An Evolutionary View of the Biogenesis and Function of Rice Small RNAs

Small RNAs are key players in transcriptional and posttranscriptional gene silencing. The rice genus Oryza comprises two domesticated species and 22 wild species. Using deep-sequencing technology, a variety of small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been characterized in Asian-cultivated rice (Oryza sativa) and its wild relatives. These RNA species are processed by different types of DICER-LIKE proteins (DCL) and/or RNA-dependent RNA polymerases (RDRs) and are loaded into distinct types of ARGONAUTE (AGO) family members. Compared with Arabidopsis, rice has an expanded number of core genes in RNA-silencing pathways, resulting from multiple gene duplication events, and functional diversification of these genes remains largely unexplored. Rice also has an evolutionarily dynamic small RNA repertoire, with several special classes of small RNAs unique to rice or to monocots. While miRNAs can serve as a driving force for rice domestication, knowledge about evolutionary trajectories and specialized functions of rice small RNAs is still lacking to a large extent. In this chapter, we summarize our current understanding of the evolution of biogenesis and functional diversity of rice small RNAs.