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United States Department of Agriculture

Agricultural Research Service

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Research Project: Determine Genetic Diversity and Develop Tools for Genetic Improvement of Oyster Stocks for the Pacific Northwest

Location: Forage Seed and Cereal Research

2011 Annual Report

1a. Objectives (from AD-416)
Objective 1: Assess the potential for genetic gain, and trade-offs among economically important traits in currently available Pacific oyster germplasm in order to develop a framework for informed decisions regarding alternative selective breeding strategies. Sub-objective 1.A. Estimate the additive genetic, non-additive genetic, and environmental covariance matrices for larval, nursery, and field performance in currently available germplasm of the Pacific oyster using a multi-year animal model approach. Sub-objective 1.B. Use the estimates obtained in Sub-objective 1.A. to design an efficient genetic improvement strategy for Pacific oysters. Objective 2: Evaluate and optimize mixed-family breeding strategies for Pacific oysters. Sub-objective 2.A. Determine at which stage larval progeny derived from controlled crosses of Pacific oysters can be mixed in equal proportions and not have those proportions drastically skewed at the field plant-out stage. Sub-objective 2.B. Compare the results and costs of mixed family selection protocols to current procedures in which families are reared separately from spawn to harvest. Objective 3: Identify genetic markers for economically important traits in Pacific oysters to enable marker-assisted selection. Sub-objective 3.A. Examine the relationship between among-family variance in the expression levels of previously identified candidate genes and family-specific growth and survival in the field. Sub-objective 3.B. Use standard QTL mapping approaches and quantitative assays of the levels of expression of candidate genes to identify regions of the Pacific oyster genome that control the transcription of the most promising candidate genes from Objective 3.A.

1b. Approach (from AD-416)
Utilize quantitative and molecular genetics techniques to elucidate the genetic architecture of, map quantitative trait loci for, and identify expression QTL for candidate genes that control economically important traits in cultured Pacific oysters. Utilize this new information to integrate rigorously-estimated breeding values and marker-assisted selection into the NIFA-funded Molluscan Broodstock Program, which currently selects only on post-larval yield using among-family selection. Explore the utility of marker-based pedigree reconstruction from mixed-family evaluations to mitigate family-specific environmental effects on families reared separately without replication during the larval and nursery stages and family-specific density effects on growth during field trials caused by differential survival of families.

3. Progress Report
Progress was made on Objectives 2 and 3 and their subobjectives, all of which fall under National Program 106, Component I, Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources, and Component 2, Enhancing Animal Performance, Well-being, and Efficiency in Diverse Production Systems. Research on Objective 1 was delayed due to technical limitations of the collaborator’s hatchery facility which did not permit meaningful comparison of genetically distinct families of oysters. Accordingly, progress on this project focused on Problem 1C, the need for genomic and bioinformatics infrastructure for oysters and 2A, the need for identification of genes and pathways leading to improved growth, nutrient utilization, and product quality. To address Problem 1C, we conduct gene mapping experiments to identify genes that control the expression of previously identified stress-related genes and reproductive effort in Pacific oysters. This research will enable marker-assisted selection to enhance stress tolerance directly and indirectly by reducing reproductive effort and the associated metabolic disturbances that contribute to summer mortality in cultured Pacific oysters. We established collaboration with researchers at the University of Rhode Island to apply deep “next generation” DNA sequencing and advanced bioinformatics to develop molecular tools to identify and characterize genes that impact complex traits of economic importance in Eastern oysters. We also released Kumamoto oysters from the Ariake Sea for commercial production to revitalize existing Kumamoto breeding stock. To address Problem 2A, we established collaboration with researchers at the University of Oregon to understand the genetic basis of high mortalities of Pacific oyster larvae in commercial shellfish hatcheries. Standardized protocols to challenge oyster larvae with bacterial pathogens and experimentally acidified seawater were developed and laboratory experiments to identify genes for larval resistance to these stresses were completed.

4. Accomplishments
1. Release of novel Kumamoto oyster breeding stock, “Ariake Kumo.” Existing U.S. Kumamoto oyster breeding stock has been hybridized with Pacific oysters and subjected to excessive inbreeding, producing undesirable characteristics and making larval culture difficult. In 2006, ARS researchers at Newport Oregon, in collaboration with the Molluscan Broodstock Program at Oregon State University, the University of Southern California, and Taylor Shellfish Farms collected a genetically diverse sample of Kumamoto oysters from the Ariake Sea in southern Japan and used molecular markers to confirm their species identification. From 2007-2010, we raised an entire generation under strict quarantine conditions and conducted extensive disease testing on the imported parents and their first- and second-generation progeny to preclude the introduction of non-native pests and pathogens. This non-inbred and non-contaminated breeding stock is currently being used and evaluated by commercial producers and is likely to replace or revitalize current stocks and thus enhance the production of Kumamoto oysters.

Review Publications
Camara, M.D., Vadapolas, B. 2009. Genetic aspects of restoring Olympia oysters and other native bivalves: Balancing the need for action, good intentions, and the risks of making things worse. Journal of Shellfish Research. 28(1): 121-145.

Taris, N.G., Lang, R.P., Reno, P.W., Camara, M.D. 2009. Transcriptome response of the Pacific oyster (Crassostrea gigas) to infection with Vibrio tubiashii using cDNA AFLP differential display. Animal Genetics. 40:663-677.

Lang, R.P., Langdon, C.J., Taris, N.G., Camara, M.D. 2010. Use of laboratory assays to predict subsequent growth and survival of Pacific oyster (Crassostrea gigas) families planted in coastal waters. Aquaculture. 306:68-79.

Taris, N.G., Boudry, P., Bonhomme, F., Camara, M.D., Lapegue, S. 2009. Mitochondrial and nuclear DNA analysis of genetic heterogeneity among recruitment cohorts of the European flat oyster, Ostrea edulis. Biological Bulletin. 217:233-241.

Lang, R.P., Bayne, C.J., Camara, M.D., Cunningham, C., Jenny, M.J., Langdon, C.J. 2009. Transcriptome profiling of selectively bred Pacific oyster Crassostrea gigas families that differ in tolerance of heat shock. Marine Biotechnology. 11:650-668.

Camara, M.D. 2011. Changes in molecular genetic variation at ALFP loci associated with naturalization and domestication of the Pacific oyster (Crassostrea gigas). Aquatic Living Resources. 24:35-43.

Last Modified: 06/22/2017
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