Identifyng microRNAs in plant genomes

The ability to control gene expression during development in plants could be used for improving crop yields, resistance to disease, and environmental adaptability. It has been suggested that microRNAs, or miRNAs, control developmental processes such as meristem cell identity, organ polarity, and developmental timing by interfering with the expression of mRNAs. Our preliminary analysis focuses on the miR166 family since it has been shown to mediate repression of rolled-leaf1 (rdl1) in maize. Based on maize sequences derived from degenerate primers, we computationally identified miR166b, miR166c, miR166d, and four more closely related putative maize precursors. Patscan, a pattern-matching program that allows RNA basepairing and mismatches, was used to identify functional elements in the putative hairpins. Each hairpin was further supported by their stable secondary structures determined with Mfold. Using this pattern matching approach we expanded the analysis for 19 Arabidopsis miRNA families in rice and maize.