Ontology highlight
ABSTRACT:
PROVIDER: PRJNA488534 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7768550_1.fastq.gz | Fastqsanger.gz | |||
| SRR7768550_2.fastq.gz | Fastqsanger.gz | |||
| SRR7768560_1.fastq.gz | Fastqsanger.gz | |||
| SRR7768560_2.fastq.gz | Fastqsanger.gz | |||
| SRR7768570_1.fastq.gz | Fastqsanger.gz |
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Project description:A grape-bud-oriented genomic platform was produced for a large-scale comparative analysis of bud responses to two stimuli of grape-bud dormancy release, hydrogen cyanamide (HC) and heat shock (HS). The results suggested considerable similarity in bud response to the stimuli, both in the repertoire of responding genes and in the temporary nature of the transcriptome reprogramming. Nevertheless, the bud response to HC was slower, more condensed and stronger, as reflected by a higher number of regulated genes and a higher intensity of regulation compared to the response to HS.
2009-12-01 | GSE16173 | GEO
Project description:Photoperiod regulation of grape bud dormancy
| PRJNA118913 | ENA
Project description:A grape-bud-oriented genomic platform was produced for a large-scale comparative analysis of bud responses to two stimuli of grape-bud dormancy release, hydrogen cyanamide (HC) and heat shock (HS). The results suggested considerable similarity in bud response to the stimuli, both in the repertoire of responding genes and in the temporary nature of the transcriptome reprogramming. Nevertheless, the bud response to HC was slower, more condensed and stronger, as reflected by a higher number of regulated genes and a higher intensity of regulation compared to the response to HS. To facilitate large-scale comparative analysis of early changes in the bud transcriptome by cDNA microarray, HC and HS were applied to canes collected from three vineyards, located in different regions, in three different years. This experimental scheme resulted in two true biological replicates for each treatment, differing in both timing and location, and loop design of technical replicates within time series. Consistent with our previous studies, both application of 5% Dormex (HC) and incubation for 1 h in 50oC water (HS) resulted in increased bud-break rates compared to respective controls. Bud break of HS-treated and HC-treated buds started 10 to 12 days after treatment. Three weeks after treatment, HS-treated buds exhibited 100% bud break while HC-treated buds had reached 80% bud break. The control showed significantly lower levels of bud break during this period. Bud material was collected from control, HC- and HS-treated cuttings at six time points (3, 6, 12, 24, 48 and 96 h) after the treatments and used to prepare total RNA samples.
2010-05-19 | E-GEOD-16173 | biostudies-arrayexpress
Project description: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.
2019-12-19 | GSE127322 | GEO
Project description:Bud dormancy in perennials in boreal and temperate ecosystems is crucial for survival in harsh winter. Dormancy is released by prolonged exposure to low temperatures and is followed by reactive growth in the spring. Lysine acetylation (Kac) is one of the major post-translational modifications (PTMs) involved in plant response to environment signals. However, little information is available on the effects of Kac modification on bud dormancy release. Here, we report the dynamics of lysine acetylome in hybrid poplar (Populus tremula x alba) dormant buds. A total number of 7,594 acetyl sites from 3,281 acetyl proteins were identified, representing the largest to date dataset of lysine acetylome in plants. Of them, 229 proteins were differentially acetylated during bud dormancy release and were involved mainly in the primary metabolism. Site-directed mutagenesis enzymatic assays showed that acetylation strongly modified the activities of two key enzymes of primary metabolism, pyruvate dehydrogenase (PDH) and isocitrate dehydrogenase (IDH). We thus propose that Kac of enzymes could be an important strategy for reconfiguration of metabolic processes during bud dormancy release. In all, our results reveal the importance of Kac in bud dormancy release and give a new perspective to understand the molecular mechanisms of tree’s seasonal growth.
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Project description:Grapes are a valuable fruit and an important economic crop in the world, where wine production is a major industry. In grapevine, the environmental regulation of bud dormancy varies among its diverse genotypes. Certain grapevine genotypes become dormant in response to decreasing photoperiod and others require low temperature or both environmental cues to induce dormancy. This study used a proteomic approach to gain an understanding of the underlying molecular events involved in bud dormancy commitment.
2018-06-29 | PXD001627 | Pride
Project description:Bud dormancy is a crucial stage in perennial trees and allows survival over winter and optimal subsequent flowering and fruit production. Environmental conditions, and in particular temperature, have been shown to influence bud dormancy. Recent work highlighted some physiological and molecular events happening during bud dormancy in trees. However, we still lack a global understanding of transcriptional changes happening during bud dormancy. We conducted a fine tune temporal transcriptomic analysis of sweet cherry (Prunus avium L.) flower buds from bud organogenesis until the end of bud dormancy using next-generation sequencing. We observe that buds in organogenesis, paradormancy, endodormancy and ecodormancy are characterised by distinct transcriptional states, and associated with different pathways. We further identified that endodormancy can be separated in two phases based on its transcriptomic state: early and late endodormancy. We also found that transcriptional profiles of just 7 genes are enough to predict the main cherry tree flower buds dormancy stages. Our results indicate that transcriptional changes happening during dormancy are robust and conserved between different sweet cherry cultivars. Our work also sets the stage for the development of a fast and cost effective diagnostic tool to molecularly define the flower bud stage in cherry trees.
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Project description:This study investigated changes in gene expression of controlled environment chilled (4C) grape overwintering buds as they accumulated from 0 to 2000 chilling hours. Keywords: time course, chilling, endodormancy release, axillary bud, grape
2009-06-03 | GSE9903 | GEO
Project description:Bud dormancy – the repeated phase of rest that punctuates periods of growth in the life cycles of many perennial species. In temperate fruit trees, fulfillment of chilling requirement and subsequent heat requirement enable dormant buds to have uniform blooming in field. However, effects of environmental factors such as chilling underlying dormancy release and bud break has not been fully understood. Histone modification is an important epigenetic regulation system which plays an important role in gene expression in various developmental and adaptive processes. Taking advantage of next-generation sequencing, we generated epigenome and transcriptome profiling at different stages before chilling, after chilling and just before bud break in apple (Malus x domestica). We found H3K27me3 may play dominant role during chilling and the genes involved in lignin and lipid metabolic process showed histone modifications. Interestingly, the higher ratio of genes in chilling-associated network exhibited histone modifications, suggesting crucial epigenetic roles in regulating gene expressions in response to chilling during dormancy. Furthermore, H3K4me3 may play more important role during bud break and the genes related to cell wall modification/organization were strongly modified. Taken together, this study provides important insights into the chromatin-based gene regulation underlying chilling-mediated dormancy release and bud break in apple.
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