Genomics and Genetics of Switchgrass Cell Wall Quality

Utilization of second-generation biofuels from biomass of low-input, perennial crops such as switchgrass (Panicum virgatum L.) has potential to reduce greenhouse gas emissions from transportation. The availability of a partially assembled draft switchgrass genome has opened the toolbox of genomic methods toward improving bioenergy-relevant traits of switchgrass.  Among traits requiring improvement is the ease with which switchgrass biomass, mostly consisting of secondary cell walls, can be degraded by enzymes during biochemical conversion to biofuels. Toward understanding and improve the quality of secondary cell walls (SCWs) for enzymatic digestion, we are using phylogenomics, gene expression, and genome-wide association analyses. Several Arabidopsis R2R3 MYB transcription factors regulate SCW gene expression. Phylogenetic analysis of R2R3 MYB proteins from grass and dicot genomes suggests that grasses utilize similar SCW regulators as dicots based on phylogenetic and gene expression conservation. Furthermore, several unstudied MYBs from clades with more members in grasses than in dicots exhibit expression patterns similar to MYBs that regulate SCWs. Consistent with a role in SCW regulation, transcripts for a subset of these proteins are differentially regulated according to RNA Seq results contrasting enzymatically recalcitrant and degradable switchgrass genotypes. In addition, the RNA Seq dataset also reveals differentially regulated genes in a genomic interval associated with enzymatic glucose release. These analyses reveal novel targets for use as markers in genetic improvement of switchgrass and for further study via reverse genetics toward better understanding the complex trait of enzymatic digestibility in grasses for biofuel production.