Scientific Objectives and Approaches. Endogenous small regulatory RNAs, including short interfering RNAs (siRNAs) and microRNAs (miRNAs), mediate development and responses to stress in plants as in other eukaryotic organisms. Knowledge of the number, sequence and expression pattern of such small RNAs as well as their regulatory targets is essential in order to understand the basic biology of plants as well as to develop high yielding, stress resistant crops. Experiments are to extensively analyze the sequence and expression patterns of all or nearly all of the small RNAs expressed in two important crop plants, rice and maize. The first aim is to clone and sequence small RNAs isolated from rice and maize (~10,000/organism), providing the first extensive systematic examination of small RNA populations in both species. miRNAs in the small RNA populations of both plants will be identified using both experimental and computational approaches and the number and location of rice miRNA genes annotated. The last two aims focus on understanding the biogenesis and function of the monocot miRNAs, establishing miRNA expression patterns during development and in response to various kinds of stress and mapping the ends of the primary precursor RNAs for rice miRNA genes and a subset of those in maize. A web interface to all data generated in the proposal will be made available to the research community, including a database of all small RNA sequences, predicted miRNA precursors and targets and other associated information through a searchable website. Broader Impacts. The recent discovery that endogenous siRNAs and miRNAs play important roles in the regulation of eukaryotic gene expression has put small RNA biology at the forefront of experimental science. The work will extend the current database of small RNAs in plants. The project is a three-University collaborative effort that offers unique mentoring opportunities. Two of the participating Universities are EPSCoR institutions in South Carolina: University of South Carolina (USC), with a large female (54%) and minority (22%) enrollment and Claflin University, the oldest historically black University in the state. The third is University of California, Davis (UC Davis). An exchange program will be established between Claflin University, USC and UC Davis, allowing promising young Claflin and USC students to participate in cutting edge research activities at each University. Specific deliverables to the research community: 1) An extensive database of small RNA sequences and associated information will be made freely available via the project website. 2) A candidate miRNA-target dataset generated by the findMiRNA algorithm that will enable further bioinformatic analysis of miRNAs and their targets. 3) Microarrays of all identified rice miRNAs sequences and all putative maize miRNAs will be made freely available to the community as soon as the methodology is established at a small cost to include producing the array as well as shipping expenses. Distribution of microarrays will be handled by the University of South Carolina Institute for Biological Research and Technology (IBRT).
