Transcript profiling in Paoenia ostii during chilling induced endo-dormancy release
Ontology highlight
ABSTRACT:
ORGANISM(S): Paeonia ostii Paeonia suffruticosa
PROVIDER: GSE40004 | GEO | 2014/08/01
SECONDARY ACCESSION(S): PRJNA172838
REPOSITORIES: GEO
Similar Datasets
Project description:To better understanding the genetic and physiological changes behind the dormancy process in tree peony, we performed customized cDNA microarray to investigate gene expression profiling in tree peony M-bM-^@M-^XFeng Dan BaiM-bM-^@M-^Y buds during chilling induced dormancy release. Endo-dormant tree peony plants were exposed to 0-4M-BM-0C from 5 November to 30 December 2009 in Qingdao, Shandong, China. Buds were collected after 0 d, 6 d, 12 d, 15 d, 18 d and 24 d chilling endured. DNA microarrays were customized using Agilent eArray 5.0 program, containing spots with 14,957 gene-specific 60-mer oligonucleotides representing 14,957 non abundant ESTs obtained from 454 sequencing normalized cDNA of tree peony buds during chilling duration (TSA, 65,217). Total 3,174 significantly differentially-expressed genes (P<0.05) were observed through endo-dormancy release, and the number of up-regulated (1,611) and that of down-regulated (1,563) was almost same. Expression of differentially-expressed genes associated with GA biosynthesis and signaling, cell growth and development was confirmed by quantitative RT-PCR, which displayed similar trends pattern in expression. Transcript profiling of tree peony was measured during chilling (0-4M-BM-0C) induced dormancy release. Mixed buds, three buds for each individual, were collected after 0, 6, 12, 15, 18 (endo-dormancy release), 24 days (eco-dormancy) chilling requirement fulfilling. Three replications (3 plants/ replication) were harvested between November and December.
2014-08-01 | E-GEOD-40004 | biostudies-arrayexpress
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next season’s growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. ‘Nanko’ vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release.
2014-03-26 | GSE49368 | GEO
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next seasonM-bM-^@M-^Ys growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. M-bM-^@M-^XNankoM-bM-^@M-^Y vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release. In this study, we used chilling exposed bud samples (0, 40, 60 days starting at November) and seasonal monthly bud samples (June to March). For the samples in dataset 1 (three different time points during chilling treatment), three technical replicates (60K M-CM-^W 3 per sample) with three biological replicates were averaged, whereas three technical replicates were averaged for the samples in dataset 2 (10 different seasonal time points)
2014-03-26 | E-GEOD-49368 | biostudies-arrayexpress
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.
2024-03-31 | GSE171131 | 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.
2024-03-31 | GSE128041 | GEO
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: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: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:Leafy spurge (Euphorbia esula) is an herbaceous perennial weed that produces vegetatively from an abundance of underground adventitious buds. The objectives of this study were to determine how mimicking natural seasonal conditions (photoperiod and temperature) under controlled environmental conditions affect dormancy and flowering competence; to determine molecular mechanisms associated with well-defined phases of seasonal dormancy transitions based on transcript profiles obtained by microarray analysis; and to link mechanisms regulating induction and release of endodormancy and flowering competence. Reduction in temperature (27 to 10°C) and photoperiod (16 to 8 h) over a three-month period induced a para- to endo-dormant transition in crown buds. An additional eleven weeks of prolonged cold (5-7°C) and short-photoperiod treatment resulted in accelerated shoot growth from crown buds, and 99% floral competence when plants were returned to growth promoting conditions. Exposure of paradormant plants to short-photoperiod and prolonged cold treatment alone had minimal affect growth potential or on flowering (~1%); whereas endodormant crown buds without prolonged cold treatment, had delayed shoot growth and approximately 2% flowering when returned to growth promoting conditions. Transcriptome analyses revealed that 373 and 260 genes were differentially expressed (p<0.005) during para- to endo-dormant and endo- to eco-dormant transitions, respectively. Transcripts from flower competent vs. non-flower competent crown buds identified 607 differentially expressed genes, and genes involved in cell cycle and DNA processing, oxidative stress, flower regulation, and proteolysis were over-represented. Further, sub-network analysis identified expression targets and binding partners associated with circadian clock, dehydration/cold signaling, phosphorylation cascades, and response to abscisic acid, ethylene, gibberellic acid, and jasmonic acid, suggesting these central regulators affect well-defined phases of dormancy. Potential genetic pathways associated with these dormancy transitions and flowering were used to develop a proposed conceptual model.
2009-12-01 | GSE19217 | GEO