Variation in transcriptional responses to salt stress in rice
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE98455 | GEO | 2018/01/01
SECONDARY ACCESSION(S): PRJNA385135
REPOSITORIES: GEO
Similar Datasets
Project description:A submergence tolerant indica rice cultivar FR13A, was also reported to withstand salt stress and proven in our experiments. The mechanism of tolerance is yet to be studied by forward genetics approach. However, it is known that salt stress tolerance is governed by several QTLs and not by a single gene. To understand the mechanism of such a complex mechanism of salt tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype 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 constitutive and salt stress conditions at seedling stage. Keywords: Mechanism of salt tolerance
2007-12-21 | GSE6600 | GEO
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
2016-01-13 | GSE73181 | GEO
Project description:A submergence tolerant indica rice cultivar FR13A, was also reported to withstand salt stress and proven in our experiments. The mechanism of tolerance is yet to be studied by forward genetics approach. However, it is known that salt stress tolerance is governed by several QTLs and not by a single gene. To understand the mechanism of such a complex mechanism of salt tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype 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 constitutive and salt stress conditions at seedling stage. Experiment Overall Design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice plant tissues during salt stress treatment. We used two contrasting rice genotypes (FR13A tolerant and IR24 susceptible) differing in salt stress response. Plants were grown in growth chambers and treated with 150 mM salt concentration at 14th DAS. Sampling was done in both constitutive and treated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the RNA from tolerant samples against the susceptible lines on the same slide.
2008-06-15 | E-GEOD-6600 | biostudies-arrayexpress
Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
2021-06-15 | E-MTAB-10653 | biostudies-arrayexpress
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice. Leaf and root mRNA profiles of Dongxiang wild rice at the seedling stage with or without salt stress were generated by deep sequencing, on Illumina Hiseq 2000 platform.
2016-01-13 | E-GEOD-73181 | biostudies-arrayexpress
Project description:We report the application of small RNA sequencing (Illumina) technology for the identification of miRNA from root and leaf and flower tissues of pusa basmati rice cultivar grown under normal and salt stress conditions. We used this data to predict and identify known and novel miRNAs.
2021-02-01 | GSE111768 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2016-06-30 | GSE76613 | GEO
Project description:Both barley (Hordeum vulgare) and rice (Oryza sativa) belong to Poaceae family, but differ greatly in salt tolerance. In order to understand molecular mechanisms in the difference of salt tolerance between the two species, the responses of transcriptomic profiles to salt stress were compared between rice (cultivar Nipponbare) and barley (accession XZ26) to reveal how alternative splicing (AS) coordinates with transcriptional regulation in adaptation to salt stress. Physiological study showed that XZ26 had higher salt tolerance than Nipponbare, as reflected by less growth inhibition, lower shoot Na+ concentration and higher K+/Na+ ratio when exposed to salt stress. Transcriptomic analysis showed that XZ26 had higher ROS scavenging ability, less degradation of protein kinases and enhanced anti-oxidation. Moreover, AS genes related to ion transporter genes and transcription factors could enhance and amplify K+/Na+ homeostasis and signal transduction cascades. We proposed that higher salt tolerance of barley accession XZ26 is attributed to its superior K+/Na+ homeostasis, tissue detoxication and less energy consumption. The present results provide insights at transcriptomic levels into reasons why barley has higher salt tolerance than rice.
2019-06-05 | GSE132183 | GEO
Project description:Study of gene expression under no salt condition from total leaf RNA and gene expression after five days of salt stress in 150mM NaCl from total leaf RNA of PcINO1 and OsINO1 introgressed IR-64 transgenic rice lines.
2019-11-01 | GSE122850 | GEO
Project description:Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation. Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. Transcriptomic analysis showed that salt stress caused 333 genes to be upregulated and 1,765 to be downregulated. However, adding Spd during salt treatment significantly altered this pattern: 2,298 genes were upregulated and 844 were downregulated, which indicated Spd reverses some transcriptional changes caused by salt stress. KEGG pathway analysis suggested that Spd influenced key signaling pathways, including MAPK signaling, plant hormone signal transduction, and phenylalanine metabolism. Additionally, the bZIP transcription factor OsbZIP73 was upregulated after Spd treatment, which is confirmed by Western blot. Further insights into the interaction between OsbZIP73 and Spd were gained through fluorescence polarization experiments, showing that Spd enhances protein OsbZIP73's affinity for RNA. Functional enrichment analyses revealed that OsPYL1, OsSPARK1, and various SAUR family genes involved in Spd-affected pathways. The presence of G/A/C-box elements in these genes suggests they are potential targets for OsbZIP73. Conclusions: Our findings suggest a strategy of using spermidine as a chemical alleviator for salt stress and provide insights into the regulatory function of OsbZIP73 in mitigating salt stress in rice roots.
2024-08-01 | GSE189665 | GEO