Transcriptome sequencing of the developing internode and ligular region of maize mutant Sdw3
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE127448 | GEO | 2020/07/08
REPOSITORIES: GEO
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Project description:Transcriptome sequencing of the developing internode and ligular region of maize mutant Sdw3
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Project description:The length of internodes is critical in determining the height of the castor plant (Ricinus communis L.), and is closely associated with internode elongation. However, the exact mechanisms underlying internode elongation, particularly in the main stem of the castor plant, remain uncertain. To investigate further, we conducted a study using the dwarf castor variety 071113, comparing it with the homologous high-stalk Zhuansihao as a control. Our research included cytological observation, physiological measurement, transcriptome sequencing, and metabolic determination. By integrating these findings, we discovered that the dwarf 071113 undergoes earlier main stem lignification development and has a more active lignin synthesis pathway in internode intermediate development. The plant hormone IAA also plays a role in this process. Furthermore, potential enzymes and regulators have been identified, including the auxin influx carrier AUX1 LAX, auxin response protein IAA13, ARF3, auxin-responsive protein SAUR50, peroxidase, and EXPs that regulate cell cycle, cell wall synthesis, as well as growth and development, were also. Based on these findings, we developed a model for castor internode elongation and gained a better understanding of the dwarfing mechanism of the 071113 variety. Our work lays a theoretical foundation for the future breeding of dwarf castor varieties.
2024-01-31 | GSE242985 | GEO
Project description:In order to investigate the gene expression profile related to rice internode growth under different nitrogen management practices, Agilent two color microarray chips were used to profile the differentially expressed genes of rice first internode between two nitrogen management. A rice cultivars Yin-Jing-Ruan-Zhan was used as material. First basal internode of YJRZ was taken at 30 days after transplanting, and RNA was extracted for microarray assay. Materials from OPT were label by Cy5 and FFP by Cy3.
2017-08-25 | GSE103063 | GEO
Project description:This study provides a comparison of gene expression in two tomato cultivars, Moneymaker and M82, focusing on first internode and its innermost cell type pith—under two light conditions: white light with far-red supplementation (WL+FR) and the control condition of white light (WL). The samples were harvested at four time points leading to the point where internode elongation could be measured in response to WL+FR. The timepoints were 6, 24, 30, and 48 hours after treatment initiation.
2024-02-29 | GSE255611 | GEO
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:Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2).
2012-02-12 | GSE35729 | GEO
Project description:An AGCVIII kinase (Dw2) regulates sorghum stem internode growth, but the underlying mechanism and signaling network are unknown. Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls. Phosphoproteomic analysis showed that Dw2 signaling influences the phosphorylation of proteins involved in lipid signaling (PLDδ), endomembrane trafficking, hormone, light and receptor signaling, and photosynthesis. Together
2020-11-20 | PXD020160 | Pride
Project description:Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2). Leaf tissues of 6-week-old LRK1 060615 transgenic rice and control 9311 rice (10 plants each) were selected.
2012-02-12 | E-GEOD-35729 | biostudies-arrayexpress
Project description:Plant growth regulators (PGRs) were commonly used in practical farming to restrict plant height and control lodging. Ethephon has been reported to shorten the internodes elongation and increase the harvestable grain yield of maize. In the present study, we characterized that internodes phenotypic responses to ethephon treatment induced should due to ethylene released inhibited the longitudinal growth of cells and promoted its the lateral growth. We used microarrays to detail the global programme of gene differentially expression underlying maize and identified distinct classes of up or down-regulated genes during this process.
2017-01-01 | GSE56062 | GEO
Project description:Subsequently to primary growth, most dicotyledonous plants undergo secondary growth leading to an increased diameter of growth axes. During secondary growth initiation in shoots, a cylindrical meristem, the vascular cambium, is established by the initiation of meristematic activity in interfascicular regions, a process that ultimately leads to the formation of a continuous cylinder of vascular tissue along the shoot axis. In Arabidopsis this happens in a reduced area at the very base of the stem. In this study, a transcriptional comparison between the base and the first internode has been performed in order to asses the physiological state of both sample types and search for potential key regulators of the process. Total RNA was extracted from the base and the first internode from stems of 15cm tall Arabidopsis plants (ecotype Col-0). After RNA amplification, Cy3 or Cy5 targets were produced. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap.
2010-06-05 | E-GEOD-15446 | biostudies-arrayexpress