2009 Annual Report 1a.Objectives (from AD-416) To generate an integrated physical and genetic map for rainbow trout. 1b.Approach (from AD-416) Use BAC DNA fingerprinting to construct a physical map and BAC end sequencing to identify genetic markers for integration of the physical and gentic maps. 3.Progress Report Developing species-specific molecular tools such as chromosome maps is critical for identifying genes affecting production traits. The types of chromosome maps and genetic maps characterize inheritance of genetic markers throughout generations, physical maps characterize the location and order of genetic markers and chromosomes. In an effort to integrate the rainbow trout genetic map and bacterial artificial chromosomes (BAC) physical map, the NCCCWA mapping reference families were genotyped with approximately 200 new microsatellite markers developed from the physical map. The integrated map facilitates gene identification and characterization. In collaboration with researchers from the University of California-Davis, we generated BAC DNA fingerprints and end sequences from approximately 10,000 clones from two new BAC libraries, which will contribute to the expansion of the current integrated map and the generation of a more robust second generation physical-genetic map of the trout genome. The ADODR is in frequent contact with the cooperator through phone calls, email, and annual site visits in addition to receipt of written reports.