Location: Pacific Shellfish Research Unit
2025 Annual Report
Objectives
Shellfish aquaculture is a well-established sustainable industry on the United States West Coast (USWC) with harvested products valued at more than $224 million annually in 2022. Despite this high value and increasing demand, expansion of the USWC shellfish aquaculture industry is currently constrained by: 1) high oyster mortality during grow-out and 2) the need to comply with environmental regulations concerning the role and impact of shellfish farming practices in the estuarine environment. This project is designed to: 1) proactively address the risk posed by the Ostreid Herpesvirus-1 microvariant (OsHV-1 µVar) to Pacific oyster aquaculture by advancing a new Pacific Oyster Genomic Selection project (POGS) to select for increased survival to OsHV-1 µVar and provide OsHV-1 tolerant families of broodstock to the USWC industry, 2) characterize the genetic architecture and polygenic mechanisms influencing Pacific oyster response to OsHV-1 µVar and non-viral stressors that contribute to oyster mortality, and 3) explore relationships between shellfish aquaculture, burrowing shrimp, and eelgrass and the functional role of habitats at the estuarine seascape scale to provide growers and resource management agencies strategies for adopting practices including integrated pest management at larger scales. Objective 1: Develop genetic improvement strategies and improved stocks having increased resistance to Ostreid herpesvirus-1 (OsHV-1). Sub-objective 1.A: Use family breeding to increase survival to OsHV-1 using a paired laboratory and field approach. Sub-objective 1.B: Develop a high-throughput and low-cost genetic workflow to implement genomic selection in Pacific oysters. Sub-objective 1.C: Identify and characterize the genetic and physiological basis of disease tolerance and persistency of OSHV-1 in Pacific oysters. Objective 2: Develop strategies to reduce on-farm mortalities from Pacific oyster mortality syndrome and environmental stressors in Pacific oyster aquaculture. Sub-objective 2.A: Investigate and quantify the interactions between the oyster genome and biotic and abiotic environmental factors involved in summer mortalities. Sub-objective 2.B: Evaluate oyster sex determination, fecundity and reproduction as a determining factor for growth and condition index leading to stress during summer. Sub-objective 2.C: Assess the extent of genotype-by-environment interaction in field survival between an OsHV-1 positive estuary and an OsHV-1 negative estuary. Objective 3: Develop methods to quantify the environmental impacts and ecosystem services of Pacific oyster aquaculture. Sub-objective 3.A: Quantify the interaction between oyster aquaculture, burrowing shrimp and aquatic vegetation at the estuarine seascape scale and verify models across estuaries. Sub-objective 3.B: Quantify and model burrowing shrimp populations in seascapes that include both oyster aquaculture and shrimp dominated areas in US West Coast estuaries. Sub-objective 3.C: Quantify the function of intertidal habitats including oyster aquaculture, aquatic vegetation and burrowing shrimp dominated habitat for managed species of fish and invertebrates at the estuarine seascape scale.
Approach
Objective 1 – Genetic improvement strategies and improved POGS breeding stocks that demonstrate increased survival to the Ostreid herpesvirus will be achieved using paired laboratory and field exposures where juvenile oysters are deployed in the laboratory for short term exposures to OsHV-1 µVar as well as at a field location where OsHV-1 is present. Survival will be monitored and animal models used to estimate heritability and generate pedigree estimated breeding values for each family. An imputation-based method of genomic selection will be evaluated to increase the speed of genetic gain. Genes that confer increased tolerance to OsHV-1 will be investigated in laboratory trials using oyster families selected based on previous year survival and challenged with OsHV-1 µvar. Concurrent water and tissue samples will be used to compare transcriptomes. Latent OsHV-1 infections that present an extreme risk to the oyster industry will be investigated utilizing differential accumulation of RNA species from asymptomatic tissues.
Objective 2 - Strategies to reduce on-farm mortalities in farmed USWC Pacific oysters will be investigated by examining factors contributing to field mortality during summer. Survival, growth, and gene expression patterns in juvenile oysters will be examined in laboratory experiments using toxic and non-toxic algae to determine if exposure renders oysters more susceptible to secondary bacterial infections. Oyster sex, fecundity, and reproductive investment leading to stress during summer will be examined by comparing gene expression in triploid and diploid animals to determine the genetic basis of undesirable increased fecundity. The extent of genotype-by-environment interaction in field survival will be assessed by deploying POGS breeding families in a second OsHv-1 negative estuary, establishing an environmental monitoring program at both breeding sites, and deploying families of oysters from different lines alongside POGS cohorts to assess survival more frequently and sample tissues for RNA/DNA analyses to explore correlations with environmental data.
