Skip to main content
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

2016 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 2011-2012 year class (YC11-12) salmon in the National Cold Water Marine Aquaculture Center (NCWMAC) salmon breeding program. Fish from YC12-13 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. Crude lipid and fatty acid analysis was conducted on the fish used for harvest evaluation. The results demonstrated that different families contain varying levels of omega-3 fatty acids as well as crude lipid levels. The combined information could be used to reduce the cost of salmon diets and produce fish with desirable amounts of fat in the fillet. 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 YC13-14 families for both phenotypic and genotypic resistance to sea lice infection. To this end, 1000 fish from 120 different YC13-14 families were challenged with sea lice. These challenges yielded phenotypic estimated breeding values for each fish with overall heritability estimates ranging between 0.43±0.1 and 0.19±0.1 depending on the variables included in the models. Based on the phenotypic results, 585 tissue samples from both the challenged fish and the existing broodstock being held for the 17 most resistant families were sent for analysis on the 288 single nucleotide polymorphism (SNP) chip that was created by the Center for Aquaculture Technologies. Research at the NCWMAC shellfish program in Kingston, Rhode Island continued to define resistant and susceptible phenotypes associated with Dermo disease in the eastern oyster. Survival data from the 2015 challenge were analyzed to identify the most resistant and most susceptible families. Tissue samples from these families were processed for DNA and RNA. DNA samples were subject to quantitative PCR to estimate parasite loads and RNAseq libraries were generated from RNA samples collected from oysters post-dermo exposure. In winter 2015/spring 2016 oyster feeding experiments were designed and conducted to test the hypothesis that variation in survival among oyster families exposed to the Dermo-causing parasite through feeding can be explained, at least in part, by variation in feeding behavior. The most susceptible family exhibited the highest feeding rate that was independent of Dermo concentration. The most resistant family exhibited a moderate feeding rate in the absence of Dermo, but slowed its feeding as Dermo concentration increased. Four oyster families spawned in 2015 with genetic links to resistant and susceptible families evaluated in 2015 (spawned in 2014) were challenged with Dermo in an attempt to disentangle variation for Dermo resistance from variation for Dermo tolerance. Experimental oysters were monitored for mortality and parasite load. In addition, oyster tissue samples were collected post-exposure to track progression of the disease and for gene expression and sequencing analysis. Single nucleotide polymorphism (SNP) genotyping assays have been developed for 67 of the novel SNPs mined from previously published oyster sequence data. These assays enabled the validation of 20 SNP markers thus far.

1. Improved resistance to seal 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 2013-2014 year class (YC13-14) to be at 0.19, 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. The genotypic and combined estimated breeding values will be calculated once the genotyping results have been reported back to the National Cold Water Marine Aquaculture Center. Utilization of 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. It is not known how selected oyster lines will perform in different grow-out sites. ARS scientists in Kingston, Rhode Island conducted a field experiment to evaluate the performance (growth, mortality, and yield) of six mass-selected oyster lines at five grow-out sites with varied environmental conditions. Significant oyster line x grow-out site interactions were detected for mortality and yield, and peak mortality at each site coincided with the most prominent oyster pathogen at that site. Selected lines generally performed best at their native site, and some lines exhibited above average performance at multiple sites. Characterization of interactions between oyster lines and where they are grown will 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.