Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1023695 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohoromones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array
2009-11-18 | GSE18987 | GEO
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:In plant axillary bud dormancy and outgrowth are regulated by phytohormones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array 4 samples were used in this experiment
2009-11-17 | E-GEOD-18987 | biostudies-arrayexpress
Project description:We investigated differential gene expression patterns in Populus vegetative buds between paradormant, endodormant, and ecodormant dormancy states. Our primary objectives were to (1) identify which individual genes, biological processes, molecular functions, and regulatory pathways were differentially expressed among dormancy states, (2) classify the differentially expressed genes into contrasting gene expression patterns, and (3) identify cis-acting elements associated with each gene expression group. For more details consult Howe et al. (Frontiers in Plant Science, 2015, pending).
2015-06-26 | GSE70260 | GEO
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq. Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays. Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy. Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-05-07 | GSE174017 | GEO
Project description:Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.
2021-11-30 | GSE189658 | GEO
Project description:Comparison of gene expression levels between different dormancy stages
| PRJDB14938 | ENA
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 A loop design with 3 biological replicates (RNA from buds collected at 0, 500, 1000, 1500, and 2000 hr of chilling in 2002, 2004, and 2005).
2010-05-18 | E-GEOD-9903 | biostudies-arrayexpress
Project description:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
2022-02-23 | PXD008958 | Pride