GEO DataSets

(Submitter supplied) Seedlessness is a highly relevant trait in grapevine berries that are intended for fresh consumption or raisin production. Corinto Bianco (CB) is a parthenocarpic somatic variant of the seeded cultivar Pedro Ximenes (PX). Both variants were compared to understand the basis of this parthenocarpic phenotype. CB berries ripened normally although their size was six times smaller than in PX. Macrogametogenesis was aborted in CB, which was also pollen sterile. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL17894

6 Samples

Download data: PAIR

(Submitter supplied) We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

6 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

(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 array

Platform:

GPL17894

9 Samples

Download data: PAIR

(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) De-multiplexing the unique identifiers discovered data consisted of 28,808,716 clean reads from fruit samples at 40 DAF, 27,941,132 reads from 65 DAF, and 25,457,565 reads from fruit sample at 90 DAF.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18580

3 Samples

Download data: XLSX

(Submitter supplied) conducted to find out the transcriptional system that is connected with the development of leaves and production of metabolites during photosynthesis. We examine the cellular expression by use the up-to-date RNA sequencing expertise to carry out a complete analysis of the transcriptional profile of V. vinifera leaves at four different developmental stages.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

4 Samples

Download data: TXT

(Submitter supplied) The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL13936

162 Samples

Download data: PAIR

(Submitter supplied) 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. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL13936

171 Samples

Download data: PAIR

(Submitter supplied) Somatic variants spontaneously appear during the vegetative multiplication of woody crops. The new white-berried grapevine cultivar Tempranillo Blanco (TB) originally appeared as a bud sport of the black skin-berried Tempranillo Tinto (TT) cultivar. To understand the origin of this variation, TT and TB genomes were sequenced. Structural variation and genetic segregation analyses uncovered that complex chromosome rearrangements consistent with chromothripsis, a catastrophic phenomenon recently described in human cancer, generated the variant genome of TB and the deletion of the color locus functional allele. more...

Organism:

Vitis vinifera

Type:

Genome variation profiling by array

Platform:

GPL11004

12 Samples

Download data: CEL

(Submitter supplied) MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. Their action is generally mediated through complementary interactions with mRNA molecules - leading to their degradation or sequestration from the translational apparatus. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL7710

12 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived flower development transcriptome profiling (RNA-seq) of two subspecies Methods: Flower mRNA profiles of wild-type (WT) four developmental stages and the same stages of Vitis vinifera subp vinifera were generated by deep sequencing using Illumina. more...

Organism:

Vitis vinifera; Vitis vinifera subsp. sylvestris

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18580 GPL18579

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Vitis vinifera

Type:

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

Platform:

GPL18580

30 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:

Methylation profiling by high throughput sequencing

Platform:

GPL18580

12 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:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18580

18 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 have developed a method based on 454 sequencing of 3’ cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This “virtual transcriptome” provides extensive coverage depth, and can be used for the set up of a comprehensive microarray based expression analysis. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platforms:

GPL8025 GPL8024

3 Samples

Download data

(Submitter supplied) The aim of the present study was to explore commonly and preferentially expressed genes for male and female gamete development in synthetic Brassica allohexaploids. We performed differential expression analysis to identify precise genes that regulate developmental events during male and female gamete development of Brassica allohexaploids.

Organism:

Brassica carinata x Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32203

9 Samples

Download data: XLS

(Submitter supplied) In this study, we demonstrated that the grapevine NAC transcription factor VviNAC33 is directly involved in leaf degreening and organ growth. Through the application of DAP-seq approach we identified several putative targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL22427

6 Samples

Download data: TXT

(Submitter supplied) In this study we functionally characterized the grapevine VviNAC33 by its transient and stable overexpression in grapevine homologous system and the creation of its chimeric repressor. Through the application of DAP-seq approach we identified putative direct targets of VviNAC33, among which the SGR1 involved in the breakdown of chlorophyll. Stable VviNAC33 overexpressing transgenic plants displayed an obvious degreening effect on leaves and an inhibition of leaf growth. more...

Organism:

Vitis vinifera

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24368

2 Samples

Download data: TXT