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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Research Project #437692

Research Project: Improving Salmonid Health through Breeding, Vaccination and Microbiome Modulation

Location: Cool and Cold Water Aquaculture Research

Project Number: 8082-32000-007-000-D
Project Type: In-House Appropriated

Start Date: Dec 9, 2019
End Date: Dec 8, 2024

Objective 1. Genetic improvement of rainbow trout for disease resilience. Sub-objective 1.a Genetic improvement of disease resistance against Fc using the ARS-Fp-R line. Sub-objective 1.b Identify transcriptional patterns associated with host resistance. Sub-objective 1.c Define and characterize pathogen determinants influencing host genetic resistance. Sub-Objective 1.d Measure disease resistance phenotype and performance on-farm. Objective 2. Improvement of host health through pathogen characterization, vaccine development and characterization of host response to vaccination. Sub-objective 2.a Molecular-genetic characterization of virulence regulation in Yr mediated by the Rcs pathway. Sub-objective 2.b Identify virulence factors in Fc by transposon mutagenesis. Sub-objective 2.c Evaluate environmental factors affecting Fc phenotypes. Sub-objective 2.d Determine heritability of host response to vaccination. Objective 3. Identify factors in production system microbiomes that can be used in strategies to improve animal health. Sub-objective 3.a Determine the microbial composition during biofilm development in raceways. Sub-objective 3.b Reduce the amount of Fc and Fp in biofilms. Sub-objective 3.c Evolve Aeromonas to reduce the ability of Fc and Fp to invade biofilms.

Rainbow trout are a valuable finfish farmed in the U.S. and worldwide. Trout losses from infectious diseases are an important factor limiting production. Three prevalent bacterial diseases of rainbow trout are bacterial cold water disease (BCWD), enteric redmouth disease (ERM), and more recently, columnaris disease (CD). The goals of this project are to 1) develop well-characterized germplasm that exhibits on-farm resistance against multiple bacterial pathogens, 2) determine pathogen virulence mechanisms to aid vaccine development and selective breeding, and 3) characterize and manipulate the microbiome of the aquaculture environment thereby reducing pathogen outbreaks. Our approach incorporates a comprehensive and multidisciplinary strategy that combines selective breeding, quantitative genetics, immunology, and functional genomics of pathogenic bacteria. This research builds on our previous studies in which we developed and released to industry a BCWD resistant line (designated ARS-Fp-R) that has been extensively characterized, and for which we have made progress in uncovering the genetic basis of disease resistance. For the first objective, we continue to improve the ARS-Fp-R line by increasing resistance against CD, determine mechanisms of disease resistance and specificity, and evaluate this line’s on-farm performance in net-pen aquaculture. For the second objective, we characterize virulence factor regulation, evaluate new vaccine candidates for disease prevention and measure the heritability of vaccine response. For the third objective, we utilize metagenomics to define the on-farm microbiome and investigate methods to disrupt pathogen containing biofilms. Results from this research will improve animal well-being, reduce antibiotic use and increase trout production efficiency and profitability.