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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

2020 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 first 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 developed, implemented, broodstock selected, and offspring were produced. The improved germplasm was released to industry stakeholders. Paternal and maternal genome maps of a single fish of North American (NA) origin were reconstructed using long-read sequencing technology and other sequence scaffolding tools. The high-quality genome maps are in the final phase of anchoring into a chromosome-level assembly that will be submitted to a public genome repository for further functional annotation. This reference genome map will be an essential resource for conducting genome association studies, identifying QTL for production traits, and detecting genomic markers that may be used for marker-assisted selective breeding strategies. It will also be valuable for gene-expression studies and ecological and evolutionary research in Atlantic salmon. A high-quality single nucleotide polymorphism (SNP) resource database was generated through alignment of re-sequence data from 80 fish from the USDA-ARS National Cold Water Marine Aquaculture Center (NCWMAC) breeding population to the new reference genome. 50,000 SNPs with high information content were selected for a SNP array. The new SNP array will be used for genetic analyses in the NCWMAC breeding program. Approximately 70 NCWMAC families were phenotyped for sea lice resistance in 2015 to generate pedigree-based breeding values for broodstock in the next generation of the breeding program. Their offspring were phenotyped in 2019 to test the correlation between the pedigree-based genetic merit predictions of the parents from 2015 and the average family performance of their offspring in 2019. Approximately 1,000 of the fish with sea lice phenotypes from the 2015 challenge and 200 parents of fish challenged with sea lice in 2019 will be genotyped with the new 50K SNP chip. The genotype data will be used to predict genomic breeding values for the ~200 parents. We will also test the correlation between the genomic breeding value predictions and the actual average family performance of the progeny in the 2019 sea lice challenge to assess the utility of including genomic information in the selection process. Finally, broodfish for St. John River and Gaspe strains of Atlantic salmon were identified for spawning this fall. Families of fish from both strains will be sent to the Conservation Fund’s Freshwater Institute located in West Virginia and the Northern Aquaculture Demonstration Facility in Wisconsin. Another batch of eggs will be also be maintained at the NCWMAC. Fish at all three facilities will be grown in a recirculating aquaculture system and evaluated at harvest. In FY2020, the NCWMAC shellfish genetics lab focused on improving and/or developing new tools for the enhancement of eastern oyster breeding. To support our new project and a larger, Eastern Oyster Breeding Consortium (EOBC) effort, we completed a small-scale laboratory Dermo disease challenge experiment to test methods for: 1) non-destructive sampling of oyster tissues, and 2) obtaining accurate disease resistance phenotypes at the individual rather than family level. Accurate, individual-based measurements are preferred for Genome-wide Association (GWAS) studies and the application of genomic selection to breeding for Dermo resistance. We found that exposing oysters to 5% epsom salts in 15 ppt seawater for 16 hour led to sufficient shell gaping to inject the pathogen and sample tissue. We also identified the optimal time interval between repeated samplings and determined that repeated sampling of individuals at early and late timepoints post-exposure allows for better measures of Dermo resistance compared to previous protocols. Results from this experiment have contributed to the design for a large-scale Dermo challenge which will include 40 eastern oyster families from the Virginia Institute of Marine Science (VIMS) family-based breeding program. To advance a common genomic approach to address regional eastern oyster breeding needs, the NCWMAC is working directly with members of the EOBC to develop a SNP chip for high throughput genotyping of the eastern oyster. We collected, processed, and prepared 200 oysters from wild and selected populations from Maine, to North Carolina, for resequencing by a commercial provider. Sequence data are being mapped to the eastern oyster reference genome for SNP calling. High-quality, informative SNPs will be submitted to a commercial provider for the design and manufacture of a 600K SNP array.

1. Improved North American Atlantic salmon genetic selection tools. Commercial salmon farms are expected to increase 5-fold over the next three years. There is a need for an Atlantic salmon breeding program to support this industry increase. ARS researchers at Franklin, Maine, and Leetown, West Virginia, have created an improved genome reference for North American Atlantic salmon. The new chip will aid in the discovery of genetic markers for commercially valuable traits in North American Atlantic salmon. The new chip has already attracted interest from commercial breeding companies using salmon of North American origin and from companies that provide biotechnology and diagnostic services to the aquaculture industry.

Review Publications
Proestou, D.A., Sullivan, M. 2019. Variation in global transcriptomatic response to Perkinsus marinus infection among Eastern oyster families highlights potential mechanisms of disease resistance. Fish and Shellfish Immunology. 96:141-151.
Peterson, B.C., Burr, G.S., Pietrak, M.R., Proestou, D.A. 2020. Genetic improvement of North American Atlantic salmon and the eastern oyster Crassostrea virginica at the U.S. Department of Agriculture-Agricultural Research Service National Cold Water Marine Aquaculture Center. North American Journal of Aquaculture. 82:321-330.
Peterson, B.C., Chatakondi, N.G. 2020. Efffects of handling methods on cortisol response and reproductive performance to produce hybrid catfish fry. North American Journal of Aquaculture. 82:153-158.
Gao, G., Pietrak, M.R., Burr, G.S., Rexroad III, C.E., Peterson, B.C., Palti, Y. 2020. A new single nucleotide polymorphism database for North American Atlantic salmon generated through whole genome re-sequencing. Frontiers in Genetics. 11:85.
Good, C., Davidson, J., Straus, D.L., Harper, S.B., Marancik, D., Welch, T.J., Peterson, B.C., Pedersen, L., Lepine, C., Redman, N., Meinelt, T., Liu, D., Summerfelt, S. 2020. Assessing peracetic acid for controlling post-vaccination Saprolegnia spp.-associated mortality in juvenile Atlantic salmon Salmo salar in freshwater recirculation aquaculture systems. Aquaculture Research. 00:1-4.
Pietrak, M.R., Rosser, T.G. 2020. Morphologic and molecular characterization of Gyrodactylus cyclopteri Scyborskaja, 1948 from Cyclopertus lumpus L., 1758. Parasitology Research. 119:879-884.