Rice fungal microbiota
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ABSTRACT:
PROVIDER: PRJEB22764 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Plant host habitat and root exudates shape fungal diversity
| PRJEB25120 | ENA
Project description:Plant host habitat and root exudates shape fungal diversity
| PRJEB25017 | ENA
Project description:Rice root fungal metagenome Raw sequence reads
| PRJNA810017 | ENA
Project description:In this research, an array of 27,448 rice genes was used to elucidate gene expression in air-dried rice seedlings (lead and root) at various periods of treatment times. The analyses show that rice responds to drought stress mainly by down-regulating many biological processes including gene expression and regulation, protein phosphorylation, and cellular metabolism. Among strategies to actively adapt to drought, most significant are inducing protective molecules, which may be differentially regulated based on plant organs.
2012-09-21 | GSE38130 | GEO
Project description:In this research, an array of 27,448 rice genes was used to elucidate gene expression in air-dried rice seedlings (lead and root) at various periods of treatment times. The analyses show that rice responds to drought stress mainly by down-regulating many biological processes including gene expression and regulation, protein phosphorylation, and cellular metabolism. Among strategies to actively adapt to drought, most significant are inducing protective molecules, which may be differentially regulated based on plant organs. A total of 20 chips was used for the microarray analysis. Total RNAs were extracted from leaf and root of rice seedlings that had undergone 0-12 hrs acute drought. Experiments were duplicated. The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.dna.affrc.go.jp/).
2012-09-21 | E-GEOD-38130 | biostudies-arrayexpress
Project description:In order to understand the mechanisms of Drought induced susceptibility (DIS) we’ve conducted a dual RNAseq experiment on rice infected tissues by Magnaporthe oryzae. At 4 days post inoculation tissues have been collected on mock inoculated and M. oryzae inoculated plants. Rice were conducted under two type of water regime: DIS Drought during three days before inoculation, NoDIS no drought before inoculation. RNAseq was conducted both on rice and fungal RNA.
2016-10-01 | GSE84800 | GEO
Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.
2010-12-23 | GSE26280 | GEO
Project description:Plant responses to drought stress require the regulation of transcriptional networks via drought responsive transcription factors, which mediate a range of morphological and physiological changes. AP2/ERF transcription factors are known to act as key regulators of drought resistance transcriptional networks; however, little is known about the associated molecular mechanisms that give rise to specific morphological and physiological adaptations. In this study, we functionally characterized the rice (Oryza sativa) drought responsive AP2/ERF transcription factor, OsERF71, which is predominantly expressed in the root meristem, pericycle, and endodermis. Overexpression of OsERF71 either throughout the entire plant or specifically in roots, resulted in a drought resistance phenotype at the vegetative growth stage, indicating that overexpression in roots was sufficient to confer drought resistance. The root specific overexpression was more effective in conferring drought resistance at the reproductive stage, such that grain yield was increased by 23-42% over wild type plants or whole-body overexpressing transgenic lines under drought conditions. OsERF71 overexpression in roots elevated the expression levels of genes related to cell wall loosening and lignin biosynthetic genes, which correlated with changes in root structure, the formation of enlarged aerenchyma and high lignification levels. Furthermore, OsERF71 was found to directly bind to the promoter of OsCCR1, a key gene in lignin biosynthesis. These results indicate that the OsERF71-mediated drought resistance pathway recruits factors involved in cell wall modification to enable root morphological adaptations, thereby providing a mechanism for enhancing drought resistance.
2016-09-30 | GSE81325 | GEO
Project description:Magnaporthe oryzae causes rice blast, the most devastating foliar fungal disease of cultivated rice. During disease development the fungus simultaneously maintains both biotrophic and necrotrophic growth corresponding to a hemi-biotrophic life style. The ability of M. oryzae to also colonize roots and subsequently develop blast symptoms on aerial tissue has been recognized. The fungal root infection strategy and the respective host responses are currently unknown. Global temporal expression analysis suggested a purely biotrophic infection process reflected by the rapid induction of defense response-associated genes at the early stage of root invasion and subsequent repression coinciding with the onset of intracellular fungal growth. The same group of down-regulated defense genes was increasingly induced upon leaf infection by M. oryzae where symptom development occurs shortly post tissue penetration. Our molecular analysis therefore demonstrates the existence of fundamentally different tissue-specific fungal infection strategies and provides the basis for enhancing our understanding of the pathogen life style. Experiment Overall Design: We investigated global transcriptome response overtime of Mock- and M. oryzae inoculated rice root tissue in vitro. Two independant replicates were perfomed for each treatments and samples were collected at 2, 4 and 6 days post-inoculation.
2009-10-09 | E-GEOD-18361 | biostudies-arrayexpress
Project description:Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. The direct target genes were related to transmembrane/transporter activity, vesicle, plant hormone, carbohydrate metabolism, and transcription factors. The direct targets of each OsNAC are in a range of 4.0 to 8.7% of the genes up-regulated in RNA-Seq data sets. Thus, each OsNAC up-regulates of corresponding direct target genes that alters root system architectures of RCc3:OsNACs for drought tolerance. Our results provide valuable resources for functional dissection of the molecular mechanisms for plant drought tolerance.
2018-02-14 | GSE102920 | GEO