Identification and Analysis of Cell Wall/Stress-Related Genes in Switchgrass

To facilitate assembly of the switchgrass genome, we constructed two Bacterial Artificial Chromosome (BAC) libraries from the AP13 clone. We are using these BAC clones to identify genes critical for cell wall biosynthesis and modification. Because of the sequence conservation and syntenic relationship between rice and switchgrass, the knowledge gained in rice can be used to identify candidate genes in switchgrass. We screened 96,000 BAC clones with a QPCR-based strategy to identify switchgrass homologs of rice genes predicted to be involved in cell wall-related functions.

In collaboration with JGI, we have fully sequenced 310 BAC clones containing 385 genes implicated in cell wall biogenesis/degradation (glycosyl transferases, glycoside hydrolases and transporters) and more than 700 genes  (kinases and TFs) with predicted roles in cell wall assembly and remodeling. Most of the genes seem to have conserved gene order in both plant species. We have carried out a comparative phylogenetic analysis of the Glycosyl transferase 2 (GT2) family of genes, encoding cellulose synthases, in switchgrass, foxtail millet, maize, sorghum rice and Arabidopsis. Comparison of the gene expression profiles of representative genes from GT2 family among five tissue types of rice and switchgrass revealed conservation and diversification of gene expression patterns in grasses.Some of the cellulose synthase-like F (CslF) genes, involved in synthesis of mixed-linkage glucans in grasses, are conserved in gene order in both the grass genomes. Six CslF genes localize to a 118 Kb region on rice chromosome 7 and the corresponding 191 Kb region in switchgrass. Further characterization of this region is in progress.