2005 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the University of Missouri-Columbia. Additional details of this research can be found in the report of the parent project 1907-21000-014-00D Comparative Plant Genomics. Through this agreement, initiated on September 15, 2004, we focus on increasing our understanding of the maize genome organization, anchor functional elements to the genetic and physical map of maize, and identify QTL associated with crop enhancement including response to the environment and nutritional improvement. Over the past year, we have progressed toward identifying genetic markers and anchoring miRNAs to the maize physical maps. To further enhance the maize physical map, we identified unanchored contigs as well as potential simple sequence repeats (SSRs) from BAC end sequences associated with the unanchored contigs. We tested 242 SSRs for polymorphism on the parents of the IBM mapping population; 70 were found to be polymorphic and 19 failed to amplify. The features that were not polymorphic were tested on parents of six other available maize mapping populations, resulting in 66 SSRs being polymorphic. Across the parents of the seven populations tested, 56% of the markers were found to be polymorphic. In the past year, the Davis lab has been anchoring predicted miRNA and their gene targets to the maize physical map using a BAC pooling strategy, resulting thus far in the successful positioning of 33 of 37 miRNA genes. The data generated from this project will improve the quality of the maize physical map, develop criteria for selection of potential genetic markers for fine mapping based on available sequence from the maize physical map, and anchor genes known to be involved in important developmental processes to the genetic and physical maps of maize.