Oryza sativa
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-13735
PROVIDER: PRJNA110799 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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
2010-07-07 | GSE13735 | GEO
Project description:Expression data from rice stem bases in two different genotypes
| PRJNA309529 | ENA
Project description:Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.
2016-07-20 | PXD004603 | JPOST Repository
Project description:Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Keywords: stress response
2009-07-16 | GSE14403 | GEO
Project description:Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance.
2012-12-21 | GSE38023 | GEO
Project description:Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice (Oryza sativa L. ssp. japonica and indica) to drought stress at the late vegetative stage and harvested leaves for protein extraction and subsequent label-free shotgun proteomics. Gene ontology analysis revealed some differentially expressed proteins were induced by drought in all eight genotypes; we speculate that these play a universal role in drought tolerance. However, some highly genotype-specific patterns of response to drought suggest that some mechanisms of metabolic reprogramming are not universal. Such proteins had largely uncharacterized functions, making them biomarker candidates for drought tolerance screens.
2020-01-17 | PXD016150 | Pride
Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
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
2010-07-07 | E-GEOD-13735 | biostudies-arrayexpress
Project description:Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to observe the response of two wild rice species (Oryza barthii and O. glaberrima) and two O. sativa genotypes (cv. Nipponbare and f. spontanea) to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, chlorophyll concentration and fluorescence showed that the wild species present higher level of leaf damage, increased accumulation of H2O2 and lower photosynthetic capacity when compared to O. sativa genotypes under infested conditions. Infestation decreased tiller number, except in Nipponbare. Infestation also caused the death of wild plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa genotypes, the number of panicles per plant was affected only in f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) genotypes under control and infested conditions. O. barthii has a less abundant antioxidant arsenal and is unable to modulate proteins involved with general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes and energy production, suggesting that, under infested condition, the primary metabolism is maintained more active compared to O. barthii. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors. These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming increased tolerance to mite infestation.
2021-09-09 | PXD020940 | Pride