To facilitate scientific advances and crop improvement, the thousands of maize genes being discovered during the maize genome sequencing project must be ordered relative to a genetic map. This project builds on prior NSF investments in genomics to meet this challenge. A validated PCR-based approach will be used to genetically map 4,500 genes. The resulting high-density transcript map will enhance our understanding of the organization and evolution of the maize genome. These thousands of mapped genes will also provide the necessary sequence-based cross-links to facilitate the alignment of the rice physical map with the maize genetic map. This will provide a means to determine the linear order on maize chromosomes of maize genes. 1,000 co-dominant PCR-based genetic markers (IDPs) that will be suitable for use in a wide variety of genetic experiments will also be generated and distributed to the public via web-based databases. The bioinformatic strategy and tools that will be developed to enhance PCR primer design will be of great value to other genome projects.