Objective 3 - The interaction between oyster aquaculture, burrowing shrimp and eelgrass at the estuarine seascape scale will be quantified using models and verified across USWC estuaries. Data collected from unmanned aerial vehicles will be used to follow change in habitat mosaics (shellfish culture, eelgrass and open unstructured sand/mudflat) over time. Populations of burrowing shrimp will be monitored annually at long-term monitoring sites within dense shrimp colonies and burrow counts used to estimate shrimp abundance at two scales including widely spaced grid points across the mosaic of shellfish and adjacent shrimp beds and at closer grid points across individual oyster beds or borders to distinguish shrimp recruitment from movement of larger individuals. The function of these intertidal habitats including shellfish aquaculture for managed species of fish and invertebrates will be assessed using remote underwater cameras to capture data over multiple days and tidal cycles and beach seines to directly sample fish and invertebrates.
Progress Report
This report documents progress for project 2076-10600-001-000D, "Improving the Sustainability of Pacific Oyster Aquaculture", which started December 2024, and continues research from project 2076-63000-005-000D, "Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries".
Sub-objective 1.A focuses on the use of family breeding to increase the survival of Pacific oysters to ostreid herpes virus (OsHV-1) using a paired laboratory and field approach. Pacific oysters from the ARS Pacific Oyster Genomic Selection (POGS) project were challenged with a more virulent strain of the virus (OsHV-1 microvariant) from San Diego Bay in controlled laboratory experiments and planted on commercial aquaculture farms in California and Washington. Genetic data generation for the laboratory experiments is ongoing, with field deployed animals growing well and being monitored at both locations to date.
Sub-objective 1.B is designed to develop a high-throughput and low-cost genetic workflow to implement genomic selection in Pacific oysters. A panel of microhaplotype markers is being developed for Pacific oysters. The panel has been tested in multiple rounds of sequencing, with continual improvement in each round. The non-finalized panel is able to assign parents to offspring with a high level of certainty, but further work is needed to refine the panel for breeding program scale use.
Sub-objective 1.C identifies and characterizes the genetic and physiological basis of disease tolerance and persistence of OsHV-1 in Pacific oysters and addresses two research avenues and hypotheses. Hypothesis 1.C.1 is that genes that confer increased tolerance to OsHV-1 are present in Pacific oyster populations being cultivated in the U.S Pacific Northwest. Progress includes finishing a gene expression profiling in Midori oysters (originating from Southern Japan) and Miyagi oysters (originally from Miyagi prefecture in Northern Japan) challenged with OsHV-1 microvariant in a controlled laboratory setting. Mixed families were used due to lack of family-level performance data. Analysis has been completed leading to the detection of immunity pathways involved in response to the virus. Increased tolerance appears to be related to constitutively expressed genes. Hypothesis 1.C.2 is that OsHV-1 and its microvariants can remain latent (present but without sign) in tissues using similar mechanisms as other viruses within the Herpesviridae family. These mechanisms include non-coding long RNA species and small RNAs expressed to repress the basal immunity of oysters. A pilot experiment was run on previously OsHV-1 positive Pacific oysters from Tomales Bay, California, provided by collaborators at Hog Island Oyster Company. Polymerase chain reaction (PCR) confirmed the presence of latent virus; however, no viral RNA was detected after deep sequencing of hemolymph from these oysters. Alternative approaches for a new experiment are being explored.
Sub-objective 2.A investigtes and quantifies the interactions between the oyster genome and biotic and abiotic environmental factors involved in summer mortalities. A biological safety level 2 certification was recently obtained after modifying and equipping spaces. ARS researchers in Newport, Oregon, obtained toxic and non-toxic algae strains from the same genus to carry out laboratory-controlled comparisons. Three pilot experiments were carried out so far to obtain clearance rates of these algae and algae regularly fed to Pacific oysters. A protocol has been developed to sample challenged oyster tissue.
Sub-objective 2.B evaluates oyster sex determination, fecundity, and reproduction as a determining factor for growth and condition index leading to stress during summer. Triploid oysters were obtained from collaborators at the Pacific Aquaculture and Coastal Resources Center (PACRC) at the University of Hawai’i in Hilo, Hawaii. The gametogenic condition of these oysters varied from very fecund to non-fecund. RNA was extracted from these oysters, and ARS researchers in Newport, Oregon, performed a real-time polymerase chain reaction (qPCR) on five pre-selected genes in sex-determination and maturation pathways. Genes encoding for FOX-L2 and Beta-catenin were found to be differentially expressed in correlation with fecundity, with higher levels in more fecund oysters. Messenger RNA (mRNA) was fully sequenced from these oysters to find additional markers, and the data are being analyzed. A new batch of triploid oysters will be sent in FY2026 for additional testing and to confirm these results. These results will help to understand the reversion of triploids from sterile to non-sterile and having substantial gonad development as well as the basis of reproductive sterility in triploids.
