YIA NSF Proposal
Scientific Objectives
In this proposal, we will study gene colinearity and the movement of orthologous segments between rice chromosome 1 and the orthologous segments of the maize and sorghum genomes. I will first build a rough map of shared segments between rice, sorghum and maize using existing public data. I will then close gaps in the comparative maps by selecting candidate rice genes to use as additional anchor points and map them to orthologous positions in the sorghum and maize genetic and physical maps. The final product will be a high-resolution comparative map of rice 1 with the corresponding regions of sorghum and maize. The information developed in this in this project will be released in peer-reviewed publications and through the Gramene web site.
Our Specific aims are to:
- Develop BAC based comparative maps of maize and sorghum to rice chromosome 1.
- Determine the three-way level of gene synteny and colinearity between rice, maize and sorghum for analysis of chromosome evolution within the cereals.
- rain one summer intern and develop a pilot curriculum for high school students on "Colinearity of Genes in Cereal Genomesā" in order to increase the exposure of students to plant biology.
Broader Impact
The broader impact of this proposal will be to provide a better understanding of genome organization of agronomically important cereal crops. The structure of cereal genomes and the genes contained within them are key to understanding the evolutionary relationships within this important family. However, due to the size and complexity of these genomes it is unlikely in the next few years that we will have complete sequences from each of these genomes. Although there has been much work on cereal macro and micro-colinearity, gene dense islands, and links between gene amplification and gene movement among the cereal genomes, there has been no large-scale analysis of these phenomena to date. We will take an unbiased large-scale approach to identify whether these are indeed true trends or represent selected events in cereal genomes. The proposed comparative physical maps will be a starting point for studies to understand the organization of the three cereal genomes and their evolutionary relationship. In the process, we will have developed methods for building and finishing comparative maps, which can be applied to genome-scale projects in the future. It will also serve as a valuable resource for the identification of genes involved in agronomically important traits.