Morag Clinton | Geology Reports

USGS2026

Transcriptional changes in wild Yukon River Chinook Salmon associated with Ichthyophonus infections

Objective We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality. Methods Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000 km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures. Results Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction—all processes that are known to be influenced by senescence during spawning migrations. Conclusions Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).

Journal of Aquatic Animal Health↗

USGS2026

Biomarkers of mortality risks in Yukon Chinook salmon

Premature mortality of spawning adult Pacific salmon ( Oncorhynchus species) can strongly influence population dynamics and complicate escapement-based management. Heat stress and Ichthyophonus infections have been identified as probable drivers of premature mortality in Yukon River Chinook salmon ( Oncorhynchus tshawytscha ) and likely contributors to low spawning abundance. We leveraged a multiagency study focused on Ichthyophonus using lethally collected heart tissue as a rare opportunity to investigate these two stressors jointly in the same individuals to accomplish two tasks: (1) provide a more comprehensive premature mortality risk index that combines heat stress and Ichthyophonus detection and (2) investigate the feasibility of using skeletal muscle tissue gene transcription (mRNA of select genes) as a non-lethal biomarker of Ichthyophonus . Water temperatures ranged from ~12–22°C across four sites and two years. In both 2023 and 2024, effects were identified in ~30% of salmon at Pilot Station, Alaska, and ~70% of salmon by the time they reached mid river (Rapids, Fort Yukon). Mortality risk is presumably highest among fish with multiple stressors, which were detected in ~25% of Chinook salmon in the middle river sites in 2023 when it was warmer and 9—18% in 2024 when it was cooler. We explored Chinook salmon genes that respond to Ichthyophonus with a full transcriptome analysis that measured mRNA of 17,569 genes and identified 53 that were related to Ichthyophonus infection. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction– all processes known to be influenced by senescence during spawning migrations and imply accelerated senescence of infected fish. Primers were developed for 21 of the differentially expressed Chinook salmon genes for qPCR measurements of their mRNA that could be used in classification models. Attempts to statistically deduce Ichthyophonus infection from Chinook salmon gene transcription at the individual and group levels included some potential for separating fish where Ichthyophonus was not detected compared to those with high infection intensities (as judged by qPCR that directly detects Ichthyophonus DNA). Fish with relatively low infection intensities did not have a separate gene transcription signature and grouped with the undetected Ichthyophonus fish in two-thirds of the cases and high infection in onethird of cases. Among the genes with the most utility to predict Ichthyophonus infection were retinoic acid receptor beta (regulates cellular states) and lysozyme CII (immune system gene). Interannual variation in the gene transcription of fish with undetected Ichthyophonus was a complicating factor that demonstrated a need for additional refinement and testing. Overall, this study identified two broad findings: (1) The proportion of migrating fish with one or both of the assessed stressors ( Ichthyophonus infections and/or elevated levels of heat shock protein) can be very high (~70%) and (2) we recommend measuring interannual variation of gene transcription in any study that seeks to develop gene transcription as a biomarker.

Alaska↗