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Chromatin and transcription dynamics regulate flower development during chilling accumulation in peach buds

ABSTRACT: In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.

ORGANISM(S): Prunus persica

PROVIDER: GSE190586 | GEO | 2022/04/06

REPOSITORIES: GEO

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Chromatin and transcription dynamics regulate flower development during chilling accumulation in peach buds

Project description:In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.

2022-04-06 | GSE189882 | GEO

Trancriptomic analysis of flower bud dormancy in sweet cherry

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.

2019-12-16 | GSE130426 | GEO

Seasonal variation in leafy spurge crown bud gene expression

Project description:These experiments were designed to follow the seasonal changes in the transcriptome of field-grown leafy spurge crown buds. The goal was to identify specific signaling pathways and marker genes characteristic to the changes that occur when the buds transitioned from paradormancy through endodormancy and into ecodormancy. Keywords: Time course seasonal dormancy

2005-12-29 | GSE3913 | GEO

Photoperiod induction of endodormancy in Vitis riparia axillary buds.

Project description:This study compares age matched V. riparia axillary buds at one time point during long photoperiod (paradormancy maintenance) and short photoperiod (endodormancy induced). Keywords: endodormancy, photoperiod, paradormancy, grape, axillary bud

2005-08-05 | GSE3052 | GEO

Expression analysis of leafy spurge crown buds during dormancy transitions and release.

Project description:This submission contains the RNAseq data from one (just the study on paradormancy release) of several studies used to assemble the leafy spurge tranacriptome. These assembled transcrptome was built from 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (this study). 2) A study of leafy spurge crown buds through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy (Series GSE71321). 3) A study identical to #2 above but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 4) A previously submitted study (Series GSE56509) of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome. The paradormancy study (#1) contained 4 time points (0hr, 6h, 1d, 3d) with 3 biological replicates at 0hr and 4 biological replicates at each of the other time points.

2015-08-05 | E-GEOD-71317 | biostudies-arrayexpress

A hydrogen cyanamide-responsive transcriptome of sweet cherry flower buds from endodormancy to flowering

Project description:Perennial plants, like fruit trees grown in temperate regions, are characterized by bud dormancy, a rest state that protects the bud from cold during winter. At the same time, these plants have developed a requirement for winter chill for correct flowering. However, winters are becoming increasingly warm in temperate regions, resulting in dramatic effects on the flowering output and therefore crop yield. A compound that successfully compensates for missing winter chill is hydrogen cyanamide, which has been used to synchronize and advance flowering time in a range of commercially important fruit crops. Hydrogen cyanamide also represents a unique tool for researchers to study controlled endodormancy release. Here, we treated dormant sweet cherry flower buds with hydrogen cyanamide, sampling flower buds at different time points after treatment. RNAseq revealed more than 6,000 hydrogen cyanamide-responsive genes. In accordance with these results, hydrogen cyanamide treatment increased the levels of jasmonoyl-isoleucine (JA-Ile) and the cytokinins trans-zeatin riboside (tZR), dihydrozeatin (DZ) and dihydrozeatin riboside (DZR). Furthermore, hydrogen cyanamide affected the expression of antioxidant- and cell wall loosening-associated transcripts. These results suggest a complex mechanism of action for hydrogen cyanamide-induced endodormancy release, including key roles for JA-Ile, zeatin-type cytokinins and hydrogen cyanide.

2017-06-01 | GSE94290 | GEO

Expression analysis of leafy spurge crown buds during seasonal dormancy transitions.

Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

2015-08-05 | E-GEOD-71321 | biostudies-arrayexpress

Vitis riparia bud transcriptome in response to long and short photoperiod.

Project description:The transition of axillary grapevine buds from paradormancy to endodormancy is an important mechanism for winter survival. Maintenance of paradormancy and transition to endodormancy may be synchronized by factors including phytohormones, genes, transcription factors and other molecular regulators. In the present study we used age matched buds from vines subjected to 28 days of short day (SD; 13h) treatment or continued long day (LD; 15h) photoperiod for high throughput transcriptome profiling.

2021-04-28 | GSE95429 | GEO

Expression analysis of leafy spurge crown buds during dormancy transitions and release.

2015-08-05 | GSE71317 | GEO

Expression analysis of leafy spurge crown buds during seasonal dormancy transitions after glyphosate treatments.

Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

2015-08-05 | E-GEOD-71406 | biostudies-arrayexpress

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