2007 Annual Report 1a.Objectives (from AD-416) The objectives of this cooperative research project are to increase our understanding of plant genome organization through sequence evaluation, and to develop methodologies to leverage emerging sequencing technologies for the purpose of sequencing and genotyping plant germplasm. 1b.Approach (from AD-416) 1) Development of physical markers for Cereals. We will use regions of synteny established between the rice genome sequence and cereal sequences to identify rice gene models for physical marker development. The sequences will be used to generate primers for PCR amplification from cereal BAC clones. The results will enrich comparative cereal maps and anchor cereal genes to their respective physical maps.. 2)Genomic cereal sequences will be generated from cereal BACs for the purpose of surveying cereal genomes. . 3)Finished genome sequence will be generated from BACs associated with QTL for the purpose of identifying genes associated with crop improvement. 3.Progress Report This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Cold Spring Harbor Laboratory. No funds were used. The collaboration focused on evaluation discussions and preliminary runs of maize sequence using the new Solexa/Illumina sequencers of which Dr. McCombie’s laboratory is a beta test site. Management and Communication: Discussion and review of the objectives are done at least twice a year in conference calls or in personal meetings as well as email exchanges and conference calls.