Gene Expression vs. Cell Wall Composition Correlations Vary Dramatically Among Switchgrass Genotypes

Efficient conversion of lignocellulosic biomass, such as that of switchgrass, into “second-generation” biofuels is influenced by the biomass' composition and structure. In grasses, lignin and other phenylpropanoids, such as p-coumaric acid (p-CA) and ferulic acid, reduce cell wall sugar accessibility hampering biochemical fuel synthesis. Transgenic silencing of lignin biosynthesis enzymes and regulators improves cell wall digestibility; however, questions remain as to the relative contribution of different molecular players in controlling biomass content. In this study, we characterized cell wall parameters and lignin biosynthesis gene expression in three switchgrass genotypes (AP13, A4, and VS16) for tillers at three developmental stages (V3, E4, and R3) and for the E4 stage, three segments (S1-S3). The genotypes have similar patterns of cell wall content across development but distinct gene expression. Correlation analysis between gene expression and components reveals that comparing expression at stage N to cell wall content at stage N+1, abolishes many unexpected correlations between sugar content and lignin gene expression compared with N vs. N comparisons. For the whole data set, expression in the Nth stage of “COMT3” is most highly correlated with lignin and p-CA in the N+1th stage. Still, gene-component correlation patterns for each genotype are distinct, and in some cases opposite in different genotypes. This may be due to the complexity of functions of cell walls, expansion of biosynthesis gene families in tetraploid switchgrass, and multiple layers of regulation. Moreover, approaches for improving biomass content in switchgrass that rely on gene silencing may not be generalizable across genotypes.