2008 Annual Report 1a.Objectives (from AD-416) Conduct research on the quantitative and molecular genetics of oysters leading to improvement in broodstock management and selective breeding for enhanced production efficiency and product quality. Develop reference families, molecular genetic markers and elucidate key genes and sequence information for traits of economic importance. Assess genetic diversity of potential germplasm resources. 1b.Approach (from AD-416) Utilize traditional and molecular genetic techniques to estimate the heritability and genetic correlation structure and to map quantitative trait loci for economically important traits such as growth/rate efficiency, reproduction, survival, disease resistance and product quality. Utilize this new information to integrate marker-assisted selection and traditional phenotypic approaches to provide the shellfish industry with improved genetic stock. Coordinate activities with, and utilize the genetic resources of the Molluscan Broodstock Program at the Hatfield Marine Sciences Center. Explore utility of non-native germplasm for the identification and incorporation of important traits and genes for pacific shellfish production. FY02 Program Increase $216,000. Add 1 SY. FY04 Program Increase $120,783. Replacing 5358-31000-001-00D (2/05). 3.Progress Report GENETIC IMPROVEMENT: The Shellfish Genetics Program has completed all laboratory work on two large projects to identify genes that differ in their expression patterns in response to heat shock and bacterial exposure between stress-tolerant and stress-susceptible families of Pacific oysters (C. gigas). This work is aimed at improving the efficiency of selective breeding in oysters by facilitating the ability to directly target the genes that contribute to stress resistance, a major component of Summer Mortality Syndrome. The Shellfish Genetics Program has also completed all field work and data collection on a large gene mapping experiment for growth and survival genes in Pacific oysters. Genotyping should be completed by Spring 2009. This work is intended to identify chromosomal regions that contain genes for growth and survival with the aim improving selective breeding efforts. The Shellfish Genetics Program has collected genetic marker information from all known naturalized populations of C. gigas in US waters as well as several populations in New Zealand and Japan. Statistical analyses of the distribution of molecular genetic variation within and among these populations, genetic distances between them, and a genome scan looking for loci under selection are in progress. This work will identify potential sources of genetically distinct and novel germplasm for future selective breeding efforts and provide an indication of the degree to which populations are locally adapted. In collaboration with the Molluscan Broodstock Program, we collected novel germplasm of both Pacific and Kumamoto oysters from the Ariake Sea in Japan and we are currently raising the first US generation under strict quarantine to preclude the introduction of pathogens. We have completed DNA extractions and are beginning genotyping work on a large laboratory experiment examining how family representation changes over time in mixed larval cultures and a “side-by-side” field experiment comparing mixed-family and separate-family selection schemes for C. gigas. This work will be used to optimize novel approaches to selective breeding that mix families in common rearing units rather than raising them separately. AQUACULTURE PRODUCTION SYSTEMS: In response to bacterial outbreaks in 2005 and 2006, we collaborated with the Molluscan Broodstock Program to develop improved water treatment systems incorporating micro-filtration, UV sterilization, foam fractionation, and biological filtration. Commercial shellfish hatcheries have had similar problems, and in 2008 at least one commercial hatchery adopted and scaled up this approach resulting in dramatic improvements. SUSTAINABILITY AND ENVIRONMENTAL COMPATIBILITY OF AQUACULTURE: We developed genetic markers for the native Olympia oyster, O. concaphila, and used them to examine remnant populations in British Columbia, Washington, Oregon, and Northern California. This work addresses both the potential for aquaculture production of this native species and how natural populations are impacted by past and current aquaculture practices.. Analyses of population structure are in progress. This addresses NP 106, Components 1, 5, 6. 4.Accomplishments 1. New water treatment protocol established. As a result of bacterial outbreaks in 2005 and 2006 that caused mass mortalities of larval and juvenile oysters in the research hatchery at the Hatfield Marine Science Center, the ARS Shellfish Genetics Program collaborated with the Molluscan Broodstock Program to develop improved water treatment systems that include filtration, UV sterilization, foam fractionation, and biological conditioning. Recently, commercial shellfish hatcheries experienced similar problems that nearly eliminated commercial-scale larval production. In 2008, the Whiskey Creek shellfish hatchery - the largest supplier of oyster larvae for independent growers – was considering closing as a result of similar problems. This closure was avoided when the hatchery operator replicated and scaled up the systems developed and implemented by the Molluscan Broodstock Program and ARS resulting in dramatic improvement that partially restored production although more work is needed on this problem. Contributes to National Program 106 Aquaculture, Component V. Aquaculture Production Systems b) Production Intensity. 5.Significant Activities that Support Special Target Populations None. 6.Technology Transfer Review Publications Taris, N.G., Lang, R.P., Camara, M.D. 2008. Sequence polymorphism can produce serious artifacts in real-time PCR assays: lessons from Pacific oysters. BioMed Central (BMC) Genomics.9:234. Matson, S.E., Camara, M.D., Eichert, W., Banks, M.A. 2008. P-loci: a computer program for choosing the most efficient set of loci for parentage assignment. Molecular Ecology Resources.8:765-768. Camara, M.D., Evans, S., Langdon, C. 2008. Parental relatedness and survival of Pacific oysters from a naturalized population. Journal of Shellfish Research.27(2):323-336. Camara, M.D., Davis, J.P., Sekino, M., Hedgecock, D., Li, G., Langdon, C.J., Evans, S., Hedgecock, D. 2008. The Kumamoto oyster Crassostrea sikamea is neither rare nor threatened by hybridization in the northern Ariake Sea, Japan. Journal of Shellfish Research.27(2):313-322.