Decoding Hatchery Effects: An Integrative Transcriptomic and Functional Analysis of Coho Salmon
Shruthi Balasubramanian
Mentor: Dr. Tom Iwanicki, Ph.D. Earth Commons institute.
Date/Time: August 25th, 2026 at 2:30 PM.
Abstract: Pacific salmon are ecologically, culturally, and economically important species whose populations have declined across portions of their native range (Walsh et al., 2020). Hatchery programs supplement vulnerable populations by rearing juvenile salmon before release, yet hatchery-reared salmonids often experience lower post-release survival than their wild counterparts (Gaffney et al., 2026a). Improving hatchery practices may therefore better prepare fish for survival after release. Recent work in Coho salmon (Oncorhynchus kisutch) has shown that environmental enrichment can substantially reduce vateritic deformities of the otoliths, inner-ear structures important for hearing and balance, particularly when introduced early in development, while stocking density has weaker and less consistent effects (Gaffney et al., 2026a, 2026b). Building upon this work, we investigated whether environmental enrichment, rearing density, and an enriched diet produce detectable transcriptional responses in hatchery-reared Coho salmon.
Juvenile Coho salmon were reared under paired hatchery conditions manipulating environmental enrichment, stocking density, or feed composition, including a black soldier fly-based diet. Gill and pyloric caeca tissues were collected during the freshwater hatchery phase before marine transition, and RNA sequencing was used to compare gene expression among treatments. STAR-derived gene counts were analyzed with DESeq2 across all three conditions in both tissues. Gill was selected as an indicator of physiological condition because its gene-expression profiles can reflect environmental stress, health, and survival (Akbarzadeh et al., 2021; Grønvold et al., 2024). Pyloric caeca were examined because the salmon gut undergoes major physiological changes during the freshwater-to-marine transition (Veillette et al., 2005). Differentially expressed genes (DEGs) were identified and compared across all six tissue-condition combinations. Because Coho salmon have limited functional annotation, eggNOG-mapper was used to expand annotations through orthology and support GO, GSEA, and KEGG pathway analyses.
Notably, the magnitude of transcriptional responses did not mirror previously observed phenotypic effects. Stocking density produced the strongest and most broadly shared response across DEG, GO, and GSEA analyses, consistent with evidence that rearing density can influence salmonid physiology and post-release survival (Avila et al., 2025). Caeca also showed substantial responses to density and feed, with considerable DEG overlap and pathway-level changes across metabolic and cellular processes. In contrast, environmental enrichment, despite its previously observed phenotypic effects, produced relatively few significant DEGs and only one shared between gill and caeca. However, GSEA using DESeq2 Wald statistics identified coordinated changes across several biological processes, such as cytoplasmic translation, extracellular matrix organization, and cell adhesion. Thus, moderate changes across functionally related genes revealed an enrichment response not apparent from individual DEG analysis alone.
This disconnect between phenotypic and gene-level responses suggests that environmental enrichment may induce coordinated but subtle transcriptional changes or stronger effects localized to other tissues. Previous work from this experimental system found substantial enrichment-associated reductions in otolith deformities, suggesting that stronger molecular responses may occur in tissues directly involved in otolith development (Gaffney et al., 2026b). Because only gill and pyloric caeca were available, additional tissues are needed to distinguish broader systemic responses from targeted, tissue-specific mechanisms. Ultimately, understanding how hatchery conditions shape these molecular responses may help identify rearing practices that better support salmon health and post-release success.
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