Comparative analysis of aligned plant chromosomal regions have exceptional, but largely untested, potential for the discovery of genes, new classes of mobile DNAs, and the nature, rates and mechanisms of evolutionary change. Moreover, comparative analysis of closely related genomes that differ greatly in size can indicate both the origin(s) of that genome size difference and, equally important, determine whether the small genome could be used for map-based cloning of significant genes in the large genome species. In this project, maize and sorghum have been chosen for such an analysis because of their importance as crop plants and as model genetic systems. In particular, we plan (1) to uncover basic genomic composition of several gene-rich regions, (2) to use this two genome approach to improve and test annotation (including gene prediction) programs, (3) to determine whether the compactness of the sorghum genome can be used to physically link maize genes that have been genetically mapped to be as close as one map unit, and (4) to characterize the chromosomal composition of maize and its relationship to the origin of the sorghum genome for gene clusters and intergenic regions. The content of contiguous DNA sequence from different chromosomal locations in maize and sorghum totaling five megabases will be characterized. The size of the regions characterized will differ between the two genomes because of their differential gene density. In maize, a minimum of two BAC clones whose overlap hybridizes to a designated nucleation probe will be used. In sorghum, the probe will be centered within a single BAC. By selecting gene sequences as probes to genic regions of the respective genomes, a number of clusters, each with a predicted 10-20 genes, and their intergenic regions will be obtained. By comparing gene clusters in a bi-genomic fashion, better computational programs for predicting gene boundaries and repeat elements will emerge. In a number of cases, gene sequences will be discovered with known phenotypes because of the integration of genetic and DNA sequence data. Current projects to increase the density of DNA markers and phenotypes on both maize and sorghum maps will also benefit from this analysis because it will provide extensive evidence on the feasibility/difficulty of positional cloning in maize or its relatives. Evolutionary studies of cereal genomes based on gene islands will now be enhanced by the analysis of gene clusters and intergenic regions.