miRNAs in switchgrass have recently been studied using both bioinformatics and experimental approaches (Matts et al. 2010; Xie et al. 2010), providing a first glimpse of the miRNA components and their possible target genes in switchgrass.

Using bioinformatics approaches, Matts et al. (2010) identified a total of 16 conserved miRNA families in switchgrass, among which 12 families are conserved between monocotyledonous and dicotyledounous, whereas 3 families (miR437, miR444, and miR528) are conserved only among monocotyledonous plants. The predicted fold-back structures of these switchgrass miRNAs are also conserved (Matts et al. 2010). With different criteria for computational strategies, Xie et al. discovered 121 conserved miRNAs belonging to 44 miRNA families (Xie et al. 2010). Unlike Matts et al. who only discovered one member in miR444 family similar to that in wheat (Yao et al. 2007) and Brachypodium distachyon (Unver and Budak

2009) , Xie et al. identified 13 members in miR444 family. Another interesting discovery from Xie et al. study is that they identified miR414 family, which had previously been discovered only in Arabidopsis, rice and moss (Wang et al. 2004; Fattash et al. 2007), but supposedly should exist in all plant species because of its existence in both dicot (Arabidopsis) and monocot (rice) as well as moss (Xie et al. 2010). Xie et al. also discovered one miRNA cluster (including miR2118a and miR2188b), and miR164 with an antisense miRNA in switchgrass (Xie et al. 2010).

Using experimental approaches, Matts et al. identified 34 conserved miRNAs from 16 families in switchgrass. Based on frequencies of different miRNAs in the library, miR172 family and miR156 family are the most abundant (Matts et al. 2010). Expression analysis of these miRNA families in different organs and developmental stages demonstrated that most miRNA families are expressed ubiquitously, whereas a few showed a distinct tissue-specific pattern. They also discovered that unlike other plant species in which miR395 and miR399 are induced in sulfate and phosphate deficit conditions (Jones-Rhoades and Bartel 2004; Fujii et al. 2005; Jagadeeswaran et al. 2009; Matts et al. 2010), miR395 and miR399 are detected to be expressed in relatively high basal level in switchgrass under optimal growth conditions, and their expression levels are only slightly changed under low sulfate and phosphate conditions, indicating the potential of switchgrass adaptation to sulfate — and phosphate-deficit soil (Matts et al. 2010).

Based on high complementarities between plant miRNAs and their targets, Matts et al. predicted 37 targets for conserved miRNAs in switchgrass, most of which are transcription factors (including SBP, MYB, TCP, NAC, ARFs, Scarecrow-like, AP2, MADS and CBF families), whereas others are transport inhibitor response 1 protein, Argonaute 1-like protein, plant acyanin and ubiquitin conjugating enzyme (Matts et al.

2010) , indicating a diverse role switchgrass miRNAs play in development, reproduction and stress response through regulating different targets. Of the predicted targets, only 4 (NAC for miR164, HD-zip for miR166, SPL for miR156 and AP2—like for miR172) are confirmed by modified 5’RACE (Matts et al. 2010). Xie et al. (2010) identified a total of 839 potential targets for switchgrass miRNAs. They also conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to predict biological processes and metabolic pathways these miRNAs-targets may be involved in (Xie et al. 2010). Their analysis indicated that 19 miRNAs might play a role in biofuel-related metabolic pathways and have the potential to contribute to enhancing biofuel production from switchgrass in the future (Xie et al. 2010).