Innovating transcriptomics for practitioners in freshwater fish management and conservation: best practices across diverse resource-sector users

Thriving freshwater fish populations contribute to people's economic prosperity and wellbeing. Yet, freshwater fish populations are in critical condition around the globe. Most stressors to freshwater fishes, fisheries, and culture stem from habitat impacts, water-quality issues, and aquatic invasive species. Logistical difficulties of monitoring fish health are compounded by the limitations of conventional (capture-based) sampling methods, which provide only a temporal "snapshot" and generate data lacking in sensitivity and prognostic ability. Here, we propose an innovative genomics approach to develop a health toolkit that will allow resource-sector users to determine the health status of freshwater fishes, including their coping capacity, to environmental stressors. The stress-response transcription profile (STP)-chip is a suite of quantitative gene transcription assays that represents key gene pathways broadly associated with fish functional responses to environmental stress; therefore, the differential expression of well-selected genes can provide sensitive fish-health status indicators. Despite the scientific achievement of using genomics tools, actualizing the toolkit in practice is only successful if resource-sector users have full buy-in. We present seven case studies representing different practitioners and resource users - Indigenous rightsholders, environmental consultants (industry), commercial aquaculture, environmental charities (ENGO), and fishery commissions and managers (government) where each explores the benefits and risks associated with the adoption of a genomics fish-health toolkit. Using a co-production approach, wherein practitioners and resource users are engaged from the outset, these case studies reveal translational pathways that would be needed to overcome barriers to technological adoption and, hence, accelerate the responsible uptake of genomics-based applications in fisheries assessment, management, and conservation.