Transcriptome profie of rice in response to temperature and oxidative stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Indica Group
PROVIDER: GSE19983 | GEO | 2012/05/31
SECONDARY ACCESSION(S): PRJNA120141
REPOSITORIES: GEO
Similar Datasets
Project description:Genome wide expression profiles of 10-day-old seedlings in response to prior exposure with OS followed by heat stress or cold stress as well simultaneous exposure to OS along with HS/CS was done to study the transcriptional changes in response to combination of stresses. 10-day old rice seedlings were used for experiments. Transcript profiling was done in 10-day old rice seedling following oxidative Stress prior to High Temperature Stress (PO_HS) or Low Temperature Stress (PO_CS) and Oxidative Stress during High Temperature Stress (DO_HS)/ during Low temperature stress (DO_CS). Unstressed seedlings were used as control. For each condition, three biological replicates were processed in a similar manner for the microarray analysis.
2012-12-26 | E-GEOD-32704 | biostudies-arrayexpress
Project description:To comprehend the gene expression profile in rice panicle under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice panicle of post-meiosis at 0 min, 10min, 20 min, 60 min, and 2 hr after the treatment of 40 degree centigrade, and the differentially expressed genes at the time course were involved in binding, catalysis, stress response, and cellular process. The significantly expressed genes were mainly up-regulated. Among HR genes, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. The MapMan analysis demonstrated that, under heat treatment, the HR genes were enriched in the pathways related to biotic stress, abiotic stress including heat and cold, and cell cycle and development, ubiquitin-proteasome , lipid and secondary metabolisms, which revealed the great importance of cross-talk and protein homeostasis in response to heat in rice panicle of post-meiosis.
2013-11-27 | GSE51426 | GEO
Project description:Genome wide expression profiles of 10-day-old seedlings in response to prior exposure with OS followed by heat stress or cold stress as well simultaneous exposure to OS along with HS/CS was done to study the transcriptional changes in response to combination of stresses.
2012-12-26 | GSE32704 | GEO
Project description:Heat stress is one of the extreme weather disasters potently decreasing cereal plant production. Recent studies have demonstrated that protein degradation and rRNA homeostasis as well as transcription factors are involved in thermoresponse in plants. However, how 5-methylcytosine (m5C) RNA modification contribute to heat stress response in plant remains largely unknown. Herein, we identified OsNSUN2 as the mRNA m5C methyltransferase in rice. The osnsun2 mutants specifically displayed severe phenotypes of temperature- and light-dependent lesion mimic and heat stress hypersensitivity. Heat stress enhanced mRNAs m5C methylation involving photosynthesis and detoxification systems, such as β-OsLCY, OsHO2, OsPAL1, and OsGLYI4, in an OsNSUN2-dependent manner, which then increased the protein synthesis. Consistently, the photosystem of the osnsun2 mutants was vulnerable to high ambient temperature and failed to be repaired under tolerable heat stress. Furthermore, OsNSUN2 mutation reduced photosynthesis efficiency and accumulated excessive reactive oxygen species upon heat treatment. Our findings demonstrate an important mechanism of mRNA m5C-dependent heat acclimation in rice.
2020-04-15 | PXD017187 | Pride
Project description:To better understand the mechanisms that regulate the heat stress response in rice, we conducted a comparative analysis of transcriptome profile in panicles from two rice lines, heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082) using rice Affymetrix GeneChip. In HTL252 panicles, 1538 differentially expressed genes (DEGs) genes with at least four-fold expression changes compared with the control under heat treatment were considered heat-responsive (HR). Of these DEGs, 522 genes were up-regulated while 1016 genes were repressed. Among DEGs in HSL082, 496 genes were induced and 1707 genes were repressed. Out of the 370 common DEGs found between HTL252 and HSL082, 129 genes were induced and 241 genes were repressed.
