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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cytosolic glutathione reductase (OsGR2) regulates plant development and salt stress tolerance in rice

ABSTRACT: Rice genome contains three genes that encode for glutathione reductase (GR) viz., OsGR1, 2 and 3. GR is an important component of the anti-oxidative machinery of plant cells. GR2 down-regulated plants were produced by RNAi mediated down-regulation of GR2 (GR2-Ri). GR2-Ri plants were significantly smaller and have significantly lower grain yield (grain number per panicle) compared to WT(Wild type), under control conditions. RNA-Seq analysis of panicles (differentiation stage) identified genes known to affect grain size to be differentially regulated in GR2-Ri compared to WT, respectively, under control conditions.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Oryza sativa

SUBMITTER: Chwan-Yang Hong

PROVIDER: E-MTAB-7172 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cytosolic glutathione reductase (OsGR2) regulates plant development and salt stress tolerance in rice

Project description:Rice genome contains three genes that encode for glutathione reductase (GR) viz., OsGR1, 2 and 3. GR is an important component of the anti-oxidative machinery of plant cells. GR2 down-regulated plants were produced by RNAi mediated down-regulation of GR2 (GR2-Ri). GR2-Ri plants were significantly smaller /reduced plant height compared to WT(Wild type), under control conditions. Microarray analysis was carried out to identify the genes which are differentially regulated in GR2-Ri compared to WT, respectively, under control conditions.

2024-08-30 | E-MTAB-7171 | biostudies-arrayexpress

SWATH-MS quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling

Project description:Modern rice cultivars have large panicle, however, yield potential of these cultivars is often not fully achieved due to the poor grain-filling of their late-flowering inferior spikelets (IS). Our earlier work suggests broad transcriptional reprogramming during grain filling and shows a difference in gene expression between IS and the earlier-flowering superior spikelets (SS). However, the links between the abundance of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied between SS and IS. A total of 304 proteins, ranging from cellular components to biological processes, were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundance of most of the differentially expressed proteins is not correlated to the transcript levels, indicating an extra layer of gene regulation which may exist during rice grain filling. These findings raise an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

2017-07-03 | PXD005401 | Pride

Unravelling the proteomic profile of rice meiocytes during early meiosis

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Gene expression profiling in leaf and panicles of non-transgenic and HMB4 over-expression line.

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2014-09-01 | E-GEOD-55984 | biostudies-arrayexpress

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Transcription profiling of barley maturing and germinating grains

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2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress

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2022-02-23 | PXD006883 | Pride

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

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2011-12-21 | E-MTAB-2037 | biostudies-arrayexpress

Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

Project description:Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation with current criteria of about 400 annotated miRNAs and the finding that among these, about 150 had siRNA-like characteristics. Seventy nine new miRNAs were identified and miRNAs were distinguished that are regulated in response to water stress, nutrient stress, or temperature stress. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be controlled in the panicle. This high resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae. Examination of different tissue types and tissues treated with various environmental and nutrient stresses in rice by high throughput sequencing for small RNA profiling

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