Location: National Cold Water Marine Aquaculture Center
2023 Annual Report
Objectives
Objective 1: Expand and optimize approaches for multi-trait selection in Atlantic salmon. Component 2: Problem Statement 2A
Subobjective 1A. Develop a multi-trait selection index in Atlantic salmon germplasm selected for carcass weight, fillet fatty acid levels, and sea lice resistance.
Subobjective 1B. Generate a reference genome assembly and genomic research resources for North American Atlantic salmon.
Subobjective 1C. Evaluate and validate genome-enabled selection strategies for resistance to sea lice in North American Atlantic salmon.
Subobjective 1D. Characterized genetic × environment interactions of Atlantic salmon selected for performance in net pens through evaluations in recirculating aquaculture systems.
Objective 2: Advance genetic improvement technologies for the eastern oyster. Component 4: Problem Statement 4A
Subobjective 2A. Integrate laboratory disease challenge protocol for measuring Dermo resistance in a family-based breeding program.
Subobjective 2B. Discover and validate candidate SNP markers for Dermo resistance from RNA-seq data.
Objective 3: Improve Fish Health in Atlantic salmon aquaculture by determining the susceptibility of North American Atlantic salmon selected for performance to new and emerging pathogens and develop strategies to improve fish health.
Component 2: Problem Statement 2A
Objective 4: Optimize production efficiency in recirculating aquaculture systems. This new objective will focus on developing breeding strategies and management practices that ensure the productivity and profitability of raising fish in recirculating aquaculture systems while maintaining high standards of animal well-being.
Approach
U.S. marine aquaculture industries, which consist primarily of molluscan shellfish and Atlantic salmon were valued at $192 million in 2016. Cold water marine aquaculture production has great potential for expansion, and both Atlantic salmon and eastern oysters are widely accepted as seafood by American consumers. Due to increased demand for high quality seafood and advances in genomic and breeding technologies, the East Coast marine aquaculture industry is projected to double in value over the next five years. Commercial salmon and oyster producers predominantly utilize stocks that are not many generations removed from wild, unselected stocks, so there is a need for continuous support to this industry through breeding programs. The NCWMAC is the only Federal research program supporting the U.S. cold water marine aquaculture industry by developing genetically improved salmon which are optimized for aquaculture production efficiency. Aquaculture of the eastern oyster is a large segment of shellfish aquaculture in the US, and minimal selective breeding has been accomplished in this species. In both species, there is a need to improve the performance of existing stocks. This project plan proposes to meet this need through the following objectives: 1) expand and optimize approaches for multi-trait selection in Atlantic salmon and 2) advance genetic improvement technologies for the eastern oyster. Research accomplished during this project will result in the development of genetically improved Atlantic salmon for release to U.S. producers. Experimental protocols and genomic tools developed for the selectively breeding eastern oysters will facilitate and accelerate the development of high-performing, disease resistant oyster lines and will support the East Coast shellfish aquaculture industry.
Progress Report
This is the fourth annual report for Project 8030-31000-005-000D. With respect to Atlantic salmon, carcass weight, fillet fatty acid levels, and fillet astaxanthin content were measured and analyzed from fish cultured in net pens. A multi-trait selection index was implemented for growth (70% weighted) and sea lice resistance (30% weighted) using genotypic estimated breeding values. Broodstock were selected and offspring produced. The improved germplasm was released to industry stakeholders through a material transfer research agreement.
Utilizing the North American Atlantic Salmon single nucleotide polymorphism (SNP) chip produced in FY2022, approximately 750 2018/2019 year-class fish phenotyped for sea lice resistance were used to identify approximately 2,000 potential brood fish within the National Cold Water Marine Aquaculture Center (NCWMAC) cohort based on genomic breeding value (GBV). This selection method was compared to an alternative potential selection method using phenotypic pedigree-based estimated. The GBV accuracy did not differ significantly from traditional pedigree-based breeding values for this generation of salmon but allowed for selection to occur on an individual rather than family-specific basis, thus increasing potential genetic gains.
In anticipation of examining genotype X environment interactions, two strains of Atlantic salmon (St. John River and Gaspe) are being raised at the Conservation Fund’s Freshwater Institute located in West Virginia, the Northern Aquaculture Demonstration Facility in Wisconsin, and at the NCWMAC in Maine. Improved performance has been demonstrated in the St. Johns River fish (a 20% increase in weight compared to the Gaspe fish) at all locations. This study will conclude when the fish reach harvest size (anticipated FY2024).