2019-06-20 | GSE83542 | GEO
Project description:Purpose: understanding the complex genetic control of heat tolerance can be reached using whole transcriptome sequencing (RNA-seq) that is currently the most powerful tool to identify genes differentially regulated. Heat responses differ greatly between sensitive and tolerant genotypes, mainly in terms of the amount of genes and pathways involved in the response and differences in the expression level of constitutive genes in many pathways. The present study aims to compare the molecular response of Brazilian flooded rice cultivars with variable sensitivity to heat stress at anthesis stage and to discuss the possible processes involved in heat tolerance. Methods: Panicle mRNA profiles of cultivars IRGA 428 (sensitive) and BR-IRGA 409 (tolerant) were generated by deep sequencing, in triplicate (each replicate is composed of two plants), under three days of heat stress and control condition at anthesis stage, using Illumina Hiseq 2500. The sequence reads from each sample that passed quality filters were mapped independently, generating contigs that were aligned with the reference genome sequences in rice (cv. MH63-indica). The transcripts were analyzed at the expression level with statistic test (EdgeR – Rstudio) to identify the significant changes in the expression level of the genes for each treatment condition and cultivar follow by identification of metabolic pathways (MapMan and Cytoscape) based on different programs. Results: Using an optimized data analysis workflow, we identified 16,871 transcripts in the rice spikelet of sensitive and tolerant cultivars with HISAT workflow. Using filtered and aligned reads, transcript levels were used to find differentially expressed genes (DEGs) at different thermal condition and cultivars. We identified 2,064 genes for BR-IRGA 409 and 1,078 genes for IRGA 428 that showed a significant change in expression in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). When it was examined the multi-factor responsive genes, that is genes with an interaction between cultivar and heat stress (multi-factor analysis - cultivars vs control and high temperature), it was identified 65 DEGs in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). Comparison of our data set with other RNA-seq studies shows a significant overlap in heat responsive genes (hypergeometric enrichment test). This core set of genes common among RNA-seq studies indicates that it may be associated with basal response to heat. In the present study, genes related to light reaction pathway were induced in the panicle of the cultivar IRGA 428, while these genes in cultivar BR-IRGA 409 were already expressed highly in control conditions. The basal level of these genes in BR-IRGA 409 was as high as the heat-induced level in the sensitive IRGA 428. Photosynthesis is known to occur in rice panicles, but little has been reported about the photosynthetic characteristics of such panicles. To cope with heat stress, plants have developed a sophisticated mechanism to repair photosystem damage. Therefore, in IRGA 428 the induction of these genes suggests the activation of a repair mechanism to reverse damage on the photosynthetic apparatus caused by the heat stress. The difference in basal levels of the photosynthetic genes may be a contributing factor to the differences in spikelet fertility between the cultivars under heat stress. Conclusion: This is the first study to evaluate the heat tolerance of Brazilian rice cultivars. In panicle tissue, most canonical heat responsive genes, such as HSF family, small HSP family and FKBP family, show a similar response in both Brazilian cultivars, despite the fact that these cultivars have not been specifically selected for heat tolerance. The response of photosynthetic genes to heat stress is a major difference between the cultivars BR-IRGA 409 and IRGA 428. This study indicates that the higher basal expression of photosynthetic genes in the panicle provides improved spikelet fertility under heat stress. This may provide potential markers that can be used to identify heat tolerant genotypes among rice breeding programs. This study emphasizes that the characterization of heat stress responses in individual cultivars provides insights into both the basic mechanisms of heat response and assists with understanding the complex phenomenon of responses to high temperature stress.
2018-08-29 | GSE119109 | GEO
Project description:Background: Plant disease is a major challenge to agriculture worldwide, and it is often exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress increases host susceptibility, a tendency which could spell disaster in light of the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the molecular mechanisms that cause it. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants infected with Xanthomonas oryzae (Xo), an economically important bacterial pathogen of rice, during high temperature stress. Results: Using RNA-Seq technology, 8,499 differentially expressed genes were identified as temperature responsive in one rice cultivar, IRBB61, experiencing susceptible and resistant interactions with Xo across three time points. Many genes with gene ontology terms associated with stress response were identified. Notably, genes in the plant hormone abscisic acid (ABA) biosynthesis and response pathways were identified as upregulated by high temperature in both mock-treated plants and plants in the susceptible interaction and suppressed by high temperature in plants in the resistant interaction. A DNA sequence motif similar to known ABA-responsive cis-regulatory elements was identified in the promoter region upstream of genes upregulated in susceptible but downregulated in resistant interactions. Conclusions: The results of our study suggest that the plant hormone ABA is an important node for cross-talk between plant transcriptional response pathways to high temperature stress and pathogen attack. Genes in this pathway represent an important focus for future study to determine how plants evolved to deal with simultaneous abiotic and biotic stresses.
2017-11-07 | GSE95668 | GEO
Project description:To comprehend the gene expression profile in rice flag leaf under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice flag leaf of reproductive stage at 0 min, 20 min, 60 min, 2 hr, 4 hr, and 8 hr after the treatment of 40 degree centigrade, and the significantly expressed genes mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response were identified. Among them, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat. The metabolism pathway analysis demonstrated that, under heat treatment, glycolysis and ubiquitin-proteasome was enhanced, and TCA, gluconeogenesis, the secondary metabolism and light-reaction in the photosystem was dramatically repressed, which revealed the great importance of maintaining primary metabolism and protein homeostasis in response to heat in rice flag leaf.
2013-09-10 | GSE45259 | GEO
Project description:we utilized microRNA sequencing to identify differentially expressed miRNAs in rice heat-tolerant line and heat-sensitive line under high night temperature stress .
2023-02-04 | GSE224013 | GEO
Project description:we utilized transcriptome sequencing to identify differentially expressed genes in rice heat-tolerant line and heat-sensitive line under high night temperature stress .
2023-02-20 | GSE225259 | GEO