2006 Annual Report 4d.Progress report. This report serves to document research conducted under a 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. We have been able to spawn and deploy into the field 24 mapping families to be used to identify quantitative trait lock for economically important traits, conduct an experiment to determine at what stage of development we can mix genetic families without biasing their representation at the plantout stage, and conduct several heat shock experiments that use DNA microarrays and cDNA-AFLP techniques to examine changes in the transcriptome of the Pacific oyster in response to heat shock and bacterial challenges. In addition, a subset of the MBP samples has been genotyped at 12 microsatellite markers and we have shown that the breeding program has resulted in a substantial loss of allelic diversity and that inbreeding depression in Pacific oysters is detectable even with very low levels of parental relatedness. The inbreeding work has been submitted for publication. Further, we have completed and published a study of the heritability of heavy metals bioaccumulation in Pacific oysters.