Drought Response Time Course in Two Genotypes of Switchgrass (Panicum virgatum)

Switchgrass (Panicum virgatum) is a target lignocellulosic biofuel species in part due to its drought tolerance. Nonetheless, drought tolerance still varies greatly between switchgrass genotypes. Relatively little is known about changes in gene expression in response to drought in tolerant and susceptible switchgrass genotypes. With this motivation, we grew switchgrass lines Alamo (tolerant) and Dacotah (susceptible) in pots in a greenhouse and subjected plants to increasingly stringent water deprivation over 30 days. Leaf samples were collected at 6, 12, 18, 24 and 30 days, and RNA was extracted and sequenced. While ~12,000 genes were found to be statistically significantly differentially expressed between Alamo and Dacotah, the expression of ~2,500 genes demonstrated a genotype x treatment (GxE) interaction. The genes with significant GxE interactions were subjected to coexpression analysis that identified 11 modules of genes with similar expression patterns. GO analysis indentified modules enriched for genes involved in photosynthesis, signal transduction, phosphorylation and RNA processing/modification. Alamo and Dacotah switchgrass are tetraploids, and the recent annotation of the switchgrass genome has identified the constituent subgenomes (K and N) of the Alamo reference genome. We performed synteny analysis on the two subgenomes and found ~10,000 syntenic gene pairs from the two subgenomes. We found no evidence of subgenome dominance using our drought stress time course expression data. However, we do see evidence for divergent gene function as the expression of some syntelogs is responsive to drought stress while their syntenic pairs were not differentially expressed in this experiment.