Multi-tissue RNAseq reveals genetic and temporal differences in acute viral (IHN) infection among three selected lines of rainbow trout with varying resistance

Authors: Bledsoe, Jacob; MA, JIA - University Of Idaho; CAIN, KEN - University Of Idaho; BRUCE, TIM - Auburn University; Rawles, Anna; Abernathy, Jason; Welker, Thomas; Overturf, Kenneth - Ken

Submitted to: Fish and Shellfish Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2022
Publication Date: 4/6/2022
Citation: Bledsoe, J.W., Ma, J., Cain, K., Bruce, T., Rawles, A.A., Abernathy, J.W., Welker, T.L., Overturf, K.E. 2022. Multi-tissue RNAseq reveals genetic and temporal differences in acute viral (IHN) infection among three selected lines of rainbow trout with varying resistance. Fish and Shellfish Immunology. 124:343-361. https://doi.org/10.1016/j.fsi.2022.03.034.
DOI: https://doi.org/10.1016/j.fsi.2022.03.034

Interpretive Summary: Aquaculture is the fastest growing sector of animal agriculture and is projected to continue this trend for decades to come. The two most expensive aspects related to aquaculture production are the cost of feed and losses due to disease. This study evaluated the resistance of three strains of rainbow to the commercially important viral pathogen IHNV. These included a strain that has been selected for resistance against the specific strain of IHN used in our challenge for generations (VSel), a strain that has undergone selection for utilization of plant-protein based feeds and previously has shown elevated non-specific disease resistance despite no disease related selection pressures (PSel), and a commercial strain that that has been domesticated for several years but has not been selected for specific viral disease resistance (NVSel). The VSel strain, as expected, showed high resistance, 81%, the PSel demonstrated intermediate resistance, 33%, and the NVSel strain was highly susceptible, showing a survival rate of only 5%. Analysis of gene expression data from several tissues over early time points after pathogen challenge showed that the strain selected for resistance to this specific strain of virus, VSel, appeared to recognize the virus and specifically bound to virus particles preventing uptake and limiting intracellular viral replication. Both the PSel and NVSel strains showed a delayed response to the virus and then proceeded to downregulate metabolic processes and upregulate transcription of immune response genes. In contrast, the PSel demonstrated a more rapid immune response to viral infection and mounted a more robust immune response that led to increased viral resistance in this strain. The results of this study are of tremendous importance to commercial aquaculture producers that there is the potential to promote resistance non-specifically to pathogens and enhance overall disease resistance to fish without having to focus on long-term selection for disease resistance to only one pathogen.

Technical Abstract: Utilizing RNA-seq, this study aimed to compare the transcriptomic response of kidney, liver, and intestine in three improved strains (VSel, PSel, and NVSel) of rainbow trout during acute stages of challenge with infectious haematopoietic necrosis virus (IHNV). The VSel strain has been selected for resistance against the specific strain of IHN used in our challenge, PSel, has undergone selection for utilization of plant-protein based feeds and previously has shown elevated non-specific disease resistance despite no disease related selection pressures, and the final strain, NVSel, is a commercial strain that has been domesticated for several years but has not been selected for specific viral disease resistance. Following a 21-day IHNV challenge, Kaplan-Meier survival estimator curves and cumulative percent survival (CPM) showed significant differences in IHNV resistance across strains: VSel - 19.3% ± 5.0, PSel - 67.3% ± 3.0, NVSel - 94.6% ± 4.1 CPM. To evaluate acute responses to IHNV infection, whole blood, as well as samples from the kidney, liver, and intestine were collected at 0, 4, 12, 24, and 48 hours post infection (hpi). Serum lysozyme activity showed strain and temporal effects during the acute infection phase, with PSel showing the highest activity at 0 and 48 hpi. Differential gene expression responses were detected, with varying degrees, in all tissues across all strains and stepwise temporal comparisons. Evaluation of upregulated immune related genes showed the highest expression of unique genes expressed by the PSel strain in both kidney and intestine with NVsel having the greatest number in liver. A significant number of genes were shared between Psel and NVsel in all tissues while the Vsel strain only had a limited number of genes in which it shared expression with the Psel strain and none were shared directly with the NVsel strain. The Vsel strain showed upregulation for a particular subset of viral recognition genes early in the infection and rather limited upregulation of immune genes later while continuing to maintain regulation of metabolic regulatory genes as a consistent level. The NVsel strain showed a downregulation of metabolic related genes and a limited upregulation of immune genes while the Psel strain showed similar downregulation of metabolic genes when compared to the NVsel strain yet it had a much more robust expression of innate immune genes.