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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Research Project #437429

Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

2021 Annual Report

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

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 second annual report for Project 8030-31000-005-00D, which officially began on 10/28/2019. With respect to Atlantic salmon, carcass weight, fillet fatty acid levels, and astaxanthin were measured and analyzed for fish grown in net pens. Additionally, siblings of these fish were infected with sea lice and evaluated for sea lice resistance. A multi-trait selection index was implemented, broodstock selected, and offspring were produced. The improved germplasm was released to industry stakeholders. In the past year, we tested and refined the genome assembly algorithm and bioinformatic pipeline to generate a better quality sequence scaffold. We are currently using the genotype data from the new 50K single nucleotide polymorphism (SNP) array to generate a new high-density linkage map for anchoring and ordering the scaffolds onto complete chromosome sequences. The new SNP array is commercially available and has attracted much interest from commercial breeding companies and companies that provide biotechnology and diagnostic services to the aquaculture industry. It was used to genotype over 2,000 fish from more than 100 full-sib families. With this combined pedigree and genotypes dataset, we can generate the high-density linkage map necessary for improved reference genome assembly. The SNP array will be used in the selective breeding strategy this fall. St. John River and Gaspe strain Atlantic salmon broodstock were spawned and approximately 4,000 eggs from each strain were sent to the Conservation Fund’s Freshwater Institute located in West Virginia and the Northern Aquaculture Demonstration Facility in Wisconsin. Another batch of eggs was kept and maintained at the National Cold Water Marine Aquaculture Center (NCWMAC). Atlantic salmon parr are being compared at each of the three locations. The fish will be grown in a recirculating aquaculture system and evaluated at harvest. In FY2021, the USDA ARS NCWMAC shellfish genetics lab focused on improving and developing new tools to enhance eastern oyster breeding. To support our project and a larger, Eastern Oyster Breeding Consortium (EOBC) effort funded by the Atlantic States Marine Fisheries Commission (ASMFC), we performed a laboratory disease challenge experiment in fall/winter 2020 to evaluate 30 2019 year class (YC) families for resistance phenotypes and measure genetic parameters for Dermo resistance traits. We also collected tissue samples from resistant and susceptible oysters for RNAseq and Genome-Wide Association (GWAS) studies to identify genetic markers/genomic regions associated with Dermo resistance. We observed significant differences in resistance phenotypes across families (e.g. survival ranged from 13 % to 75 %) and modest heritability for survival in response to challenge (h2und = 0.12). Processing of tissue samples for the RNAseq study was delayed due to COVID-19 restrictions. A second challenge with 40 2020 YC families is currently underway. To advance a common genomic approach for regional eastern oyster breeding needs, one of our scientistsworked with members of the EOBC to develop a SNP chip for high throughput genotyping of the eastern oyster. A total of 270 oysters collected from throughout the species U.S. range were resequenced to identify SNPs. Over 3M candidate SNPs were submitted to Thermo Fisher for a 600K axiom SNP array design. The 600K array was screened with ~1000 oysters to identify the best performing SNPs. Approximately 280,000 SNPs on the array performed well and were informative. These SNPs were filtered according to Axiom guidelines to construct a 60K breeding array. The 60K array design was finalized, and 60K array manufacture was completed in June 2021. This high-density, high throughput genotyping tool will facilitate the Dermo resistance GWAS study and genomic selection in the Eastern oyster. The NCWMAC developed a Non-Assistance Cooperative Agreement (NACA) with the University of Maine starting in September 2020. For the first year, the University of Maine used the funding for personnel, graduate student stipends, undergraduate interns, and project-specific equipment purchases at the Darling Marine Center and the University of Maine Cooperative Extension Diagnostic and Research Laboratory. Two faculty members were hired that specializes in finfish nutrition, an aquaculture innovation specialist was hired for shellfish work and to manage the experimental farm, a part time administrative assistant was hired to track the USDA ARS budget and reporting specifically, and other existing support staff are being funded to work on project objectives. Equipment was purchased for the Darling marine center that allows for research to evaluate the field performance of genetically selected Eastern oysters in varying geographic regions and develop localized selective breeding strategies that improve performance for economically important traits, including growth and disease resistance, and for gear to operate the experimental marine farm (Objective 2). Equipment was purchased for the University of Maine Cooperative Extension Diagnostic and Research Laboratory to determine North American Atlantic salmon's performance in response to new and emerging pathogens and develop strategies to improve fish health. In particular, a suite of advanced molecular equipment will be used to optimize assays to detect Infectious Salmon Anaemia Virus Highly Polymorphic Region 0 (ISAV HPR0) in water and fish tissues (Objective 2). Some early successes of the NACA include convening the Aquaculture session in the Regional Association for Research on the Gulf of Maine (RARGOM) Annual Science Meeting, teaching a Shellfish Techniques course at the Darling Marine Center to prospective aquaculturists, installing an experimental aquaculture station growing eastern oysters, sea scallops, and kelp, and deploying oceanographic instrumentation at multiple sites along the coast to inform aquaculture site selection models. Preliminary site selection products are available at and and have been introduced to growers in the Aquaculture in Shared Water course and our Shellfish Techniques course. The NCWMAC developed a NACA with Auburn University starting June 1, 2020. Some early successes of the NACA include the creation of a functional, on-site, oyster ecophysiological lab, training of students in the use of new research equipment (i.e., respirometry system), and conducting preliminary experiments examining effects of thermal stress on metabolic depression in oysters and the relation of metabolic depression to critical thermal maxima. Novel research into the relationship between sperm activity and low salinity was published (Nichols et al., 2021). In addition, the team developed collaborative research with a multi-university regional oyster selective breeding program. Auburn University Shellfish Laboratory (AUSL) continues to maintain multiple lines of tetraploids used by hatcheries to produce triploid oysters for farm production. A field-based project was established in August 2020 withhalf-sibling seed oysters for performance evaluation of triploid oysters produced from different tetraploid lines compared to diploid oyster seed at several cooperating commercial oyster farms. AUSL continues work on two new strains of tetraploids to broaden the genetic diversity and availability of tetraploid lines, and develop improved diploid lines targeting shell shape for Gulf-wide use.

