2007 Annual Report 1a.Objectives (from AD-416) The objective of this cooperative research project is to elucidate the genetic architecture underlying economically important traits in cultured Pacific oysters (Crassistrea gigas) and to use this information to develop marker-assisted selection technology that enhances broodstock development with improved characteristics such as growth rate, reproduction, survival, disease resistance, and product quality. Information will be utilized from existing archived samples and genetic maps and new information will be contributed to mapping databases by mapping quantitative trait loci (QTL) for traits of economic importance. The development of these tools will allow the integration of marker-assisted selection with traditional breeding approaches to provide the shellfish industry with improved genetic stock. The program is dependent upon coordination with the Molluscan Broodstock Program (MBP) at the Hatfield Marine Science Center (HMSC), an administrative unit of Oregon State University. 1b.Approach (from AD-416) The levels of genetic (co)variation available in existing and potential shellfish germ plasm resources for economically important phenotypic characters as well as the number of loci contributing to these traits and the nature of their effects (genetic architecture) will be examined through a combination of quantitative and molecular genetic approaches. These include reconstructing and verifying pedigrees of broodstock animals using molecular markers, traditional quantitative genetic variance partitioning among families of animals of known relatedness and quantitative trait locus mapping. The patterns of available genetic (co)variation and genetic architecture are critical information for the design and execution of effective selection protocols for genetic improvement. Identifying QTL contributing to economically important traits will allow for the development of marker-assisted selection strategies that will improve the efficiency of selective breeding by allowing direct selection of favorable genotypes and by reducing the interval between spawning and selection and the need to maintain undesirable genotypes through the entire life cycle. Documents NFCA with Oregon State University. Formerly 5358-31000-001-01N. 04/2005. 3.Progress Report This report serves to document research conducted under Non-Funded Cooperative Agreement 5358-31000-002-01N between USDA ARS and Oregon State University, Hatfield Marine Science Center. Additional details of this research can be found in the report for the in-house associated project 5358-31000-002-00D "Genetic Characterization and Improvement of Shellfish Breeding Stocks for the Pacific Northwest". This project focuses on the development of genetically improved shellfish stocks through selective breeding using both quantitative and molecular genetic approaches. In the past year, we have collected new germplasm of both Pacific and Kumamoto oysters from their native range in the Ariake Sea in Japan and produced the first captive generation under strict quarantine conditions at the Hatfield Marine Science Center. We have also conducted extensive disease testing and hybridization experiments between these two species. We also produced 24 F2 mapping families of Pacific oysters from last year’s F1 families which will be used to identify quantitative trait lock for economically important traits, conducted a large scale analysis of population structure in native Olympia oyster populations in Washington, Oregon, and California, and produced a software package that identifies the most informative genetic markers for pedigree re-construction from mixtures of families. ADODR monitored the research progress and kept the cooperator informed