2006 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 1907-21000-023-00D "Comparative Genomic Analyses, Bioinformatics and Resource Development for Cereal Genomes." This agreement, initiated on September 15, 2004, focuses 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. In the past year, the Davis lab continued work of anchoring predicted miRNA and their gene targets to the maize physical map using a BAC pooling strategy. This work was further extended to include additional maize expressed ESTs.