2008 Annual Report 1a.Objectives (from AD-416) A major constraint to increasing the production efficiency of the Nation's cool and cold water aquaculture industry is the lack of genetically improved strains of fish for aquaculture. There is only limited genetic information on traits that will enhance production efficiency and yield a better quality fish. Identification and characterization of genes affecting aquaculture production traits will facilitate the development of genetically improved strains to increase aquaculture production efficiency. The objectives of the research outlined in this agreement focus on the identification of genes affecting oocyte maturation and embryogenesis in rainbow trout. Characterization of these genes will result in more in-depth understanding of the biology of reproduction and embryonic development and will impact strategies for improving developmental characteristics in broodstock. 1b.Approach (from AD-416) Collaborators at the USDA/ARS/NCCCWA and West Virginia University have worked to develop resources for conducting functional genomic research in rainbow trout. Resources which specifically target studies on embryogenesis include large volumes of expressed sequence tag data from oocyte and embryonic developmental stages and a cDNA panel representing oocytes thru day 50 post fertilization for gene expression analyses. Strategies will include analyses of gene expression and proteomic data in NCCCWA Broodstock to identify and characterize novel-oocyte specific genes, similar strategies will be employed to characterize gene expression throughout embryonic development. 3.Progress Report A rainbow trout high density oligo-array representing 37,394 unique cDNA clusters was constructed using Agilent's SurePrint technology. Several bioinformatics pipelines were evaluated for their ability to detect single nucleotide polymorphisms (SNPs) from expressed sequence tag data. A library of microRNAs from a pool of unfertilized eggs and early stage embryos was constructed. Sequence analysis of random clones identified 14 miRNAs, 4 of which are novel to rainbow trout. The ADODR is in frequent contact with the cooperator through phone calls, email, and annual site visits in addition to receipt of written reports. National Program 106, Component 3, Genetic Improvement.