Extensive transcriptome changes during vegetative bud dormancy in Populus
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ABSTRACT:
ORGANISM(S): Populus trichocarpa
PROVIDER: GSE70260 | GEO | 2015/06/26
SECONDARY ACCESSION(S): PRJNA288121
REPOSITORIES: GEO
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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). Nimblegen whole genome microarrays (n=10 arrays) were hybridized with total RNA isolated from axillary buds collected on five dates between August and March. On each date, RNA was isolated from two P. trichocarpa trees (clone Nisqually-1) growing in the field. After cDNA synthesis and labeling, the samples were sent to NimbleGen for fragmentation, hybridization, and detection. The Nimblegen microarray was designed for the Populus v1.0 genome assembly, but for data analysis, the 60-mer probes were reassigned to the Populus v3.0 gene models.
2015-06-26 | E-GEOD-70260 | biostudies-arrayexpress
Project description:To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with gibberellins, abscisic acid, and cytokinin. We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA. Analogies between flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).
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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
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds
2007-08-24 | GSE8849 | GEO
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:Dormancy of buds is a critical developmental process that allows plants to survive extreme seasonal variations in climate. Dormancy transition in leaf buds of Japanese pear leading cultivar ‘Kosui’ were investigated using 10 K cDNA microarray. Leaf buds collected on October (early endodormancy) and February (breaking stage) were used to monitor the changes in the transcriptome. Over 1000 genes were differentially expressed (p value < 0.05 and 2 fold change) when the early endodormant stage and breaking one were compared to each other. Functional classification revealed that the majority of genes were involved in response to abiotic/biotic stimulus and stress, signal transduction, and transcription. Among them, 76 and 22 genes were significantly (over 10 fold change) highly expressed in early endodormant stage and breaking stage, respectively, this result suggests that even in the endodormant stage, gene expression in the buds is high. Among them, several transcriptional factors were included. The quantitative real-time PCR analysis showed that at least three of their seasonal changes during endodormancy transition phases were similar to two DAM (dormancy-associated MADS box) genes isolated from Japanese pear, suggesting that they might be novel candidate genes associated to dormancy.
2013-01-22 | GSE34845 | GEO
Project description:Dormancy of buds is a critical developmental process that allows plants to survive extreme seasonal variations in climate. Dormancy transition in leaf buds of Japanese pear leading cultivar M-bM-^@M-^XKosuiM-bM-^@M-^Y were investigated using 10 K cDNA microarray. Leaf buds collected on October (early endodormancy) and February (breaking stage) were used to monitor the changes in the transcriptome. Over 1000 genes were differentially expressed (p value < 0.05 and 2 fold change) when the early endodormant stage and breaking one were compared to each other. Functional classification revealed that the majority of genes were involved in response to abiotic/biotic stimulus and stress, signal transduction, and transcription. Among them, 76 and 22 genes were significantly (over 10 fold change) highly expressed in early endodormant stage and breaking stage, respectively, this result suggests that even in the endodormant stage, gene expression in the buds is high. Among them, several transcriptional factors were included. The quantitative real-time PCR analysis showed that at least three of their seasonal changes during endodormancy transition phases were similar to two DAM (dormancy-associated MADS box) genes isolated from Japanese pear, suggesting that they might be novel candidate genes associated to dormancy. The gene expression profiles between dormant and released leaf bud were compared.
2013-01-22 | E-GEOD-34845 | biostudies-arrayexpress
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset
2007-08-23 | E-GEOD-8849 | biostudies-arrayexpress
Project description:Correlation analysis of the expression of bud dormancy-related genes in 10 peach cultivars, with different chilling requirements for dormancy release.
2012-01-15 | E-MEXP-3201 | biostudies-arrayexpress
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