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

Abstract

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.

Unraveling Aspects of Bacillus amyloliquefaciens Mediated Enhanced Production of Rice under Biotic Stress of Rhizoctonia solani

“…Furthermore proteases from SN13 may be inducing nitrogen limitation for fungal partner and induce immune response as reported for proteases from pathogenic sources during sheath blight disease ( Suarez et al, 2005 ; Zheng et al, 2013 ). The observations clearly demonstrate role of SN13 in employing plants’ system to elicit defense that not only maintains the cell wall integrity but also resists pathogen invasion by degrading fungal cell wall polysaccharides, as evident earlier ( Nakano et al, 2013 ).…”

“…Controlled intracellular redox in SN13 + R. solani is in accordance to the down-regulation of defense responsive genes and enzymes. Down-regulation of NADPH oxidase family such as ferric reductase (Os08g35210), a key producer of ROS in SN13 + R. solani (0.5-fold) emphasizes relatively unstressed conditions ( Figure 6 ) as stated earlier ( Nakano et al, 2013 ). These cell wall interactions and elicitation lead to kinase mediated signaling, as evident by overexpression of serine-threonin protein kinase (Os01g66860) of MAPKinases (fivefold) and phospholipase D (by threefold in SN13 as compared to control) that functions in response to ROS accumulation.…”

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

“…Between Panel I and II, interestingly four locus (RM259, RM5633, RM1026 and RM5961) harboring five genes (LOC_Os01g13360, LOC_Os04g23030, LOC_Os04g23040, LOC_Os09g39320 and LOC_Os11g34070) were common and identified to be linked to key plant physiological production traits in rice. Gene expression analysis revealed the gene (LOC_Os01g09550) associated with SLA to be highly expressed in internode of rice dwarf mutant Fukei71 [ 83 ], treatment with gibberellin [ 84 ] and brassinosteroid [ 85 ]. The loci RM259 associated with chlorophyll content underlying gene, LOC_Os01g13360 was found to highly express in endosperm [ 86 ] and caryopsis [ 87 ].…”

Association Mapping of Drought Avoidance and Agronomic Traits in Rice (Oryza Sativa L.) Landraces with SSR Markers and Genotyping-By-Sequencing Approach

“…Between Panel I and II, interestingly four locus (RM259, RM5633, RM1026 and RM5961) harboring ve genes (LOC_Os01g13360, LOC_Os04g23030, LOC_Os04g23040, LOC_Os09g39320 and LOC_Os11g34070) were common and identi ed to be linked to key plant physiological production traits in rice. Gene expression analysis revealed the gene (LOC_Os01g09550) associated with SLA to be highly expressed in internode of rice dwarf mutant Fukei71 91 , treatment with gibberellin 92 and brassinosteroid 93 . The loci RM259 associated with chlorophyll content underlying gene, LOC_Os01g13360 was found to highly expressed in endosperm 94 and caryopsis 95 .…”