Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27315377_1.fastq.gz | Fastqsanger.gz | |||
| SRR27315377_2.fastq.gz | Fastqsanger.gz | |||
| SRR27315378_1.fastq.gz | Fastqsanger.gz | |||
| SRR27315378_2.fastq.gz | Fastqsanger.gz | |||
| SRR27315379_1.fastq.gz | Fastqsanger.gz |
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Project description:To gain more insight into cellular responses to mercury, we have undertaken a large-scale analysis of the rice transcriptome during mercury stress.More transcripts were responsive to mercury during short (pooled from 1- and 3-h treatments) , as compared to long (24 h) exposures. After short exposures, these induced genes can be divided into different functional categories, mainly on the basis of cell wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response. Molecular mechanisms for the mercury toxicity in rice roots.
2014-05-28 | GSE41719 | GEO
Project description:To gain more insight into cellular responses to mercury, we have undertaken a large-scale analysis of the rice transcriptome during mercury stress.More transcripts were responsive to mercury during short (pooled from 1- and 3-h treatments) , as compared to long (24 h) exposures. After short exposures, these induced genes can be divided into different functional categories, mainly on the basis of cell wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response. Molecular mechanisms for the mercury toxicity in rice roots. Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 25mM Hg during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 Hg-treated replicates (short and long exposures).
2014-05-28 | E-GEOD-41719 | biostudies-arrayexpress
Project description:Endophytic fungi are fungi that live inside the roots of plants. They can promote plant growth through a variety of direct and indirect mechanisms. Direct mechanisms include the production of phytohormones, such as auxin and gibberellins, which can stimulate plant growth. Endophytic fungi can also fix nitrogen, solubilize phosphate, and produce siderophores, which are compounds that chelate iron and make it available to plants. In addition, some endophytic fungi produce antimicrobial metabolites that can protect plants from pests and pathogens. Indirect mechanisms include the induction of systemic resistance, which is a plant's ability to defend itself against pests and pathogens. Endophytic fungi can also help plants to tolerate abiotic stresses, such as drought, salinity, and heavy metals. In this study, we used a proteomic approach to identify the proteins that are expressed in rice plants after they are treated with endophytic fungi. We found that the treatment with endophytic fungi resulted in the expression of a number of proteins involved in plant growth, stress response, and defense. These results suggest that endophytic fungi can promote plant growth and improve plant resilience to stress.
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Project description:Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. AM-regulated DEGs in cell wall modification and peroxidases categories were mainly upregulated in shoots, suggesting AM symbiosis might assist in relaxing the cell wall and scavenging reactive oxygen species (ROS). AM symbiosis indeed improved ROS scavenging capacity in rice shoots under salt stress. In addition, genes involved in Calvin cycle and terpenoid synthesis were enhanced by AM symbiosis in shoots and roots under salt stress, respectively. AM-upregulated cation transporters and aquaporin in both shoots and roots were highlighted. Strikingly, “protein tyrosine kinase activity” subcategory was the most significantly over-represented GO term among all AM-upregulated and downregulated DEGs in both shoots and roots, highlighting the importance of kinase on AM-enhanced salinity tolerance. Overall, our results from the transcriptomic analyses indicate that AM symbiosis uses a multipronged approach to help plants achieve salt stress tolerance.
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Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
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Project description:Salt Stress response of salt-tolerant genotype FL478 compared to IR29 Rice GeneChip was used to find differential expression between two rice genotypes under control and salt stress conditions Keywords: genotype and treatment comparison Roots (tips) tissue was used for hybridization to GeneChips
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Project description:The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64), but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.
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Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
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