Project description:To reveal the underlying molecular mechanism of Gif1 action in the control of grain filling and yield improvement, we performed transcriptional profiling of wild type Zhonghua11 and mutant gif1 plants in early filling stage on a global scale using the Affymetrix GeneChip Rice Genome Array Keywords: Filling stage

2007-11-02 | GSE9498 | GEO

Global gene expression profiles of Oryza sativa wild type Nipponbare and mutant coi1-13

Project description:To reveal the underlying molecular mechanism of jasmonate inhibits gibberellins signaling in rice, we performed transcriptional profiling of wild type nipponbare and mutant coi1-13 plants on a global scale using the Affymetrix GeneChip Rice Genome Array Rice young uppermost internodes were harvested and three biological repeats were performed on Nippombare (wild-type) and coi1-13 (mutant), respectively.

2011-12-01 | E-GEOD-29577 | biostudies-arrayexpress

Expression data from Oryza sativa and Arabidopsis thaliana

Project description:The goal of this work is to identify the gene regulatory hubs that control nitrogen-use in Oryza sativa, one of the most important crop plants, by using a combination of genomics, bioinformatics and systems biology approaches. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of N and L treatment conditions. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide. We also study the interspecies conservation, comparing rice with Arabidopsis thaliana nitrogen transcriptomes, to help identify conserved nitrogen regulation.

2015-06-10 | E-GEOD-38102 | biostudies-arrayexpress

Oryza sativa strain:Zhonghua11 Transcriptome or Gene expression

Project description:In the current study, we characterized an miRNA, OsmiR397, which was found to be associated with increased grain size, more rice panicle branching and higher grain productivity. We also elucidated the molecular mechanisms by which OsmiR397 increased grain yield. This miRNA downregulated the expression of its target gene, OsLAC, which then affected the sensitivity of plants to brassinosteroids. These results should be useful for breeding high-yield crops through genetic engineering. We performed RNA-seq on the young panicles of the wild-type, OXmiR397b and OXLAC plants and found that lots of brassinosteroid-related genes were differentially expressed between the three samples

2013-07-17 | E-MTAB-4429 | biostudies-arrayexpress

Global tanscriptome analysis in Oryza sativa identifies genes regulated by copper in the medium

Project description:Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. Different iron-related genes are expressed under either copper deficiency and excess, such as those that encode ferredoxin and transcriptional regulator IRON-RELATED TRANSCRIPTION FACTOR 2 (OsIRO2), respectively. As expected, the expression of OsCOPT1, which encodes a high affinity copper transport protein, was up-regulated under copper deficiency, and the expression of OsIRO2 targets were increased under copper excess. Arabidopsis COPT1 overexpression (C1OE) in rice causes root shortening under copper excess, modifies the expression of the putative Fe-sensing factor HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE- AND ZINC-FINGER (OsHRZ1) and enhances the expression of OsIRO2 and its targets, which suggests a role of copper in iron signaling. Our studies conducted under simultaneous copper and iron deficiencies indicate that C1OE plants are more sensitive than the wild-type controls to root growth inhibition. The C1OE rice plants grown on soil contained higher endogenous iron concentration in grains than the wild-type plants (both brown and white grains). The results obtained herein showed the interaction between homeostatic networks of iron and copper, and suggest that strategies to obtain crops with optimized nutrient concentrations in edible parts should take into account this interaction.

2017-06-20 | GSE89109 | GEO

Oryza sativa extracellular vesicles proteins

Project description:Cross-kingdom molecular exchange between hosts and interacting microbes is essential for the survival of both plants and their pathogens. Recent studies showed plants transfer their small RNAs (sRNAs) and massager RNAs (mRNAs) into fungal pathogens to suppress infection. However, whether and how plants send defense proteins into pathogen cells remains unknown. Here, we show that rice plants send defense proteins into the fungal pathogen Rhizoctonia solani via extracellular vesicles (EVs). These vesicles enrich host defense proteins and are taken up by the fungal cells. Reducing EV-mediated host protein transfer leads to increased disease susceptibility. Thus, plants send defense proteins via EVs into fungal pathogens to combat infection, providing a mechanism of protein exchange between plants and pathogens that helps reduce crop disease.

2025-01-06 | PXD048458 | Pride

Eschericha coli proteomics with Tanaka and Tachikawa

Project description:Relative comparison of Escherichia coli proteome between wild-type and pta mutant

2021-06-21 | PXD020753 | JPOST Repository