2005 Annual Report 1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? Despite the implementation of modern hatchery and grow-out technologies among the most advanced in the world, the west coast shellfish farming industry still largely depends on essentially wild animals as broodstock, without the economic benefits that domestication and genetic improvement have brought to land-based agriculture. Furthermore, typical commercial hatchery practices have been shown to result in a small number of individuals contributing to the gene pools of cultured populations, reducing genetic variability. This will, in the long term, almost certainly reduce yields due to inbreeding depression, eliminate rare but useful alleles from cultured populations, and limit the potential for future improvement through traditional selective breeding and modern genetic manipulation. Shellfish farmers also currently tolerate sometimes-catastrophic mortality, mostly due to a poorly understood syndrome called 'summer mortality,' believed to result from the interaction of stress and opportunistic pathogens. Specific genetic factors for tolerance to abiotic and biotic stressors are virtually unknown aside from the roles of heat shock proteins and genes related to exposure to heavy metals. As a consequence, the future growth of the oyster industry on the West Coast will depend on hatchery production of improved genetic strains. Characters requiring improvement are growth and survival (yield), disease and stress tolerance, allocation reproductive effort, shell shape, and shell and meat color. Developing and maintaining such strains demands an improved understanding of the quantitative and molecular genetic variation available and of the functional genetic mechanisms underlying desirable traits. Limited information on the availability of genetic variation and the lack of genetic markers to sort inferior and superior genotypes early in the life cycle make current selective breeding efforts inefficient, especially if genotype-by-environment interactions unwittingly select different genotypes in different locations or if unrecognized negative genetic correlations among desirable characteristics force trade-offs among traits. The overall research objective is to conduct a research program that employs state-of-the-art molecular genetics and breeding theory towards providing the commercial aquaculture industry with improved shellfish stocks. Marker-assisted selection will be developed to enhance breeding improvements in factors such as growth rate/efficiency, reproduction, survival, disease resistance, and product quality. Information will be utilized from existing genetic maps and new information will be contributed to mapping databases. Marker-assisted selection will be integrated with breeding approaches to provide the shellfish industry with improved genetic stock. The program is coordinated with the Molluscan Broodstock Program at the Hatfield Marine Science Center. The project has four specific objectives for the immediate future:. 1)to conduct a quantitative genetic characterization of current germplasm resources for Pacific oysters, assess their potential for genetic gain, and investigate trade-offs among traits in order to develop a framework for informed decisions regarding alternative selective breeding strategies,. 2)to identify or develop appropriate molecular markers for population genetics, parentage analysis and most importantly QTL mapping in Pacific (Crassostrea gigas) and Kumamoto oysters (Crassostrea sikamea) and conduct a molecular genetic characterization of currently available breeding stocks, and . 3) to identify quantitative trait loci (QTL) for economically important characters in C. gigas. This program falls within the Genetic Improvement Component of NP 106 - Aquaculture, and specifically addresses three of the problems identified within the National Program Action Plan: a) Conserve, characterize, and utilize genetic resources, b) Selective breeding for economically important traits, c) Genomic resources. Information on genetic variation in shellfish broodstocks will provide benefits to shellfish breeders and farmers. Improved germplasm can substantially reduce losses to summer mortality, enhance yields, and increase marketability by stabilizing the supply and improving quality. The growth of shellfish aquaculture can provide ecologically sustainable economic growth in hard-pressed coastal communities and decrease pressure on over-exploited capture fisheries. U.S. consumers will benefit from increased availability of high quality, safe, competitively priced, nutritious and appealing shellfish products. Increasing the supply of fresh shellfish will provide exportable products to satisfy high global demand and reduce the U.S. trade deficit. Finally, the expansion of domestic and export markets for farmed shellfish will create jobs in industries that supply equipment, post-production processing and distribution. 