Discovering the sRNA-mRNA Regulatory Networks In Perennial Grasses for Bioenergy.

Discovering the molecular mechanisms controlling biomass traits could accelerate the development of sustainable bioenergy from feedstock grasses. Small RNA (sRNA) plays crucial roles in the regulation of plant genes  important in development, responses to stress, and genome evolution. Regulatory networks of sRNAs and mRNAs are known to control plant development and thus the quality and quantity of biomass, as well as other traits such as perenniality. We have investigated these networks in three potential bioenergy crop speciess: Miscanthus, switchgrass, and prairie cordgrass. We used high-throughput sequencing technology to sequence and profile mRNA, sRNA, and cleaved mRNA (degradome) from multiple developmental tissues and organs of the feedstock grasses. By applying this approach to Miscantus X giganteus (Mxg), we predicted 120 new miRNA families and identified 61 orthologs of previously annotated miRNAs. We predicted 824 miRNA-mRNA interactions, of which 265 were also validated by sequencing the cleaved mRNA products .  In addition to confirming many previously identified miRNA-mRNA interactions from other model plant systems, we documented novel interactions that include several mRNAs that were cleaved by multiple miRNAs. The majority of the newly discovered miRNAs from Mxg showed peak expression in the inflorescence and rhizome tissues, potentially implicating them in the regulation of perennial growth. Similarly, we identified miRNAs regulating genes associated with cell wall synthesisduring stem development. Integrated sRNA, mRNA, and degradome sequencing experiments are underway for switchgrass and prairie cordgrass. Our results suggest that miRNAs regulate the expression of genes that control biomass deposition and the perennial habit of Mxg.