2006 Annual Report 4d.Progress report. This report serves to document research conducted under a non-funded cooperative agreement between ARS and The University of Victoria, Victoria, British Columbia, Canada. Additional details of research can be found in the report for the parent CRIS 1930-31000-008D Identification and Characterization of Genes Affecting Cool and Cold Water Aquaculture Production. This agreement entitled, “Transcriptome Analyses in Salmonids” has the goal of identifying representatives for all salmonid genes by coordinating expressed sequence tag projects for Atlantic salmon and rainbow trout. New tissues for gene discovery including stages of embryonic development have been targeted to increase the probability of identifying novel genes. In FY2006 the first phase of this project was completed, involving partial sequencing of 100,000 genes from rainbow trout. Future analyses will be conducted within and between species to identify common genes and estimate the amount of representation for each transcriptome.