Ontology highlight
ABSTRACT:
PROVIDER: PRJNA822865 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18591502_1.fastq.gz | Fastqsanger.gz | |||
| SRR18591502_2.fastq.gz | Fastqsanger.gz | |||
| SRR18591503_1.fastq.gz | Fastqsanger.gz | |||
| SRR18591503_2.fastq.gz | Fastqsanger.gz | |||
| SRR18591504_1.fastq.gz | Fastqsanger.gz |
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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:Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes. Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, e.g. enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into glycinebetaine and H2O2 in a single step. It is possible that H2O2 /GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unraveled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signaling and cellular metabolism. Overall, 165 genes show more than 2 folds up-regulation at P value <0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes. Experiment Overall Design: Rice (Oryza sativa L.), transgenic plants expressing codA gene from Arthrobacter globiformis were compared with untransformed plants at seedling level
2009-06-24 | E-GEOD-15448 | biostudies-arrayexpress
Project description:Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes. Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, e.g. enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into glycinebetaine and H2O2 in a single step. It is possible that H2O2 /GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unraveled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signaling and cellular metabolism. Overall, 165 genes show more than 2 folds up-regulation at P value <0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes.
2009-06-03 | GSE15448 | GEO
Project description:Environmental stresses influence the growth of plants and the productivity of crops. Salinity is one of the most important abiotic stresses for agricultural crops. PCD is induced by various biotic and abiotic stresses in algae and higher plants, including high salinity treatment. OsPDCD5, an ortholog to mammalian-programmed cell death 5, is up-regulated under low temperature and NaCl treatments. We found that the transgenic rice which constitutively expressed anti-OsPDCD5 increased salt stress tolerance in unique ways. By using the Rice Genome Microarray, we identified target genes that were regulated in transgenic rice plants by anti-OsPDCD5.
2011-11-01 | GSE28209 | GEO
Project description:Expression analysis of abiotic stress-treated rice
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Project description:The OsCPK4 gene is a member of the complex gene family of the Calcium-dependent protein kinases (CPKs) in rice. Expression of OsCPK4 is induced by high salinity, drought and the phytohormone abscisic acid. The OsCPK4 protein localizes to the plasma membrane. Transgenic rice overexpressing OsCPK4 enhances tolerance to salt and drought stress, the transgenic plants having stronger water-holding capability than control plants. Microarray analysis of OsCPK4 rice plants revealed up-regulation of genes involved in metabolism, particularly lipid metabolism, as well as genes involved in oxidative stress and redox control. Meanwhile, OsCPK4 overexpression has no impact on the expression of the well-characterized abiotic stress-associated transcription factors (i.e. DREB and NAC), or the typical salt and drought-inducible genes (i.e. LEA genes, including Dehydrin genes). Under salt stress conditions, the OsCPK4 transgenic lines showed lesser membrane lipid peroxidation as compared to control plants, indicating that OsCPK4 rice plants have a better capacity to prevent oxidative damage in cellular membrane lipids. Collectively, our data suggest that OsCPK4-mediated processes protect the plant cell from uncontrolled redox reactions affecting membrane functions, which, in turn, results in salt and drought tolerance. OsCPK4 shows great promise for genetic improvement of tolerance to abiotic stress in rice.
2014-07-03 | GSE52353 | GEO
Project description:Drought, salinity and sub-optimal temperatures are stresses that cause adverse effects on the growth of plants and the productivity of crops. In this study, we have analyzed the expression profiles of rice genes under control and abiotic stress conditions using microarray technology to identify the genes differentially expressed during various abiotic stresses. Keywords: Stress treatment
2007-05-17 | GSE6901 | GEO
Project description:The inbuilt mechanisms of plant survival have been exploited for improving tolerance to abiotic stresses. We have investigated the subcellular interactions of rice stress-associated proteins (SAPs) using yeast two-hybrid and FRET approaches and found that A20 domain mediates the interaction of OsSAP1 with self, its close homolog OsSAP11, and a rice receptor-like cytoplasmic kinase, OsRLCK253. Such interactions between OsSAP1/11 and with OsRLCK253 occur at nuclear membrane, plasma membrane and in nucleus. Functionally, both OsSAP11 and OsRLCK253 could improve the water-deficit and salt stress tolerance in transgenic Arabidopsis plants via a signaling pathway affecting the expression of several common endogenous genes. The yield in transgenic plants is also protected indicating the agronomic relevance of OsSAP11 and OsRLCK253 in conferring abiotic stress tolerance. Arabidopsis transgenic plants expressing rice genes OsSAP11 and OsRLCK253 were compared with untransformed plants at seedling level
2011-05-01 | E-GEOD-27861 | biostudies-arrayexpress
Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.
2021-12-20 | GSE167342 | GEO
Project description:Rice plants cultivated on mountain areas are frequently exposed to acid fog and natural fog events. In this report, we analyzed the expression profiles of the rice plant with acid fog (SiAF) or neutral fog (SiNF) treatment for 1 and 7 days. Microarray results suggested that ROS generation was induced by not only SiAF, but also SiNF treatment, and it occurred in apoplast, not in organelles. Genes for defense- and stress-responses was also induced by both SiAF and SiNF treatments. The induction occurred in plants treated with SiAF for both 1 day and 7 days, and it was also detected in plants treated with SiAF for 7 days. These results suggest that both SiAF and SiNF treatments are abiotic stresses accompanying ROS generation in apoplast.
2012-07-01 | GSE31196 | GEO