Location: Pacific Shellfish Research Unit
Project Number: 2076-10600-001-000-D
Project Type: In-House Appropriated
Start Date: Dec 14, 2024
End Date: Dec 13, 2029
Objective:
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.
