SGER: Conserved Noncoding Sequences (CNS) in Grasses

University Of California-Berkeley, Berkeley CA

Investigators

Abstract

Many grasses, including some economically important crops, are considered "orphan systems" because they do not have sequence databases that permit efficient genetic fingerprinting, mapping and gene fragment identification. Modern breeding depends on molecular tools such as these. The justification for support of this project as a Small Grant for Exploratory Research (SGER) is that this is a short-term, proof-of-concept project that will develop an urgently needed tool to meet these needs. This project will begin to develop a database of Conserved Non-Coding (CNS) sequences to cover the grasses. The CNS sequences are large, exact phylogenetic "footprints" in the non-protein coding parts of genes. They can be obtained by pair-wise comparison of sequences from whole genome and Expressed Sequence Tag (EST) collections. CNS sequences make excellent Polymerase Chain Reaction (PCR) primer sites. Since the CNS sequences are highly conserved, a PCR primer designed by comparing, for example, maize and rice, will work in the other 10,000 grasses as well. This project will determine the feasibility of finding CNS sequences and designing primer pairs using the available sequence resources. If it is successful, the long-term goal will be to develop about 4000 primer sequence pairs that amplify specific polymorphic fragments of known, mapped genes, across all grasses. These sequences will be valuable tools for understanding genome architecture across the grasses, as well as for mapping. Broader impacts The results will be made available through a project web site that will include viewing tools to enable the user to sort and select sequences of interest. The outcomes of the project will have a broad impact, facilitating research on grasses, and allowing tools from well characterized systems such as maize and rice to be leveraged for less well developed, but agronomically important relatives such millet.