Oryza sativa cultivar:Indica
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ABSTRACT:
PROVIDER: PRJNA643146 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:We used RNA-Seq to systematically investigate the global transcriptomes of rice which was inoculated with viruliferous SBPH, or inoculated with insect-derived RSV or plant-derived RSV by mechanical inoculation, and generated a useful resource for the immune reaction of rice in face of different kinds of RSV. The changes in the expression of candidate transcripts may provide valuable information for future studies on molecular mechanisms of rice stripe disease.
2015-10-18 | E-MTAB-5025 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.
2010-01-01 | GSE19050 | GEO
Project description:Comparative transcriptome analysis among closely related rice strains
2014-10-27 | E-MTAB-4280 | biostudies-arrayexpress
Project description:Rice plants exhibiting bacterial blight resistance at high temperature suppress abiotic response
| PRJNA377880 | ENA
Project description:Climate change is affecting the unprecedented drought scenario and frequent occurrence of pathogen infection in rice. Simultaneous occurrence of these stresses could lead to more crop loss. Transcription response of genes involved in combined stress would provide relevant candidate gene to develop climate resilient rice. We report individual drought, Xoo infection and combined stress on rice. RNA Seq of contrasting genotypes BPT5204 and TN1 has revealed many candidate genes. A meta-analysis further filtered out some candidate genes which could be used for breeding programme. Several genes identified were already characterized by other groups for individual stress condition. However the genes involved in drought and pathogen infection could be further used for genetic manipulation studies in future.
2022-06-16 | GSE197133 | GEO
Project description:The rice gene SUB1A-1 confers flooding tolerance restricting shoot growth during submergence. Rice with SUB1A also show more rapid recovery after submergence ends, but mechanisms by which SUB1A improves recovery from submergence had not been examined. In this study, the transcriptome was sequenced at five time points over a 24 hour submergence recovery period in near-isogenic rice genotypes with and without SUB1A.
2017-09-01 | GSE102494 | GEO
Project description:The impact of global warming on weather patterns raises concerns for agriculture management. Using NGS technologies, we identified the miRNA profile that is expressed in rice cultivar grown at two different temperatures. We observed 118 and 100 miRNAs uniquely expressed at 35°C and 25°C respectively. Potential targets of these miRNAs have been identified. An interesting example, would be mir1863b which targets Os07g46670.3; a homologue of the ERD15 gene in Arabidopsis which is involved in dehydration stress response.
2016-12-31 | GSE72160 | GEO
Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
2017-11-13 | PXD004870 | Pride