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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Research Project #428104

Research Project: Genetic Improvement Of Marine Fish and Shellfish

Location: National Cold Water Marine Aquaculture Center

2017 Annual Report

1: Define phenotypic measures, estimate genetic and phenotypic parameters, and develop a selection index in Atlantic salmon for commercially important traits such as carcass weight, cold tolerance, fillet color, fat content, and sea lice resistance. 1A. Define phenotypic measures and estimate genetic parameters for sea lice resistance and fillet fatty acid levels in Atlantic salmon. 1B. Develop a multi-trait selection index in Atlantic salmon germplasm for carcass weight, fillet fatty acid levels, and sea lice resistance. 2: Evaluate and validate the usefulness of incorporating genotypic information into salmon selective breeding program. 3: Establish links between disease susceptible/resistant phenotypes and genotype for the Eastern Oyster, Crassostrea virginica. 3A: Define disease susceptible and disease resistant phenotypes in selectively-bred C. virginica families through disease challenges and transcriptome analysis. 3B: Discover polymorphisms in candidate genes for disease susceptibility and resistance in C. virginica and develop single nucleotide polymorphism (SNP) markers that can be genotyped in a high-throughput assay. 3C: Identify Single Nucleotide Polymorphisms (SNPs) associated with disease-susceptible and disease-resistant phenotypes in C. virginica.

The National Cold Water Marine Aquaculture Center (NCWMAC) addresses the coldwater marine aquaculture industry’s highest priority research needs. Coldwater aquaculture production has great potential for expansion, and both Atlantic salmon and Eastern oysters are widely accepted as seafood by American consumers. Commercial salmon and oyster producers predominantly utilize stocks that are not many generations removed from wild, unselected stocks. Salmon producers are legally required to culture certified stocks of North American salmon, and the NCWMAC is the only program supporting the US coldwater marine aquaculture industry and developing genetically improved salmon. 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) define phenotypes, estimate genetic and phenotypic parameters, and develop a selection index in Atlantic salmon for important traits such as carcass weight, cold tolerance, fillet color, fat content, and sea lice resistance; 2) evaluate and validate the usefulness of incorporating genomic information into a salmon breeding program; and 3) establish links between disease susceptible and resistant phenotypes and genotype 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 and consumers. Identification of genes associated with oyster disease will provide markers that can be used to enhance and accelerate the development of high-performing oyster lines through selective breeding and will support the East Coast shellfish aquaculture industry.

Progress Report
Pedigreed families were produced by spawning broodstock selected for improved carcass weight from 2012-2013 year class (YC12-13) salmon in the National Cold Water Marine Aquaculture Center (NCWMAC) salmon breeding program. Fish from YC13-14 were cultured in marine net pens in collaboration with industry, and growth data will be analyzed to obtain estimated breeding values on broodfish to be spawned as a line selected for increased carcass weight. The long-term goal of the sea lice project is to utilize both phenotypic and genotypic metrics of sea lice resistance to improve the overall resistance to sea lice infection of the Atlantic salmon strains being propagated at the NCWMAC. The primary focus over the past year has been the evaluation and screening of the YC14-15 families for both phenotypic resistance to sea lice infection and collection of tissue samples for analysis once the revised SNP chip work is completed. To this end, 1350 fish from 98 different YC14-15 families were challenged with sea lice. These challenges yielded phenotypic estimated breeding values for each fish with overall heritability estimates ranging between 0.28±0.07 and 0.17±0.1 depending on the variables included in the models. Crude lipid and fatty acid analysis was conducted on the fish used for harvest evaluation. The results demonstrated that the largest families had the highest fillet color scores because fillet color is a function of feed intake and time. We also found that more of the carotenoid, astaxanthin, is deposited in fillets of fish that consume more feed. Omega-3 fatty acid concentrations, such as Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) were also higher in larger fish for the same reasons as fillet color. In addition, our industry partner has developed markers for fillet color and verified these markers with the fish from the NCWMAC. The broodstock can be screened to ensure that the offspring have the markers that indicate the highest levels of carotenoids in the fillet. Research to define resistant and susceptible phenotypes associated with Dermo disease in the eastern oyster continued. Sequence reads from resistant and susceptible oysters exposed to the Dermo-causing parasite in 2015 were mapped to a reference transcriptome and differentially expressed genes (DEG) between exposed and control treatments at seven days post-exposure were detected. Dermo-resistant and -susceptible oysters exhibited distinct transcriptome responses to the parasite. Over 4× more transcripts were differentially expressed between injected and control treatments in the resistant vs. susceptible oysters (344 and 79 respectively) and only one DEG overlapped between resistant and susceptible groups. The majority of annotated DEGs in resistant oysters were associated with Gene Ontology (GO) terms metabolic processes, oxidation-reduction processes, and negative regulation of peptidase activity. 513 putative SNPs were identified in DEGs in the resistant group while 107 were identified in the control group. Four additional oyster families (2 resistant and 2 susceptible) subject to Dermo challenge during the summer of 2016 were processed and sequenced. More in depth analyses, including the new sequence data and using the recently released draft eastern oyster genome as a reference, are currently underway. NCWMAC’s optimized Dermo challenge protocols were applied in a large scale experiment designed to quantify resistance phenotypes in 50 oyster families included in the Aquaculture Genetics and Breeding Technology Center’s (ABC at VIMS) oyster breeding program. 5000 experimental oysters were exposed to the disease and monitored for survival. Tissues from a subset of oysters from each family were collected at 7 and 47 days post exposure to quantify parasite load and Dermo resistance. Sample processing will be completed by August 2017.

