Globle Profiling Of Gene Expression Patterns Involved In Rice Cell Wall Network Formatons And Analysis Of 4CL Gene Evolution

Plant cell walls are important compartments in planct cells, which represent the most abundant renewable biomass on the earth. Plant cell walls are mainly composed of cellulose, hemicelluloses and lignin. Despite cellulose synthase (CESA) and cellulose synthase-like(CSL) gene superfamily have been identified in plants, much remains unknown about those gene functions involved in cellulose and hemicellulose syntheses and modification, as well their biological roles in plant growth and development.As plant cell walls are complex structures that full-fill many diverse functions during plant growth and development, it is not surprising about thousands of genes involved in cell wall synthesis and maintenance. Of those genes,4-coumarate:coenzyme A ligase (4CLs) are the key enzymes involved in general phenylpropanoid metabolism by providing the precursors for both lignin and flavonoids biosynthesis.In this Ph.D. dissertion, therefore, I completed three major experiments and the results were described below:(1) A total of 45 identified members of OsCESA/CSL were classified into two clusters based on phylogeny and motif constitution. Duplication events contributed largely to the expansion of this superfamily. Using microarray data of 33 tissue samples covering the entire life cycle of rice, it has been observed about fairly high OsCESA gene expression and rather variable OsCSL expression. Furthermore, functions of OsCESA/CSL were investigated using an integrated approach comprised of phylogeny, transcriptional profiling and co-expression analyses, which provideds useful clues on CESA/CSL potentially functional complements and associations with cell wall synthesis in higher plants.(2) An integrated genomic and metabolomic framework was constructed for cell wall biology in rice. A weighted gene co-expression network was initially created from publicly available datasets, and a comprehensive cell wall dataset was then obtained by determining cell wall compositions from 29 tissues covering the whole life cycle of rice. It confirmed primary and secondary wall cellulose biosynthesis modules and the co-expressed modules that were strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. The results extended the typical co-expression approach to provide insights into cell wall biology in rice and beyond.(3) 4CLs sequence variation patterns were observed in phylogenetic framework to elucidate the evolutionary forces that lead to functional divergence. The results indicated that lignin-biosynthetic 4CLs are under positive selection. Functional divergence caused by positive selection occurs after speciation events of monocots and dicots. Most of the positively selected sites are located in substrate binding pocket and catalytic centers, suggesting that the nonsynonymous substitutions might contribute to the functional evolution of 4CL for lignin biosynthesis.