The effects of various levels of drought and heat on the rice shoot transcriptome
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE221542 | GEO | 2022/12/27
REPOSITORIES: GEO
Similar Datasets
Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase. Keywords: Drought response
2012-05-01 | GSE5978 | GEO
Project description:Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7-d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis is responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Moreover, distinctive patterns of expression of proteins in drought were observed across the entire O. australiensis proteome. An intermediate impact of drought on photosynthetic and stress-response proteins is reported in O. glaberrima relative to O. sativa but the drought response was most striking in O. australiensis. For example, photosynthetic proteins decreased when O. sativa after drought, while a narrower range of stress-responsive proteins was up-regulated. Distinctive proteomic profiles and the expression levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
2021-09-09 | PXD019885 | Pride
Project description:Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice (Oryza sativa L. ssp. japonica and indica) to drought stress at the late vegetative stage and harvested leaves for protein extraction and subsequent label-free shotgun proteomics. Gene ontology analysis revealed some differentially expressed proteins were induced by drought in all eight genotypes; we speculate that these play a universal role in drought tolerance. However, some highly genotype-specific patterns of response to drought suggest that some mechanisms of metabolic reprogramming are not universal. Such proteins had largely uncharacterized functions, making them biomarker candidates for drought tolerance screens.
2020-01-17 | PXD016150 | Pride
Project description:Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsHSFA2e loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.
2015-01-16 | E-GEOD-65025 | biostudies-arrayexpress
Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase. Keywords: Drought response We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during drought stress. We used two contrasting rice genotypes (IR64 drought susceptible and Apo drought tolerant) differing in their degree of drought tolerance. Plants were grown under green house conditions and drought stress was imposed on 33rd DAS. Leaf sampling was done in both control and drought stressed plants after 6 days of drought stress. Three replications of microarray experiments were carried out by hybridizing the control samples against the drought stressed samples.
2012-04-30 | E-GEOD-5978 | biostudies-arrayexpress
Project description:Methionine sulfoxide reductases catalyze the reduction of MetSO back to the correct Met residue. Previously, the gene of Capsicum annuum methionine sulfoxide reductase B2 was isolated and CaMSRB2-overexpressing tomato shows enhanced growth, which may trigger increased resistance to the pathogens. To assess the role of this enzyme in rice, we generated transgenic lines under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without Bar marker gene. Several physiological tests such as MV and Fv/Fm, indicators of an oxidative stress-inducing agent and a potential maximal PSII quantum yield, respectively strongly suggested CaMSRB2 confers drought tolerance to rice. Using 3′-tiling microarray covering the whole rice genes, we carried out genome-wide expression analyses with CaMsrB2-transformed rice (Oryza sativa L. cv. ILMI). Rice was grown in port for six weeks and treated with drought by water withholding for two days.
2013-04-01 | GSE41204 | GEO
Project description:Upper and lower parts (flanks) of rice (Oryza sativa sp. japonica) shoot bases at 0.5 h and 6 h after gravistimulation was used for expression analysis in control and gravistimulated samples.Targets from biological replicates of both control and gravistimulated samples were generated and expression profiles were determined Affymetrix Rice Genome arrays.
2011-09-02 | GSE31834 | GEO
Project description:Histone H2B monoubiquitination (H2Bub1) has been implicated in several important physiological and developmental processes, but its role in the regulation of stress responses remains elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found the rice (Oryza sativa) HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, interacted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, induced by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were increased in the promoters of OsbZIP46 target genes under the drought stress and ABA treatments, and the increased H2Bub1 levels were positively correlated to the increased expression levels of the target genes. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance through mediation of OsbZIP46 deactivation and degradation, can repress the H2Bub1 level in the promoters of OsbZIP46 target genes by recruiting a putative deubiquitinase OsOTLD1. Suppression of OsOTLD1 in vivo resulted in increased H2Bub1 levels and expression of drought-responsive genes targeted by OsbZIP46. These findings established an elaborate mechanism of histone monoubiquitination in the fine-turning of ABA signaling and drought response via balancing H2Bub1 deposition and removal.
2019-02-09 | GSE117047 | GEO
Project description:To impose the heat treatment similar to the Structure-seq experiment, we applied RNA-seq to 14-day-old rice (Oryza sativa) shoot tissue to investigate the effect of heat stress (42°C) as compared to control condition (22°C).
2018-11-12 | GSE100713 | GEO
Project description:To impose the heat treatment similar to the Structure-seq experiment, we applied Ribo-seq to 14-day-old rice (Oryza sativa) shoot tissue to investigate the effect of heat stress (42°C) as compared to control condition (22°C).
2018-11-12 | GSE102216 | GEO