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Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

ABSTRACT: 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.

ORGANISM(S): Oryza rufipogon

PROVIDER: GSE73181 | GEO | 2016/01/13

SECONDARY ACCESSION(S): PRJNA296071

REPOSITORIES: GEO

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Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

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

Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity

Project description:Salinity tolerance is a complex trait and, despite many efforts to obtain rice plants resistant to salt, few results have been achieved since a deeper understanding of the tolerance mechanisms is still needed. We used imaging of photosynthetic parameters, ion analysis and transcriptomic approaches to unveil differences between two rice varieties differing in salt sensitivity. Moreover, we analysed H2O2 production in roots, using a fluorescent probe, and the ensuing gene regulation. Transcriptomic analyses conducted in tolerant plants supported the set-up of an adaptive program consisting of allocating sodium preferentially to roots, restricting it to the oldest leaves and activating regulatory mechanisms of photosynthesis in new leaves. As a consequence, plants resumed growth even under prolonged salt stress. By contrast, in the susceptible variety, RNA profiling unveiled a mis-targeted response, leading to senescence and cell death. In roots of tolerant plants, an increase in H2O2 was observed as early as 5 minutes after treatment. Consequently, the expression of genes involved in perception, signal transduction and response to salt were induced at earlier times when compared to susceptible plant roots. Our results demonstrate that a prompt H2O2 signalling in roots participates to a coordinated response resulting in adaptation instead of senescence in salt treated rice plants.

2018-03-14 | GSE109341 | GEO

Expression data from roots of rice sos1 loss-of-function mutant and control plants (azygous) in normal conditions or after 4 days of salt stress

Project description:Rice (Oryza sativa) stands among the world's most important crop species and is salt-sensitive. The undue accumulation of sodium ions (Na+) in shoots has the strongest negative correlation with rice productivity under long-term salinity. The plasma membrane Na+/H+ exchanger protein SOS1 is the only Na+ efflux transporter that has to date been genetically characterized and only in dicot plants. Here, the importance of Na+ fluxes governed by the SOS system in the salt tolerance of rice was analyzed by a reverse-genetics approach. A sos1 loss-of-function mutant displayed exceptional salt sensitivity that correlated with excessive Na+ intake and impaired Na+ loading into the xylem. Thus, SOS1 controls net Na+ uptake by roots and the long-distance transport to shoots. The acute Na+ sensitivity of sos1 plants at low NaCl concentrations allowed the inspection of the transcriptional response to sodicity stress, without interference by the osmotic challenge intrinsic to high salinity treatments. The transcriptional response to salt of the sos1 mutant roots involved the preferential down-regulation of stress-related genes compared to the wild-type despite the greater intensity of the stress imposed to the mutant, which suggested impaired stress detection or inability to mount a comprehensive response to salinity.

2019-04-16 | GSE129844 | GEO

Transcriptional profiling of indica rice cultivar FR13A under salt stress condition.

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

Transcriptomic and alternative splicing analyses reveal mechanisms of the difference in salt tolerance between barley and rice

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

Transcriptome analysis provides insights into the mechanism of salt tolerance in rice colonized by arbuscular mycorrhizal fungi

Project description:Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. AM-regulated DEGs in cell wall modification and peroxidases categories were mainly upregulated in shoots, suggesting AM symbiosis might assist in relaxing the cell wall and scavenging reactive oxygen species (ROS). AM symbiosis indeed improved ROS scavenging capacity in rice shoots under salt stress. In addition, genes involved in Calvin cycle and terpenoid synthesis were enhanced by AM symbiosis in shoots and roots under salt stress, respectively. AM-upregulated cation transporters and aquaporin in both shoots and roots were highlighted. Strikingly, “protein tyrosine kinase activity” subcategory was the most significantly over-represented GO term among all AM-upregulated and downregulated DEGs in both shoots and roots, highlighting the importance of kinase on AM-enhanced salinity tolerance. Overall, our results from the transcriptomic analyses indicate that AM symbiosis uses a multipronged approach to help plants achieve salt stress tolerance.

2022-04-18 | GSE200863 | GEO

Wild and cultivated species of rice have distinctive proteomic responses to drought

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

Transcript profiling of drought responsiveness in two contrasting rice genotypes during vegetative stage stress

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

Transcript profiling of drought responsiveness in two contrasting rice genotypes during vegetative stage stress

2012-05-01 | GSE5978 | GEO

RNA sequencing of rice root in salt stress condition (250mM NaCl treatment)

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

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