With respect to eastern oyster research, data from the three previous years of Dermo challenge experiments was used in tandem with pedigree records from the Virginia Institute of Marine Science (VIMS) breeding program to estimate genetic parameters of disease resistance measures. Disease resistance phenotypes from a total of 5,805 individual oysters representing three year-classes and 109 unique full-sibling families were used. Survival status was estimated to be moderately heritable. Genetic correlation between survival status in the challenge experiment and survival status at a field test site with moderate Dermo disease pressure was low. Genetic correlation with survival status at a site with low Dermo disease pressure was close to zero. The estimated genetic parameters allow our collaborators to incorporate disease challenges into their selection index.
Oysters from the Dermo challenge experiments were genotyped with the 60K SNP array developed previously as part of this project. After quality control filtering, genotypes for a total of 5,697 individuals and 33,148 SNPs were used in an association analysis to assess trait architecture of disease resistance measures. The analysis demonstrated that the trait is highly polygenic, but still detected six loci significantly associated with survival in the disease challenge. These data will additionally be used to assess the potential for genomic selection to improve Dermo disease resistance measures.
The NCWMAC developed a Non-Assistance Cooperative Agreement (NACA) with the University of Maine (UMaine). This year, UMaine Aquaculture Research Institute (ARI) researchers contributed five unique Eastern oyster stocks for genomic assessment and potential incorporation into the NCWMAC genetic selection program. Researchers also contributed a prototype online dashboard to aid in site selection and cage type evaluation for use in commercial Eastern oyster culture.
The UMaine ARI in collaboration with the NCWMAC scientists developed an improved assay to increase the speed of phenotypic determinations of salmon pathogen Infectious Salmon Anemia Virus (ISAV). Previous methods required a days-long two-step process to meet international regulatory and trade specifications. The new 1-step assay can be completed in a few hours and demonstrated equal or better performance, sensitivity and specificity compared to previous methods. The new assay was used for industry testing to facilitate international salmon egg transfer from a company in United States to Canada and has been implemented at the NCWMAC to facilitate rapid germplasm distribution to stakeholders.
UMaine’s ARI in collaboration with NCWMAC also continued to refine the geosmin and 2-methylisoborneol test previously developed in FY2022 to detect off flavor in cultured fish and water. The sensitivity of the test was improved since last year’s report from 3 ng/L to 1 ng/L for both target compounds within water samples.
The NCWMAC developed a Non-Assistance Cooperative Agreement (NACA) with Auburn University (AUSL). This year valveometry studies using the MosselMonitor were initiated to evaluate relationships between valve closure and Vibrio counts in oysters. Initial results suggest valve closure rates are negatively correlated with Vibrio load.
To better understand ploidy effects, AUSL studied survival differences in two 4N oyster lines and reciprocal crosses of these lines in differing salinity environments. The four cohorts were deployed to look at maternal and paternal contributions to survival. We will follow this study by investigating how differing survival translates to 3N offspring. The overall goal is to produce 2N and 4N broodstock lines that improve overall survival in 3N oysters.
AUSL also completed a series of experiments to compare effects of thermal and salinity stress between diploids and triploids. When exposed to acute thermal stress, half sib families of diploid and triploid oysters both reached their critical thermal maximum for respiration at ~33 degrees Celsius, and began gaping at ~43 degrees Celsius. Both ploidies were able to recover from exposure to these thresholds but died when temperatures reached 44 degrees. The lack of a difference in physiological and behavioral responses between diploids and triploids suggests that the increased spring/summer mortalities associated with triploids is not likely due to differences in tolerance to acute thermal stress.
Accomplishments
1. Improved salmon pathogen detection assay. Infectious salmon anemia virus (ISAV) is a serious viral pathogen of salmon internationally regulated based on phenotype. Standard phenotypic detection methods require a days-long molecular assay to be performed. ARS researchers in Orono, Maine, in collaboration with University of Maine colleagues developed an improved molecular method that has increased the speed five to tenfold while maintaining equal if not better accuracy for phenotypic determination of ISAV. This improved assay has been transferred to industry stakeholders and provides a positive economic and animal welfare impact.
Review Publications
Delomas, T.A., Hollenbeck, C.M., Matt, J.L., Thompson, N. 2023. Evaluating cost-effective genotyping strategies for genomic selection in oysters. Aquaculture. 562:738844. https://doi.org/10.1016/j.aquaculture.2022.738844.
Li, N., Pan, T., Griffith, A.W., Dellatore, M., Manahan, D. 2023. Integration of physiological and gene expression analyses to reveal biomarkers for protein dynamic mechanisms regulating higher growth and survival among larval oyster families (Crassostrea gigas). Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739918.
