Transcriptomes of Rice internode before and after heading
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE51289 | GEO | 2013/10/01
SECONDARY ACCESSION(S): PRJNA222318
REPOSITORIES: GEO
Similar Datasets
Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur. Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].
2013-10-01 | E-GEOD-51289 | biostudies-arrayexpress
Project description:Stem internodes of grasses function in mechanical support, transport, and, in some species are a major sink organ for carbon in the form of cell wall polymers. To establish the rice elongating internode as a model for secondary cell wall development, we conducted cell wall composition, proteomic and metabolomic analyses of the second rice internode at booting stage. We measured major secondary cell wall components along eight segments of an elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material from the younger to the older internode segments, indicating active cell wall synthesis. With the whole elongating internode, we measured peptides via liquid-chromatography mass spectrometry (LC-MS) following trypsin digestion of size fractionated proteins. This identified a total of 3249 protein groups with at least two unique peptides, including many glycosyltransferases, acyltransferases, glycohyrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. In addition, GO over-representation analysis and KO pathway analysis indicate many proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids, flavonoids, and tepenoids. Therefore, we also used LC-MS to measure methanol-extracted secondary metabolites from the whole internode at the elongation stage and three post-elongation stages, and from leaf and root at the second post-elongation stage. The results indicate secondary metabolites in stems are distinct from those of roots and leaves, and show different profiles during stem development. This study fills a void of knowledge of proteomics and metabolomics data for grass stems, especially of rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes during internode development. This and future work is aimed at optimizing stem development and cell wall composition of grasses to improve agronomic properties and biofuel production.
2017-08-04 | PXD003676 | Pride
Project description:The resveratrol-producing rice (Oryza sativa L.) inbred line, Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in leaves and seeds. Especially, ultra-performance liquid chromatography (UPLC) analysis revealed that the biosynthesis of piceid reached peak levels at 20 days after heading (DAH) seeds. To investigate endogenous piceid biosynthesis genes (UGTs), total RNA samples of 20 DAH seeds was used for RNA-seq.
2020-12-20 | E-MTAB-9695 | biostudies-arrayexpress
Project description:We report transcriptome profiling of elongating and non-elongating peduncles of rice in two Indian cultivars, Swarna and Pokkali at the time of heading. Sequencing of twelve libraries (three replicates from each stage) yielded >6.9 billion paired-end reads.
2020-12-22 | GSE157727 | GEO
Project description:For gene expression analysis, RNA-seq was performed in seeds of Dongjin (white rice), Heukseol (black rice) and Jeokjinju (red rice) at 20 days after heading
2023-03-24 | E-MTAB-9993 | biostudies-arrayexpress
Project description:Flowering of several plant species is induced by exposure to specific photoperiods that promote the expression of florigenic proteins in the leaves and their subsequent translocation to the shoot apex, where they commit the meristem to a reproductive fate. Transition to reproductive growth at the apex is often accompanied by stem elongation, to expose flowers above the leaves and facilitate fertilization. However, how growth and inflorescence formation are coupled and how photoperiodic signals coordinate these processes at the apex is still unclear. We studied these mechanisms in rice, a short day plant. Here, we show that HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), encoding components of the rice florigenic signal, are sufficient to repress expression of PREMATURE INTERNODE ELONGATION 1 (PINE1) at the shoot apex during the transition to flowering, thus promoting culm elongation. PINE1 encodes a nuclear C2H2 zinc finger transcriptional repressor that controls the mRNA abundance of GA3ox2, a gibberellin (GA) biosynthetic gene. These data uncover the existence of a regulatory network coordinating multiple aspects of phase transition, and indicate that GA-induced growth and activity of florigenic proteins at the shoot apex need to be strictly coupled.
2018-11-30 | GSE90493 | GEO
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation.
2022-11-21 | E-NASC-15 | biostudies-arrayexpress
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Experiment Overall Design: 6 samples
2008-06-14 | E-GEOD-6148 | biostudies-arrayexpress
Project description:Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice.
2014-02-05 | GSE49020 | GEO
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Keywords: time_series_design; compound_treatment_design
2007-01-22 | GSE6148 | GEO