Reference Annotations for Small RNA-producing Genes in Plants

Project: Research project

Project Details


PI: Michael J. Axtell (Pennsylvania State University - University Park)

CoPI: Matthew Jones-Rhoades (Knox College)

Genes are discrete sections of DNA within chromosomes that encode specific functional products. Gene expression is the production of RNA copies of these discrete DNA sections that are then either used to encode for proteins, or are functional as RNAs in their own right. Gene annotations identify and characterize the location of genes throughout a complete genome sequence. Annotations of protein-coding genes have received a great deal of attention, and are at a relatively advanced state for many plant species of agricultural and economic interest. In contrast, annotations for many other types of genes are much less developed. Regulatory small RNAs are short bits of RNA that function to turn off the expression of other genes in the genome and have been implicated as key players in several important plant traits, including disease resistance, tolerance to adverse environmental conditions, and plant growth traits affecting yield. One sub-type of regulatory small RNA genes, the microRNAs, are well-studied and well-annotated. However, microRNAs account for a very small fraction of the overall small RNA gene population in plants; preliminary data indicate that a typical plant genome has just a few hundred microRNA genes, but tens of thousands of genes encoding other types of regulatory small RNAs. This project seeks to provide systematic annotations of plant genes that produce all types regulatory small RNAs for several plants of agricultural and societal interest, including rice, maize, tomato, and apple.

Knowing where in the genome the genes are, and what types of products they produce, is key information for genetic approaches to plant improvement. Regulatory small RNAs are clearly a major type of gene in plants, but their annotation is currently under-developed. Systematic and reliable gene annotations for regulatory small RNA genes will accelerate genetic, genomic, and breeding experiments to identify superior plant varieties to meet the challenge of feeding a growing population and maintaining the astounding productivity of American agriculture in the face of a changing climate. This project is also training graduate and undergraduate students in modern plant genetics through mentored research experience, and allowing the development of novel undergraduate courses. All project outcomes from this project will be made available without restriction via the project website at Sequence data will be available through long-term repositories (GEO, SRA) and small RNA gene models will be provided to community portals such as Gramene and MaizeGDB.

Effective start/end date5/15/144/30/19


  • National Science Foundation: $907,370.00


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