Sub-objective 2.C assesses the extent of genotype-by-environment interaction (GxE) in field survival between an OsHV-1 positive estuary and an OsHV-1 negative estuary. ARS researchers in Newport, Oregon, implemented a new experiment wherein two oyster populations (Midori/Miyagi) were deployed in three estuaries: 1) Willapa Bay (WB), Washington, (OsHV-1 negative), 2) Tomales Bay (TB), California, (OsHV-1 positive), and 3) San Diego Bay, California, (OsHV-1 microvariant positive). Oyster size and survival was measured at all sites and RNA samples taken every two weeks at the Tomales Bay site. Sonde instruments were deployed alongside oysters at each site to record continuous environment measurements. The POGS breeding program deployed oysters to WB and TB to assess the magnitude of a GxE effect at the family level within the breeding program population. The oysters are growing well in both estuaries and will be lethally sampled when they reach market size.
Sub-objective 3.A quantifies the interaction between oyster aquaculture, burrowing shrimp and aquatic vegetation at the estuarine seascape scale and verification of models across multiple estuaries. A geographic information system (GIS) with aquaculture and eelgrass layers was previously completed using 2020 ortho-imagery of Willapa Bay, Washington, tidal flats and used to quantify the interaction between eelgrass and oyster aquaculture at the estuarine seascape scale. ARS researchers in Newport, Oregon, completed a new GIS for Grays Harbor, Washington, and Tillamook Bay, Oregon, for this project in order to compare patterns and models across estuaries.
Sub-objective 3.B quantifies and models burrowing shrimp populations in seascapes that include both oyster aquaculture and shrimp dominated areas in U.S. West Coast estuaries. Progress was made collecting first year ground survey data in two broad areas across Willapa Bay where the distribution of burrowing shrimp has been changing and undermining oyster culture operations.
Sub-objective 3.C quantifies the function of intertidal habitats including oyster aquaculture, aquatic vegetation, and burrowing shrimp dominated habitat for managed species of fish and invertebrates at the estuarine seascape scale. Progress included a re-investigation of previously collected data using underwater cameras and a pilot scale collection effort to examine camera deployment angles that target juvenile Dungeness crab and English sole, two species of interest. GIS layers for Willapa Bay were also used to select study sites for 2026 spring and summer surveys in Willapa Bay.
Accomplishments
Review Publications
Ruesink, J.L., Mawson, C., Allen, B., Barrett, J., Beugli, D., Booth, S., Butler, L., Dewey, B., Donoghue, C.R., Dumbauld, B.R., Feldman, K., Forster, Z., Garcia, S., Gross, J.A., Hudson, B., Hull, W., Iyer, V., Katla, A., Kraft, L., Paul, B., Pruitt, C., Vashisth, A., Patten, K. 2025. Efficacy, non-target impacts, and costs of mechanical control options against a bioturbator in bivalve aquaculture. Aquaculture. 596(1). Article 741788. https://doi.org/10.1016/j.aquaculture.2024.741788.
Andersen, L.K., Thompson, N., Abernathy, J.W., Ahmed, R.O., Ali, A., Al-Tobasei, R., Beck, B.H., Calla, B., Delomas, T.A., Dunham, R.A., Elsik, C.G., Fuller, S.A., Garcia, J.C., Gavery, M.R., Hollenbeck, C.M., Johnson, K.M., Kunselman, E., Legacki, E.L., Liu, S., Liu, Z., Martin, B., Matt, J.L., May, S.A., Older, C.E., Overturf, K.E., Palti, Y., Peatman, E.J., Peterson, B.C., Phelps, M.P., Plough, L.V., Polinski, M.P., Proestou, D.A., Purcell, C.M., Quiniou, S., Raymo, G., Rexroad III, C.E., Riley, K.L., Roberts, S.B., Roy, L.A., Salem, M., Simpson, K., Waldbieser, G.C., Wang, H., Waters, C.D., Reading, B.J. 2025. Advancing genetic improvement in the omics era: Status and priorities for United States aquaculture. BMC Genomics. 26. Article 155. https://doi.org/10.1186/s12864-025-11247-z.
Anderson, E.C., Clemento, A.J., Campbell, M.A., Pearse, D., Beulke, A.K., Columbus, C., Campbell, E., Thompson, N., Garza, J.C. 2025. A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon. Evolutionary Applications. 18(5). Article e70110. https://doi.org/10.1111/eva.70110.