-11 | E-GEOD-41633 | biostudies-arrayexpress
Project description:This study aimed at investigating the effect in Grapevine of two different rootstocks (1103 Paulsen - P - and Mgt 101-14 - M) in comparison with not grafted plants - F - on the miRNome of berry skin in Pinot noir (clone Entav 115), to explore the influence of rootstock-scion interaction on grape quality. 7-year old grapevine plants were grown in 70-liters, in an open field arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized and were abundantly irrigated. Berry samples (15 per plant, 3 plants per replicate), were collected at two different developmental stage: veraison (1) and maturation (2), and dissected to separate skin tissues. Total RNA was extracted and DNase treated, small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina®), following all manufacturers' instructions. Eighteen bar-coded small RNA libraries were constructed starting from 1 µg of total RNAs.
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