2011 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 We generated a BAC DNA fingerprinting physical map (PM) of the rainbow trout genome and integrated it with the genetic linkage map through anchoring of BAC PM contigs to the chromosomes of the genetic map. BAC clones from four different libraries were used to generate the physical map. The PM is composed of 167,989 BACs of which 158,670 are assembled into 3,220 contigs and 9,319 are singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,049,643, which corresponds to an estimated physical length of 1.87 Gb (approximately 80% of the rainbow trout genome). The average number of consensus bands (CB) per contig is 326, and the estimated contig size is 580 kb. Anchoring of 230 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA) genetic map was achieved through mapping of 330 genetic markers derived from BAC end sequences (BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. The integrated physical and genetic map we produced enables detailed comparative genome analyses with other fish species, fine mapping of quantitative trait loci (QTL), positional cloning, selection of positional candidate genes for economically important traits and the incorporation of marker assisted selection (MAS) into rainbow trout breeding programs.