1. Improved Eastern oyster genomic tools. The Eastern oyster aquaculture industry grows at an annual rate of 5-10 percent, but production is limited by disease and environmental stressors exacerbated by climate change. New approaches and tools are required for genetic improvement to keep pace with the changing environment. ARS researchers at Kingston, Rhode Island, in collaboration with the Eastern Oyster Breeding Consortium (EOBC), conducted a resequencing project to identify single nucleotide polymorphisms distributed throughout the Eastern oyster genome. This collaboration resulted in the identification of over 3 million high-quality single nucleotide polymorphisms (SNPs), which were filtered to create a 600K SNP chip for high throughput genotyping. The 600K SNP chip was screened with 1000 oysters from geographically distinct wild and selected populations to identify high--performing, informative SNPs for designing and manufacturing a publicly available 60K SNP chip. The 60K SNP chip will aid in the discovery of genetic markers for commercially valuable traits and support advanced genome-based selection techniques for the Eastern oyster.

Review Publications
Sullivan, M., Proestou, D.A. 2021. Survival and transcriptomic responses to differen perkinsus marinus exposure mentiods in and eastern oyster family. Aquaculture.
Modak, T., Litterman, R., Puritz, J., Johnson, K., Roberts, E., Proestou, D.A., Guo, X., Gomez-Chiarri, M., Schwartz, R. 2021. Exceptional genome-wide copy number variation in the eastern oyster (Crassostrea virginica). Philosophical Transactions of the Royal Society B.
Colombo, S., Emam, M., Peterson, B.C., Hall, J., Burr, G.S., Zhang, Z., Rise, M. 2021. Freshwater, landlocked Grand Lake strain of Atlantic salmon (Salmo salar L.) as a potential genetic source of long chain polyunsaturated fatty acids synthesis. Frontiers in Marine Science.