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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

2019 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
This is the final report project 8030-31000-004-00D which will terminate December 2019. All planned experiments will be completed by the end of FY2019. Progress was made on all three objectives and their subobjectives, all of which fall under National Program 106, Component 1, Selective Breeding, Directed Reproduction, and Development of Genomic Tools. Progress on this project focuses on Problem A, the need to develop genomic tools and Problem B, the need to define phenotypes and develop genetic improvement programs. For the eastern oyster, with respect to Problem A, we sequenced the eastern oyster genome and identified regions of the genome associated with resistance to Dermo disease. A chromosome-level genome assembly was generated and annotated according to the NCBI annotation pipeline. The genome was released to the National Center for Biotechnology Information (NCBI) in January 2018 with reference genome status. Subsequently, genome-resequencing of 92 individuals from four geographic regions and two ecotypes within each region (representing high and low salinity/Dermo exposure environments) was completed at 30X coverage to identify Single Nucleotide Polymorphisms (SNPs) distributed across the genome. Over 30 million SNPs were discovered. Several filtering criteria were used to generate a representative 50K SNP panel and this panel was used for outlier and association analyses to pinpoint segments of the genome associated with Dermo resistance. Under Problem B, we identified components of the Dermo-resistant phenotype including parasite avoidance, parasite elimination, and tolerance, and documented variation in these phenotypes within a breeding population. More importantly, we developed efficient laboratory challenge methods for measuring Dermo-resistant phenotypes within a multi-trait selection framework. These methods will be applied on a large scale within eastern oyster breeding programs in our next project plan. In addition, we used RNAseq, differential expression analysis, and network analysis to characterize gene expression in response to Dermo exposure in eastern oyster families deemed resistant and susceptible in our laboratory challenge experiments. Resistant and susceptible families exhibit significant differences in expression patterns such that gene expression can be used to further define phenotypes for this commercially important trait. For Atlantic Salmon, under Problem B, we made significant progress in defining phenotypic measures and estimating genetic parameters for sea lice resistance and fillet fatty acid levels in Atlantic salmon. A marker panel was developed for selective breeding for sea lice resistance and salmon families were challenged with sea lice to determine heritability for resistance. Atlantic salmon with improved sea lice resistance were crossed and offspring are being evaluated using sea lice challenges. We made progress on identifying families of Atlantic salmon with improved omega-3 fatty acids. We determined that the heaviest fish families consumed the most feed, generally had the highest fillet color scores and fillet omega-3 fatty acid amounts. Fillet color is a function of feed intake and time. A multi-trait selection index for Atlantic salmon was developed, implemented, and offspring were produced. The impact of this research was that improved Atlantic salmon germplasm was developed and released to industry stakeholders.

1. Improved North American Atlantic salmon germplasm. Commercial salmon farms are expected to increase 5-fold over the next 3 years. There is a need for an Atlantic salmon breeding program to support this industry increase. ARS researchers at the NCWMAC have developed a selection index for carcass weight, fillet color, omega-3 fatty acids, and resistance to sea lice in their St. John River strain of Atlantic salmon. Eggs from the improved strain have been provided to industry stakeholders for integration and propagation on commercial farms. Development of salmon germplasm with increased growth, processing characteristics, and disease resistance will improve production efficiency and sustainability of the U.S. salmon industry.

2. Eastern oyster genome. Genomic resources are necessary to promote selective breeding practices that can keep pace with industry priorities and consumer demand. In collaboration with the Eastern Oyster Genome Consortium, ARS researchers produced a high-quality, chromosome-level genome assembly for the eastern oyster. Using the reference genome, ARS scientists and university colleagues identified millions of polymorphic markers distributed throughout the genome. These markers will facilitate the development of high-throughput genotyping tools that will be used to investigate the genetic basis of commercially important traits. The genome and polymorphic markers represent the first step toward precision, genome-enabled selection in the eastern oyster. Implementation of genome-enabled selection methods such as genomic selection has resulted in 20-100% increases in selection accuracy and genetic gain in other aquaculture species but has yet to be tested in the eastern oyster. Genome-enabled selection is particularly useful for traits that are difficult or costly to phenotype, such as Dermo resistance in the eastern oyster.

Review Publications
Jaris, H., Brown, D.S., Proestou, D.A. 2019. Assessing the contribution of aquaculture and restoration to wild oyster populations in a Rhode Island Coastal Lagoon. Conservation Genetics. 20(3):503-516.
Ben-Horin, T., Burge, C., Bushek, D., Groner, M., Proestou, D.A., Huey, L., Bidegain, G., Carnegie, R. 2018. Disease at the interface of aquaculture and wild oyster reefs. Aquaculture Environment Interactions. 10:557-567.
Peterson, B.C., Peatman, E., Ourth, D., Waldbieser, G.C. 2018. Phytogenic feed-additive effects on channel catfish rhamnose binding lectin levels and susceptibility to Edwardsiella ictaluri. Diseases of Aquatic Organisms. 129:99-106.
Peterson, B.C., Chatakondi, N.G., Small, B.C. 2019. Ontogeny of the cortisol stress response and glucocorticoid receptor expression during early development in channel catfish (Ictalurus punctatus). Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 231:119-123.
Proestou, D.A., Corbett, R., Ben-Horin, T., Small, J., Allen, S. 2019. Defining demo resistance phenotypes in an eastern oyster breeding population. Aquaculture Research. 50:2142-2154.