GEO DataSets

(Submitter supplied) Grapevine (Vitis spp., family Vitaceae) is characterized by a marked phenotypic plasticity and its ability to withstand various environmental conditions depends on the activation of highly coordinated responses, resulting from the interaction among genotypes (G) and environmental factors (E). Understanding genotype by environment (GxE) interplays is highly complex and challenging, and often the outcome of the genetic responses to field performance is not straightforward also due to the difficulties to reach a precise definition of the E component in field studies. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

18 Samples

Download data: FASTA, TXT

(Submitter supplied) Anthocyanins, total phenols, soluble sugar and fruit shape play a significant role in determining the distinct fruit quality and customer preference. However, for the majority of fruit species, little is known about the transcriptomics and underlying regulatory networks that control the generation of overall quality during fruit growth and ripening. This study incorporated the quality-related transcriptome data from 6 ecological zones across 3 fruit development and maturity phases of Chardonnay cultivars. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

54 Samples

Download data: TXT

(Submitter supplied) Grapevines cv Sauvignon Blanc were subjected to different stress regimes by simulating the most common extreme weather events occurring within the current climate change scenario. During spring, just before bud break, the vines were either flooded or kept under normal conditions. Both vines were then split in two groups and put in differnt tunnels, either undergoing a simulated heatwave or not. Berry samples were collected from the four groups of plants (control, only flooded, only heatwave, flooded + heatwave) at different timepoints before, during and after the stress. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

66 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL29591 GPL18740

10 Samples

Download data: GFF3

(Submitter supplied) Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

6 Samples

Download data: TXT

(Submitter supplied) Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

Organism:

Vitis vinifera

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18740

2 Samples

Download data: TAB, TXT

(Submitter supplied) microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18740

3 Samples

Download data: TXT

(Submitter supplied) Somatic embryogenesis (SE), a morphogenic process that takes advantage of the regenerative potential of plants to replicate whole plants starting from somatic explants, can be a source of variation with potential applications in plant breeding. It is one of the most suitable tools to apply functional genomics studies and genetic improvement in plants. However, beyond a few pioneering works mainly focused on model plants, the molecular characterization of SE mechanisms is still elusive, especially for woody species. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

24 Samples

Download data: TXT

(Submitter supplied) We determined the RNA sequence of V. vinifera cv. Victoria and V. vinifera cv. Muscat Hamburg grapes to reveal the transcriptomics variations between summer and winter berries under a double cropping system. Transcriptomics analysis showed that the upregulated VviDXSs, VviPSYs, and VviCCDs expressions might contribute to accumulations of terpenes or norisoprenoids in winter berries.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

36 Samples

Download data: TXT

(Submitter supplied) Meristem culture and somatic embryogenesis is an effective tool for virus elimination of vegetatively propagated crops including grapevine. While they both are proved to be useful to eliminate the main grapevine viruses their efficiency differs according to the virus and the variety. In our work we investigated their efficiency using small RNA high-throughput sequencing as virus diagnostic method. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids were selected for sanitation via somatic embryogenesis and meristem culture. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18740

10 Samples

Download data: TXT

(Submitter supplied) Plants have great potential to protect against pathogens and other abiotic stress, and thus the interaction between signaling networks of defense is incredible. This can be activated and express with the application of growth elicitors and antimicrobial natural compounds. In the present study we used natural polysaccharide, Chitosan (15kDa) against Grey mold in two grape varieties (Shine-muscat and Kyoho). more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

12 Samples

Download data: XLSX

(Submitter supplied) Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

27 Samples

Download data: XLSX

(Submitter supplied) Grapevine line pattern virus (GLPV) was described 30 years ago from Hungary, and in the lack of its sequence until now no additional information about its presence was reported. However High-Throughput Sequencing (HTS) applied on dsRNAs extracts recovered from a grapevine plant (accession Baco22A) infected with GLPV Grapevine line pattern virus (GLPV) allowed us to sequence it with different High-Throughput Sequencing (HTS) methods andthe assembleing of the full genome sequence of this virus. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18740

1 Sample

Download data: TXT

(Submitter supplied) Several pathogens infect grapevine, including viruses and viroids. Considering that there are no effective plant protection treatments against these pathogens and vineyards are cultivated through decades usage of high quality and pathogen-free propagation material (rootstocks and scions) is essential. Although presence of regulated pests is routinely checked using ELISA or rarely RT-PCR, these diagnostics methods can detect only particular pathogens moreover can fail to detect variant strains. more...

Organism:

Vitis vinifera

Type:

Other

Platform:

GPL18740

19 Samples

Download data: TXT

(Submitter supplied) Hydrogen cyanamide (HC) is an agrochemical compound frequently used to break bud dormancy in grapevine grown under mild winter conditions all over the world. The present study was carried out to get a better understanding of the molecular mechanism associated with HC to release bud dormancy in grapevine using RNA-seq based transcriptomic and tandem mass tag (TMT) based proteomic analysis.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

2 Samples

Download data: XLSX

(Submitter supplied) Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

42 Samples

Download data: XLSX

(Submitter supplied) Vitis vinifera is widely grown worldwide for making wine and for use as table grapes. Of the existing cultivars, some have a floral and fruity flavour, referred to as a Muscat flavour. It is well-documented that this flavour originates from a series of terpene compounds, but the mechanism of terpene content differences among the Muscat-type cultivars remains unclear. Transcript and terpene metabolite profiles were integrated to elucidate the molecular mechanism of this phenomenon. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

27 Samples

Download data: TXT

(Submitter supplied) A double cropping system has been commercially adopted in subtropical regions in southern China, where there is abundant sunshine and heat resources. In this viticulture system, the first growing season normally starts as a summer cropping cycle; then, the vine is pruned and forced by hydrogen cyanamide, resulting in a second crop in January of the next year. Due to climate differences between the two growing seasons,the transcriptome varies greatly between summer- and winter- grape berries. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

36 Samples

Download data: TXT

(Submitter supplied) Basal leaf removal has been widely practiced to increase cluster sunlight exposure, control berry rot and eventually improve grape berry quality. Early leaf removal performed in cool region appeared to benefit the accumulation of norisoprenoids and monoterpenes. However, effects of this canopy management and leaf moving on volatile profiles and transcriptome of grape berry in warm region characterized with strong sunshine and arid climate were paid less attention. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

27 Samples

Download data: TXT

(Submitter supplied) Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

6 Samples

Download data: TXT