Oryza sativa Indica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401749 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6005570.fastq.gz | Fastqsanger.gz | |||
| SRR6005569.fastq.gz | Fastqsanger.gz |
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Project description:Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).
2017-09-06 | GSE103480 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold 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 OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress
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: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.
2008-06-14 | E-GEOD-6362 | biostudies-arrayexpress
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. Keywords: Mechanism of submergence tolerance
2007-11-24 | GSE6362 | 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 cold 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 OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed
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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. Keywords: Mechanism of salt tolerance
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Project description:Purpose: The chloroplast DNA has not been primiarly analyzed in rice plants before. Hence, the objective of this study is to analyze and compare the differential methylation of chloroplast DNA in MR219 indica rice across different tissues and different developmental stages. Methods: We prepared a total of nine sodium bisulfite treated DNA libraries from three developing grain tissues, three leaf tissues at ripening stage and three leaf tissues at vegetative stage and sequenced them in Illumina Miseq platform. We performed quality trimming, alignment followed by methylation calling and differential methylation analysis using Trimmomatic v36, Bismark v16.3 and SeqMonk v40.0 on the sequencing data obtained. Statistical analysis was carried out in SeqMonk software and further validated in SPSS statistical software v22.2. Results: With an optimized data analysis workflow, we mapped around average of 26000 reads to chloroplast genome. Differential CpG and CHG methylation in SeqMonk v40.0 revealed that MR219 chloroplast DNA is differentially methylated in grain and leaf tissues and across vegetative stage and ripening stage in the leaf tissues. Chloroplast DNA from leaf at ripening stage was most methylated, followed by grain tissue and lastly leaf tissue from vegetative stage. Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated.
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Project description:Transcriptome profiling for drought tolerant and susceptible cultivars of indica rice
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Project description:Expression data for heat tolerant and susceptible cultivars of indica rice
| PRJNA177813 | ENA