Comprehensive analysis of rice transcriptome during dehydration and rehydration
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA922103 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23023933_1.fastq.gz | Fastqsanger.gz | |||
| SRR23023933_2.fastq.gz | Fastqsanger.gz | |||
| SRR23023934_1.fastq.gz | Fastqsanger.gz | |||
| SRR23023934_2.fastq.gz | Fastqsanger.gz | |||
| SRR23023935_1.fastq.gz | Fastqsanger.gz |
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Project description:Drought is a harmful abiotic stress that threatens the growth, development, and yield of rice plants. To cope with drought stress, plants have evolved diverse and sophisticated stress-tolerance pathways by regulating gene expression. Previous genome-wide studies have revealed many rice drought stress-responsive genes that are involved in various metabolism, hormone biosynthesis and signaling pathways, and transcriptional regulation. However, little is known about the regulation of drought-responsive genes during rehydration after dehydration. In this study, we examined the dynamic gene expression patterns in rice seedling shoots during dehydration and rehydration using RNA-seq analysis. To investigate the transcriptome-wide rice gene expression patterns during dehydration and rehydration, RNA-seq libraries were sequenced and analyzed to identify differentially expressed genes (DEGs). DEGs were classified into five clusters based on their gene expression patterns. The clusters included drought-responsive DEGs that were either rapidly or slowly recovered to control levels by rehydration treatment. Representative DEGs were selected and validated using qRT-PCR. In addition, we performed a detailed analysis of DEGs involved in nitrogen metabolism, phytohormone signaling, and transcriptional regulation. In this study, we revealed that drought-responsive genes were dynamically regulated during rehydration. Moreover, our data showed the potential role of nitrogen metabolism and jasmonic acid signaling during the drought stress response. The transcriptome data in this study could be a useful resource for understanding drought stress responses in rice, and may provide a valuable gene list for developing drought-resistant crop plants.
2023-05-17 | GSE222438 | GEO
Project description:Sporobolus stapfianus is a desiccation tolerant (DT) grass and a member of the Poaceae family alongside prominent crop and forage species. Despite the worldwide distribution of this family, most of its species are vulnerable to water loss within their vegetative tissues. As a DT species, S. stapfianus, could, therefore, serve as a model species for identifying the molecular changes that enabled such a rare occurrence of the DT phenotype in resurrection grasses and the implications of such a unique adaptation for agriculture. A comprehensive gene expression profiling was performed in plants subjected to a dehydration/rehydration cycle using NimbleGen microarrays hybridization method. Our results showed that most transcripts were high in the hydrated state of S. stapfianus leaf tissues and that minor dehydration (> 60% relative water content; RWC) did not induce most transcripts, but did repress photosynthetic activity, which show the importance of curtailing the production of toxic elements to the DT phenotype. It took a loss of 40% RWC for induction of most transcripts. This shows that this species is pre-equipped to deal with mild dehydration, but requires stress-induced activation mechanisms to prepare for desiccation. In agreement with our transcriptomic data, a global metabolic analysis conducted in this species has shown that most metabolites accumulate to their highest levels below 45% RWC, which suggests the importance of those late stages of dehydration in preparing resurrection grasses for desiccation and for early stages of rehydration. In most cases, a 12-h rehydration was sufficient to reinstate pre-stress expression levels, which shows that only partial damage occurred during drying. Unlike during dehydration, our metabolomic data profiled after rehydration showed that there is no clear correlation between gene expression and metabolic abundance, which suggests that most of the compounds that are produced during rehydration are quickly utilized in active metabolism of restoration. The findings of the paper show that S. stapfianus is primed to respond to mild dehydration, although severe dehydration require inducible response, with 40-30% RWC being the peak of gene expression. As for photosynthesis, this species cease its photosynthetic activity even at high water levels (85% RWC) alleviating the need to activate antioxidants activity during mild dehydration.
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Project description:We have utilized the raw sequence data from our earlier investigation of the lichen transcriptome to design a custom DNA microarray for C. rangiferina in order to study the transcripts expressed in lichen thallus during dehydration and rehydration. The aim of this study was to identify the genes most differentially expressed during the rehydration and drying processes and also to get a more integrative view of the molecular players who may play roles in the processes required for lichen desiccation tolerance and the rapid re-establishment of photosynthesis through functional annotation.
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Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant.
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Project description:Rice plants (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks under flooded lowland conditions with a 12-h light (28C)/12-h dark (25C) regimen (ca. 1500 umol photons mM-^V2 sM-^V1). The plants were subjected to dehydration treatment by growth at 28C without watering for either 2 days until the soil moisture content was 18.7% (w/w; SD = 1.3%).
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Project description:Transcriptome measurements of 14 day old rice leaves (2nd leaf) in heat stress and recovery and dehydration stress and recovery - samples collected every 15 minutes for up to 4h - 480 samples (240 conditions, 2 biological replicates)
2016-01-01 | GSE74793 | GEO
Project description:Rice plants (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks under flooded lowland conditions with a 12-h light (28C)/12-h dark (25C) regimen (ca. 1500 umol photons mM-^V2 sM-^V1). The plants were then subjected to dehydration treatment by growth at 28C without watering for 2 days until the soil moisture content was 18.7% (w/w; SD = 1.3%).
2014-03-03 | E-MEXP-3864 | biostudies-arrayexpress
Project description:Rice plants (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks under flooded lowland conditions with a 12-h light (28C)/12-h dark (25C) regimen (ca. 1500 umol photons mM-^V2 sM-^V1). The plants were subjected to dehydration treatment by growth at 28C without watering for 3 days until the soil moisture content was 15.6% (w/w; SD = 1.1%).
2014-03-03 | E-MEXP-3865 | biostudies-arrayexpress
Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant. Wild-type rice plants and a line carrying a T-DNA insertion in the third exon of the transcription factor gene (arid mutant) were subjected to dehydration stress for 90 min. Well-watered wild-type and T-DNA insertion plants were used as controls. Total RNA was extracted from roots and subjected to expression profiling using rice Affymetrix microarrays.
2013-11-30 | E-GEOD-42683 | biostudies-arrayexpress
Project description:Water-deficit or dehydration greatly influences plant development and reduces crop productivity, particularly in rain-fed areas across the world. Despite extensive research over the past several decades, little is known about dehydration management of mitochondria and cellular energy metabolism. We, for the first time, mapped dehydration-induced global changes in protein expression of the mitochondrial landscape to dissect the molecular mechanism, which might enable crop species to survive. Toward this, four-week-old rice seedlings were subjected to progressive dehydration by withholding water, and the stress severity was assessed by physicochemical reactions and mitochondrial architecture. The comparative mitochondrial proteomics analysis led to the identification of an array of stress-responsive proteins, presumably involved in a variety of cellular functions that includes energy production, organelle protein transportation and ROS detoxification, among others. The proteomics profile demonstrated that the alteration of tricarboxylic acid cycle intermediates is crucial for fuelling ATP production. Collectively, our results demonstrate that the global regulation of mitochondrial proteins is linked to dehydration response, which would favour genetic manipulation of crop species for better adaptation.
2023-09-16 | PXD022269 | Pride