2.List the milestones (indicators of progress) from your Project Plan. This project replaced CRIS project 5358-31000-001-00D effective 3/1//2005 (Normal Progression) approved through the OSQR process. Year 0 (FY 2002) Recruit a Research Geneticist to lead the project, renovate and begin equipping laboratory facilities. Year 1 (FY 2003) Complete laboratory set up. Year 2 (FY 2004) Optimize available microsatellite molecular markers on ARS equipment and screen wild and commercial populations for polymorphisms. Begin population genetic studies of Pacific oysters (Crassostrea gigas) and Kumamoto oysters (Crassostrea sikamea) based on samples available in US. Initiate quantitative genetic studies of Pacific oysters. (i.e. Spawn 48 half-sib families w/ 3 dams/sire =144 full-sib families) and collect data on larval characters. Initiate QTL experiment (Spawn 12 full sib families for mapping) and collect data on larval characters. Perform preliminary study of genetic variation for cadmium content in Pacific oysters. Year 3 (FY 2005) Deploy animals to field sites for quantitative genetic and QTL mapping experiments & monitor growth and survival. Analyze data on larval characters for quantitative genetic and QTL mapping experiments. Collect tissue samples from QTL experiment and begin genotyping. Continue collection of growth and survival data from quantitative genetic and QTL mapping experiments. Collect and begin genotyping samples of C. gigas and C. sikamea from Japan for population genetic studies. Year 4 (FY 2006) Complete genotyping and analyses of C. gigas and C. sikamea for population genetic studies. Continue collection of growth and survival data from quantitative genetic and QTL mapping experiments. Harvest both quantitative genetic and QTL mapping experiments and collect end-point data. Begin analyzing results for publication. Year 5 (FY2007) Finish analyzing results of quantitative genetic experiment and QTL mapping experiment. Finish analyzing results of population genetic studies. 4a.What was the single most significant accomplishment this past year? Determination that cadmium accumulation in oysters is under substantial genetic control: The ARS oyster geneticist, in collaboration with an ARS scientist in Corvallis discovered significant levels of genetic variation for the bioaccumulation of cadmium in Pacific oysters. Ongoing international negotiations that could limit cadmium content in seafood may impact the marketability of Pacific oysters, and there is need to know whether selective breeding can modify this character. The ARS oyster geneticist in Newport, OR collected oyster tissue samples for preliminary study of the heritability of cadmium concentration in Pacific oysters from an ongoing quantitative genetic experiment originally setup by collaborators at OSU, analyzed these samples for cadmium content in collaboration with Stephen Griffith at the ARS National Forage Seed Production Research Center in Corvallis,OR and analyzed and interpreted the data. The results provided the first evidence for quantitative genetic variation in cadmium bioaccumulation and suggested that this trait could be manipulated through selective breeding in commercial oyster stocks. 4b.List other significant accomplishments, if any. Use of DNA markers for oyster pedigree analysis. The ARS oyster geneticist demonstrated that the pedigrees of Pacific oysters can be re-constructed using a reasonable number of microsatellite DNA markers. This is important because current selective breeding protocols require that genetic families be reared separately to maintain pedigree information and that experiments be highly replicated in order to account for small scale environmental variation, making oyster breeding costly, while reducing the achievable selection intensity. The ability to mix families and reconstruct pedigrees at harvestable size could significantly streamline these protocols, reduce costs, and increase selection intensity. The ARS geneticist collected multi-locus genotypes on progeny from separately reared families of Pacific oyster and demonstrated that they can be successfully assigned to the correct parents using microsatellite DNA markers. This accomplishment provides the conceptual basis for developing mixed-family breeding strategies to be used by ongoing oyster breeding programs and potentially by commercial oyster growers. 4c.List any significant activities that support special target populations. None 4d.Progress report. None 5.Describe the major accomplishments over the life of the project, including their predicted or actual impact. Program is only in its second year. 6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? Meetings have been held with major oyster producers to identify their priorities for genetic improvement. These talks revealed that oyster markets are rapidly changing from shucked meats in cans or jars to a live half-shell product, and that these markets place a premium on presentation characters such as shell shape and color, meat/shell ration and shelf-life a rather than yield. 7.List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below). Can selective breeding reduce the heavy metals content of Pacific oysters (Crassostrea gigas), and are there trade-offs with growth or survival? Oral presentation at 59th Annual Conference of the Pacific Coast Shellfish Growers Association.