Location: Cool and Cold Water Aquaculture Research
Project Number: 8082-10600-002-000-D
Project Type: In-House Appropriated
Start Date: Dec 14, 2024
End Date: Dec 13, 2029
Objective:
Objective 1: Selectively breed rainbow trout to improve fillet yield and define new phenotypes associated with resiliency to environmental challenges.
Sub-objective 1.A: Perform the 5th and final year of selection for fillet yield in rainbow trout.
Sub-objective 1.B: Characterize the response of the ARS-FY germplasm to triploidy and hypoxic conditions.
Sub-objective 1.C: Characterize genetic control of resilience to acute and chronic temperature stress.
Objective 2: Develop strategies to improve rainbow trout egg hatch rates and survival.
Sub-objective 2.A: Evaluate the use of ultrasonography to identify and eliminate females with poor egg quality.
Sub-objective 2.B: Determine the reproductive potential of offspring from sXX male rainbow trout.
Sub-objective 2.C: Define quantitative trait loci associated with reproductive development in sXX male rainbow trout.
Objective 3: Evaluate and optimize precision breeding approaches for salmonid aquaculture.
Sub-objective 3.A: Improve genomic resources and gene annotation of the rainbow trout genome.
Sub-objective 3.B: Develop an accurate lcWGS genotype imputation pipeline for rainbow trout.
Sub-objective 3.C: Evaluate gene expression of positional candidate genes for BCWD resistance in rainbow trout.
Sub-objective 3.D: Evaluating AI-based machine learning methods for genomic predictions in rainbow trout.
Objective 4: Identify genes and mechanisms regulating performance traits as targets for genetic improvement.
Sub-objective 4.A: Characterize the biological function of Lamp2a as a regulator of growth, nutrient partitioning, and immune function.
Sub-objective 4.B: Identify viral and host genes associated with IHNV host specificity and virulence.
Sub-objective 4.C: Improve the efficiency of gene editing technologies in salmonids.
Sub-objective 4.D: Combine gene editing and germ cell transfer strategies for the production of genetically modified sterile rainbow trout on a commercial scale.
Approach:
In the United States, rainbow trout (Oncorhynchus mykiss) represent the second most valuable finfish aquaculture product. However, in 2021, the US imported approximately 40% of the rainbow trout consumed domestically, indicating an opportunity to increase production to meet current demand and improve U.S. food security. Growth of the domestic rainbow industry is achievable by increasing production efficiency. The project described herein supports this initiative through a multidisciplinary research program that integrates genetics, genomics, and systems biology research toward developing strategies that advance production efficiency. In Objective 1, genetics-based research will define selective breeding strategies to improve fillet yield and characterize the trait of resilience to thermal stress. Research outcomes will benefit production efficiency by increasing the saleable product per unit biomass and assess how selective breeding can enhance rainbow trout resiliency in the face of a warming climate. Objective 2 aims to identify husbandry strategies and genetic markers that will optimize reproductive performance and strategies to produce all-female production lots. Within Objective 3, the research will improve rainbow trout genomic resources and genotyping tools and will seek to identify the gene variants that affect resistance to bacterial cold-water disease, thus aiding the development of precision breeding strategies to improve selective breeding accuracy for superior genetics. Systems-based research in Objective 4 will characterize genetic, genomic, and physiological factors affecting metrics of fish performance, such as fish health, growth, and nutrient utilization. Defining how these factors impact biological processes contributes to developing strategies that improve production efficiency through reduced disease loss and increased product yield. Collectively, findings from this multidisciplinary project will benefit the rainbow trout aquaculture industry, improve resources for scientific researchers, and ultimately promote domestic food security.
