Intellectual Merit: Small RNAs play critical roles in development and in the plant's ability to cope with unfavorable environmental conditions and pests. Small RNAs negatively regulate the activity of select target genes recognized based on sequence complementarity. Small RNAs are further important for maintaining chromosome stability through the repression of repeated elements contained within the genome. Much of the knowledge on how small RNAs are generated and act comes from studies in Arabidopsis. Next generation sequencing technologies have been employed in Arabidopsis as well as several other plant species to analyze the small RNA content and to identify targets to elucidate their function. Despite the importance of maize as a crop, maize small RNAs remain relatively poorly characterized. Particularly, our knowledge of the maize genes and processes targeted by small RNAs is extremely limited. The limited data available indicate that while the mechanisms of small RNA production and action are largely conserved, only a tiny fraction of the millions of small RNAs identified in Arabidopsis are conserved in maize. Differences in small RNAs and their targets even exist between closely related maize varieties, and these may underlie important agronomic traits and contribute to the enhanced vigor and improved yield of hybrids. This project seeks to take advantage of the latest genomics approaches to perform a comprehensive analysis of small RNAs and targets in tissues of two diverse, commonly used lines of maize. These will be placed into distinct pathways through analysis of mutants defective in the biogenesis of microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs), and bioinformatics tools will be used to assess how the small RNA-regulated gene networks vary across tissues and genetic variants. A subset of newly identified small RNAs and their targets will be characterized in detail to address biological function, developmental regulation, and how the extensive allelic diversity contained within the genome of maize affects small RNA targeted gene networks. These experiments will provide a deeper functional understanding of small RNA-regulated processes in maize and an evolutionary perspective of miRNA- and siRNA-mediated regulatory circuits. The analysis of small RNAs in different inbreds of maize provides a unique opportunity to assess how small RNA networks vary within a species, and will shed light on the contribution of small RNAs to hybrid vigor and the phenotypic diversity present between inbred lines that is exploited for crop improvement. Thus, this study on maize will give invaluable insight into the diversity of small RNA function in plants.
Broader Impacts: An important aspect of this project is to provide excellent research opportunities for undergraduate and high school students, as well as research and professional training for two Postdoctoral Fellows. Each year, two undergraduate or high school students will contribute to genetic experiments, small RNA target analyses, and the characterization of novel small RNAs. A partnership program has been established with South Side High School in NY, which includes lectures as well as research opportunities for selected students each year. The PIs will work closely with the Cold Spring Harbor Laboratory DNA learning center on the development of web resources and teaching tools for pre-college and college students on a variety of topics, including maize genetics and plant genomics, and will develop custom bioinformatics tools that will allow students to functionally annotate novel small RNAs and their predicted targets identified in these studies.
This project is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences and by the Plant Genome Research Program in the Division of Integrative Organismal Systems.
