YIA: Genomics of Rice, Sorghum and Maize

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Cereals are a large and diverse set of agronomically important crops from the family Gramineae. They are the main source of dietary calories for most human populations whether they are consumed directly, as in rice, or indirectly as animal feed. The primary subject of this research is gene colinearity, the evolutionarily conserved order along the chromosome of genes among different species. The movement of blocks of genes of rice chromosome 1 relative to the corresponding regions of maize and sorghum will be analyzed. The research will enhance the understanding of genome organization of these agronomically important cereal crops. The structure of cereal genomes and their genes 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 complete sequences will be available 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. This project will take an unbiased large-scale approach to identify whether these are indeed true trends or represent selected events in cereal genomes. To do this, a rough map of shared segments between rice, sorghum and maize using existing public data will be generated. Gaps in the comparative maps will be closed by selecting candidate rice genes to use as additional anchor points and map them to conserved blocks 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 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, methods will be developed 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.Information generated:1.70 maize genetic markers anchored to the maize IBM map and maize physical map2.SSR database for maize and sorghum sequences3.STC database for BACs found in the maize and sorghum physical maps BAC end sequences for clones selected in the minimum tiling path 200 rice gene models anchored to maize 75 rice gene models directly sequenced from maize and sorghum 4.Integrated BAC map of maize and sorghum across colinear regions in rice chromosome 1 based upon sequence similarity and overgo hybridization.5.1 MB of cereal BAC sequences6.Develop a pilot curriculum for high school students on "Colinearity of Genes in Cereal Genomes"