Ontology highlight
ABSTRACT:
PROVIDER: PRJNA770474 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16305200_1.fastq.gz | Fastqsanger.gz | |||
| SRR16305200_2.fastq.gz | Fastqsanger.gz | |||
| SRR16305300_1.fastq.gz | Fastqsanger.gz | |||
| SRR16305300_2.fastq.gz | Fastqsanger.gz | |||
| SRR16305201_1.fastq.gz | Fastqsanger.gz |
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Project description:This study aims to provide a transcriptomics dataset for field grown rice plants subjected to mild drought concentrating on the two parents of a mapping population, Bala and Azucena. Plants were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007. Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. The drought was imposed for 24 days during which time a small amount of water was added on 3 occasions to raise soil moisture to 30% by volume. After 24 days the second youngest fully expanded leaf was taken and gene expression analysis performed. We used microarrays to detail the global programme of gene expression underlying drought in rice plants with the aim of using the data to identify candidate genes for drought avoidance QTLs detected within the a rice mapping population.
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Project description:Leaf samples were used. We exposed young seedlings to NaCl and drought. Expression study in 24hrs salt and drought condition. Salt-sensitive and salt-tolerant strains of rice exposed to NaCl or control conditions. Drought-sensitive and drought-tolerant strains of rice exposed to drought or control conditions.
2011-12-31 | E-GEOD-21651 | 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
2012-05-01 | GSE5978 | GEO
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:The aim of the study was to identify candidate genes responsible for drought tolerance trait between a pair of wheat varieties ( WL711 and C306) and correspondng progeny bulks (10 drought susceptible RILs and 10 drought tolerant RILs) by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the flag leaves showed large number of differentially expressed genes. The number of differentially expressed genes was reduced to 37 on the basis of their occurance in a major QTL region (responcible for drought tolerance) detected in RIL population derived from WL711 and C306. RNA from the reproductive stage flag leaf of wheat in irrigated and drought condition of drought susceptible parent WL711, drought tolerant parent C306 and drought susceptible and drought tolerant RIL bulks were analysed in three different biological replications (A , B and C) making total twenty four samples
2012-04-29 | E-GEOD-30436 | biostudies-arrayexpress
Project description:In order to evaluate the genome differences and find the more tolerant cultivar, first eleven Malaysian rice cultivars namely, MR219, MR276, MR220, MR211, MR219-4, MR253, Q50, Q74, MR159, Masuri and MR263 were subjected under water deficit. Then, based on the morphological and physiological traits, the more drought-tolerant and -susceptible cultivars were screened and time-course gene expression profiling established by a comprehensive transcriptome database sequencing of the leaf RNA of tolerant rice. The current investigation provides pivotal data for understanding the rice drought tolerance mechanisms.
2017-07-27 | E-MTAB-5402 | biostudies-arrayexpress
Project description:This study aims to provide a transcriptomics dataset for field grown rice plants subjected to mild drought concentrating on the two parents of a mapping population, Bala and Azucena. Plants were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007. Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. The drought was imposed for 24 days during which time a small amount of water was added on 3 occasions to raise soil moisture to 30% by volume. After 24 days the second youngest fully expanded leaf was taken and gene expression analysis performed. We used microarrays to detail the global programme of gene expression underlying drought in rice plants with the aim of using the data to identify candidate genes for drought avoidance QTLs detected within the a rice mapping population. Two rice cultivars, Bala and Azucena, were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007. Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. At 2 pm on the 83rd day after sowing (after 24 days of drought) the second youngest fully expanded leaf was taken off three plants in two plots per block, the leaves had the top and bottom 4 cm removed and the central portion of the leaf was placed in a bag and then into liquid N2. For the controls there was only one plot of the genotypes per block. There was one bag for each block and three replicate blocks. A total of 6 droughted leaf samples (3 Bala and 3 Azucena) and six control leaf samples (3 Bala and 3 Azucena) were collected for RNA extraction and hybridization on Affymetrix microarrays.
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Project description:An indica rice cultivar FR13A, is widely grown as submergence tolerant variety and can withstand submergence up to two weeks. The tolerance is governed by a major QTL on chromosome 9 and represented as sub1. Recently the gene for sub1 has been mapped and cloned. However, the trait is governed by several QTLs and not by a single gene. To understand the mechanism of submergence 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 submerged conditions at seedling stage. SUBMITTER_CITATION: Combining In Silico Mapping and Arraying: an Approach to Identifying Common Candidate Genes for Submergence Tolerance and Resistance to Bacterial Leaf Blight in Rice. Mol. Cells 2007 24:394-408. Experiment Overall Design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during submergence treatment. We used two contrasting rice genotypes (FR13A tolerant and IR24 susceptible) differing in submergence response. Plants were grown in growth chambers and treated by submerging the plants in transparent polythene bags on14th DAS. Leaf 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.
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Project description:Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403. We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.
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