R code used in "Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species"

Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, particularly in the temperate regions. This study was conducted to elucidate physiological and molecular responses of four Miscanthus genotypes species subjected to well-watered and droughted greenhouse conditions. A significant biomass loss was observed under drought conditions for all genotypes. A sterile M. x giganteus, hybrid showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under well-watered conditions, biomass yield was as good as or better than control conditions in all species tested. M. sinensis was more tolerant than M. sacchariflorus in both water stress conditions. 4,389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed among four Miscanthus species. Most of the genes were differentially expressed in a single species, but the enrichment analysis of gene ontology (GO) terms revealed that the same biological processes were regulated in all the species during stress conditions. Namely, downregulated differentially expressed genes were significantly involved in protein modification and kinase activity, cell receptor signalling and ion binding; while upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes. Twelve aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. On the other hand, downregulated differentially expressed genes were significantly involved in protein kinase activity, cell receptor signalling and phosphorylation. Candidate genes with roles in these functional categories were identified in Miscanthus. This study provides the first transcriptome data on the induction of drought-related gene expression across a range of three Miscanthus species.