Characterization of drought- and heat-responsive microRNAs in switchgrass

•MicroRNA-guided gene regulation under stress is poorly understood in switchgrass.•SmallRNA analysis enabled us to identify 29 conserved and 62 novel miRNA families.•The altered miRNA expression under drought or heat is similar as well as distinct. Recent investigations revealed that microRNAs (miRNAs) play crucial roles in plant acclimation to stress conditions. Switchgrass, one of the important biofuel crop species can withstand hot and dry climates but the molecular basis of stress tolerance is relatively unknown. To identify miRNAs that are important for tolerating drought or heat, small RNAs were profiled in leaves of adult plants exposed to drought or heat. Sequence analysis enabled the identification of 29 conserved and 62 novel miRNA families. Notably, the abundances of several conserved and novel miRNAs were dramatically altered following drought or heat. Using at least one fold (log2) change as cut off, we observed that 13 conserved miRNA families were differentially regulated by both stresses, and, five and four families were specifically regulated by drought and heat, respectively. Similarly, using a more stringent cut off of two fold (log2) regulation, we found 5 and 16 novel miRNA families were upregulated but 6 and 7 families were downregulated under drought and heat, respectively. The stress-altered expression of a subset of miRNAs and their targets was confirmed using quantitative PCR. Overall, the switchgrass plants exposed to drought or heat revealed similarities as well as differences with respect to miRNA regulation, which could be important for enduring different stress conditions.