1. Heritability and genetic markers for sea lice resistance. Improved resistance to sea lice in Atlantic salmon will reduce the need for expensive ($750,000 per farm per production cycle in Maine) chemical treatments currently used to manage this critical parasite in salmon aquaculture. ARS scientists in Franklin, Maine determined the heritability for sea lice resistance in the 2014-2015 year class (YC14-15) to be at 0.22, indicating a good potential for improvement through selective breeding. Scientists also developed a panel of genetic markers in collaboration with private industry that will be used to increase the efficiency of selective breeding for sea lice resistance. Using improved salmon germplasm will increase the profitability and sustainability of coldwater marine aquaculture in the U.S. and provide quality seafood products to U.S. consumers.

2. Improved fillet quality traits and genetic markers. Improved fillet quality traits such as color and omega-3 fatty acid levels will provide economic benefit to Atlantic salmon farmers and also potentially increase health benefits to consumers. ARS scientists in Franklin, Maine determined that the heaviest fish families generally consumed the most feed, had the highest fillet color scores, Omega-3 fatty acid concentrations, and that fillet color is a function of feed intake and time. Furthermore, our industry partner has developed markers for fillet color and verified these markers with fish from the National Cold Water Marine Aquaculture Center. Using genetic markers developed in collaboration with industry partners, salmon broodstock can now be screened to ensure that the offspring have the markers for the highest levels of carotenoids in the fillet.

3. Sequencing of the eastern oyster genome. Modest genomic resources are currently available for the eastern oyster. ARS scientists in Kingston, Rhode Island participated in the sequencing of the eastern oyster genome. The sequenced eastern oyster genome will expedite the identification of genes underlying traits of commercial importance, enhance current oyster breeding efforts, increase productivity and profitability of the shellfish aquaculture industry, and improve the quality and availability of shellfish products to U.S. consumers.

Review Publications
Nacci, D., Proestou, D.A., Champlin, D., Martinson, J., Waits, E. 2016. Genetic basis for evolved tolerance to dioxin-like pollutants in wild atlantic killifish: more than the aryl hydrocarbon receptor. Molecular Ecology. 25(21):5467-5482.
Reid, N.M., Proestou, D.A., Clark, B.W., Warren, W.C., Colbourne, J.K., Shaw, J.R., Karchner, S.I., Hahn, M.E., Nacci, D., Oleksiak, M.F., Crawford, D.J., Whitehead, A. 2016. The genomic landscape of rapid, repeated evolutionary rescue from toxic pollution in wild fish. Science. 354(6317):1305-1308.
Beldsoe, J., Peterson, B.C., Swanson, K., Small, B. 2016. Ontogenetic characterization of the intestinal microbiota of channel catfish through 16S rRNA gene sequencing reveals insights on temporal shifts and the influence of environmental microbes. PLoS One. 11(11):e0166379. DOI: 10.1371/journal.pone.0166379.
Tlusty, M., Rhyne, A., Szczebak, J., Bourque, B.D., Bowen, J.L., Burr, G.S., Marx, C.J., Feinberg, L. 2017. A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds. PeerJ. 5:e3170. DOI: 10.7717/peerj.3170.