Dayong Li,[13]‘[14] Man Zhou,2 Zhigang Li2 and Hong Luo2’*

Introduction

With the rapid development of genomics and bioinformatics, recent studies have suggested that the number of protein-coding genes is similar in many model eukaryotes whose whole genome sequences have been obtained and analyzed in detail (Matera et al. 2007; Ponting et al. 2009). Genome-wide transcriptional analyses have identified large numbers of non-coding RNAs (ncRNAs) in humans, animals and plants (Hirsch et al. 2006; Ravasi et al. 2006; The ENCODE Project Consortium 2007; Guttman et al. 2009; Amor et al. 2009; Jouannet et al. 2011). Based on their length, ncRNAs can be arbitrarily divided into small ncRNAs, intermediate-size ncRNAs and long ncRNAs (Amor et al. 2009; Jouannet et al. 2011; Liu et al. 2013). To date, the best characterized of all the ncRNAs has been small RNAs (sRNAs). Endogenous small RNAs are about 19-30 nucleotides (nt) RNA molecules that modulate

gene expression at the transcriptional and/or posttranscriptional levels and play key roles in many developmental and physiological processes in eukaryotic organisms (Zamore and Haley 2005; Bonnet et al. 2006; Zhang et al. 2006; Ramachandran and Chen 2008; Poethig 2009).

In plants, sRNAs can mainly be classified into small interfering RNAs (siRNAs) and microRNAs (miRNAs) based on their precursor structures and biogenesis processes (Vazquez 2006; Vaucheret 2006; Sunkar and Zhu 2007; Ramachandran and Chen 2008; Jin and Zhu 2010; Vazquez et al. 2010). The siRNAs are derived from double stranded RNA precursors and can be divided into heterochromatic siRNAs (hc-siRNAs), trans-acting siRNAs (ta-siRNAs), long siRNAs (lsiRNAs), natural antisense transcripts-derived siRNAs (nat-siRNAs), and others (Bonnet et al. 2006; Zhang et al. 2012). The miRNAs are distinguished from the siRNAs since they are derived from the processing of longer primary miRNA transcripts, which fold into hairpin-like stem-loop structures (Bartel 2009; Chen 2009; Chuck et al. 2009; Poethig 2009; Voinnet 2009; Zhu et al. 2009).

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass and has been recognized as a dedicated cellulosic biofuel crop because of its broad adaptation to marginal lands and high biomass production (Vogel 2004; McLaughlin and Kszos 2005; Bouton 2007; Li and Qu 2011; Mann et al. 2012). Although switchgrass has attracted great attention, little is known about its many aspects on basic biology, including ncRNAs. In this chapter, we will provide an overview of the miRNAs in this biofuel plant species and discuss their potential applications in switchgrass genetic improvement.