Ag Data Commons

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

Underlying mechanisms for selected disease resistance and enhanced non-specific resistance in rainbow trout

posted on 2024-06-11, 07:29 authored by Aquatic Animal Health Research Unit, USDA-ARS
A critical problem facing all U. S. aquaculture is loss due to disease. In the past year alone, diseases accounted for 90% of all losses of trout intended for sale, greatly impacting the livelihood of our farmers. Previously, we focused on sustainable aquaculture efforts by evaluating the effects of dietary replacement (marine-based to plant-based protein sources) on rainbow trout. Through this effort, we developed a rainbow trout strain that thrives on an all plant-protein formulated diet (PSel/UI strain). In selecting for diet tolerance, we discovered this strain has also undergone positive selection for nonspecific disease resistance to Infectious Hematopoietic Necrosis Virus (IHNV). Therefore, the goal of this project was to determine the mechanisms behind this nonspecific immunity by performing a pathogen challenge and measuring several disease performance characteristics among PSel/UI and two other trout strains commonly used in the commercial aquaculture industry, one selected for disease resistance to these pathogens for several generations and the other completely unselected. We examined lysozyme activity changes in serum and innate gene expression using RNA-sequencing by sampling kidney, spleen, intestine, and liver at time zero and at 4, 12, 24, and 48 hours post-infection with IHNV. We then integrated innate gene expression with disease performance characteristics and made comparisons among strains to identify significant differentially expressed genes and compared with the genetic background of the fish. Through these objectives, we narrowed a set of candidate genes useful in the co-selection of two aquaculturally-important traits: enhanced nonspecific disease resistance with diet utilization. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. USDA-NIFA-SRGP-006544 from the USDA National Institute of Food and Agriculture. Overall design: 270 samples of kidney, spleen, intestine, and liver tissue were taken from three trout strains at time zero and at 4, 12, 24, and 48 hours post-infection with IHNV.


Data contact name

BioProject Curation Staff


National Center for Biotechnology Information

Temporal Extent Start Date



  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

transcriptome; gene expression

Pending citation

  • No

Public Access Level

  • Public

Accession Number


Preferred dataset citation

It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA778763 in the NCBI BioProject database ("

Usage metrics



    Ref. manager