Identification and Comparative Genomic Analysis of Cell Wall-Related Genes in Switchgrass

To gain genetic control of biomass yield and quality in bioenergy grasses, identification and characterization of grass-specific cell wall-related genes is needed. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has emerged as a promising bioenergy crop. To identify cell wall-related genes in switchgrass, we constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass. We organized 96,000 clones from these libraries into pools and superpools with 7X coverage and used quantitative PCR to screen for the gene sequences predicted to be involved in cell wall-related functions. Full length sequencing of selected 300 BACs resulted in identification of 385 genes implicated in cell wall biogenesis/degradation (210 glycosyl transferases, 115 glycoside hydrolases and 60 transporters) and more than 700 genes  (397 kinases and >300 TFs) with predicted roles in cell wall assembly and remodeling. Comparative phylogenetic analysis of GT2 family genes in switchgrass, rice and Arabidopsis revealed differences/similarities in family structure and evolution. We also compared the gene expression profiles of representative genes from GT2 family in five tissue types of switchgrass and rice. The data revealed similar expression patterns for most of the genes in equivalent tissues suggesting functional equivalence of orthologous sequences in rice and switchgrass. The resources generated in this effort will be useful for initiating functional characterization of candidate genes regulating cell wall composition in grasses.