Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during infection with infectious hematopoietic necrosis virus

Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain's superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental viral infection using the CSF 220-90 isolate of Infectious Hematopoietic Necrosis virus (IHNv). At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with IHNv by static bath and one tank was mock challenged by static bath (Sham). Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. Infections were mild with mortality rates near 50% over the 21 day trial and no significant difference in mortality rates between the two strains of trout. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status. Overall design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all groups at 4 days post challenge (dpc) and 20 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain.