Transcription profiling identifies candidate genes for secondary cell wall formation and hydroxycinnamoyl- arabinoxylan biosynthesis in the rice internode

Microarray analysis was used to identify candidate genes that are involved in the formation of secondary cell walls and hydroxycinnamoyl-arabinoxylan (AX) in rice. In order to identify genes involved in secondary cell wall formation, gene expression was compared between wild-type whole internodes that contain cells with thickened secondary cell walls, such as vascular and cortical fiber cells, and wild-type internode parenchyma cells without secondary cell walls. In addition, gene expression was compared between the internode parenchyma of Fukei71 (F71), a rice dwarf mutant that accumulates large amounts of hydroxycinnamoyl-AX in pith parenchyma cells, and wild-type pith parenchyma cells to identify hydroxycinnamoyl-AX-related genes. To address the significant expression of candidate genes, gene lists were prepared for the phenylpropanoid pathway, major carbon metabolism, and cell wall biosynthesis, which is a useful platform to analyze cell wall formation in rice. The data indicated that a number of rice genes are potentially associated with secondary cell wall formation, such as the up-regulation of genes encoding cellulose synthase subunit A and ferulate 5-hydroxylase in wild-type whole internodes. Similarly, for hydroxycinnamoyl-AX synthesis, the expression of several genes changed, such as the downregulation of genes encoding cinnamoyl-CoA reductase and the up-regulation of the phosphoenolpyruvate carboxykinase gene in F71 pith parenchyma.