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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

2015 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 second generation broodstock selected for improved carcass weight from the 2014 year class of salmon in the NCWMAC salmon breeding program. Fish from the 2010 year class had been cultured in marine net pens in collaboration with industry, and growth data were analyzed to obtain estimated breeding values on broodfish to be spawned as a line selected for increased carcass weight. The mean carcass weight for 2014 year class St. John’s stock fish from the breeding program was 4.04 ± 0.02 kg compared to a mean carcass weight of 2.32 ± 0.08 kg for control fish cultured under the same conditions. Salmon were 74.13% larger than control line fish (2.32 kg) used as a control line. Data from fish cultured in net pens was used to calculate breeding values on captive sibling adult broodfish and were spawned in the fall of 2014. Breeding values of female (N=146) brood fish ranged from 234.3 to 999.0 g (mean=385.9) and male (N=69) breeding values ranged from 235.9 to 980 g (mean=401.8). A total of 133 viable families were produced with mean breeding value of 392.6 g (+0.48SD) from the population mean) for this select population. Eyed eggs were disinfected and incubated in separate hatching jars or trays. Fry were transferred to separate rearing tanks prior to first feeding and are being raised to parr size. When the fish reach 20-40 grams, individual fish will be pit tagged and cultured communally before being stocked into sea cages for performance evaluations and some fish will also be used in additional research studies evaluating sea lice resistance and evaluation of alternative ingredients in salmon diets. Research was initiated to define resistant and susceptible phenotypes associated with Dermo disease in the eastern oyster. Six oyster families with genetic links to resistant and susceptible families were exposed to the disease-causing parasite by either direct injection into oyster tissue or through feeding. Experimental oysters were monitored for mortality and parasite load. In addition, oyster tissue samples were collected at 6hr, 36 hr, 7 days, and 28 days post-exposure for gene expression and sequencing analysis. Single Nucleotide Polymorphisms (SNPs) were mined from an existing eastern oyster sequence dataset. Specifically, published sequence information was available from two oyster families, one resistant and one susceptible, that had been exposed to the bacterium responsible for Roseovarius Oyster Disease (ROD). Sequence data from the two families were compared and differentially expressed genes were identified. Differentially expressed genes are assumed to be indicative of how resistant and susceptible oysters differ in their response to the disease and therefore are good candidates for genes associated with disease resistance. Polymorphisms within differentially expressed genes were identified and further evaluated for their utility in a high-throughput genotyping assay. A total of 477 unique SNPs that meet the criteria for high-throughput genotyping were identified. Two populations of cultured oysters were sampled before and after a Dermo disease-induced mortality event and sampled individuals were genotyped at 21 genetic loci (20 microsatellites and 1 SNP). Analysis of the genotype data identified significant differences in allele frequencies in the before and after samples at two loci for both populations tested and is consistent with previous reports of genetic markers associated with disease resistance. High quality, high molecular weight DNA was extracted from oyster tissue for the sequencing of the eastern oyster genome as a collaborator in the genome sequencing project was funded by the USDA National Institue of Food and Agriculture-Agriculture and Food Research Initiative.

1. Atlantic salmon marker panel developed for selective breeding. Scientists at the National Cold Water Marine Aquaculture Center in Franklin, Maine, 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 in Atlantic salmon. The markers are evenly distributed across the salmon genome and have been validated in North American Atlantic salmon stocks. 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. Disease susceptible and resistant eastern oyster families identified. Scientists at the National Cold Water Marine Aquaculture Center, Shellfish Genetics Lab in Kingston, RI subjected eastern oysters to Dermo disease and measured survival and parasite load and identified the most and least resistant families. Dermo disease has serious and negative impacts on oyster production throughout the Northeast and Mid-Atlantic U.S. Characterization of the disease variation in cultured stocks 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.