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Gene expression profile related to rice internode growth under two nitrogen management practices

ABSTRACT: 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.

ORGANISM(S): Oryza sativa

PROVIDER: GSE103063 | GEO | 2017/08/25

SECONDARY ACCESSION(S): PRJNA400066

REPOSITORIES: GEO

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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.

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Gene expression profile related to rice internode growth under two nitrogen management practices

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