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

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Abstract

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.

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Acknowledgements

We acknowledge the many traditional and unceded territories and lands of Indigenous Peoples our Universities and partner organizations are situated on. We further acknowledge the rights and privileges of the founding peoples – First Nations and Métis peoples on land we call Turtle Island. GEN-FISH is primarily administered by the University of Windsor which sits on the traditional territory of the Three Fires Confederacy of First Nations, which includes the Ojibwa, the Odawa, and the Potawatomie. The manuscript figure was designed by Chloë Schmidt. We are immensely grateful to our partners who are willing to go with us on this journey to improve our fisheries and shared future. This paper is dedicated in memoriam to Sara K. Jamieson, without whom the success of GEN-FISH would never have been realized. An indefatigable advocate, her brilliant ideas live on.

Funding

The research described in this paper (i.e., STP-chip) is supported by Genome Canada (i.e., GEN-FISH – Genomic network for fish identification, stress and health; OGI-184)), and the Natural Sciences and Engineering Research Council of Canada (06768 to C.A.D. Semeniuk). Additional support was provided by Genome Ontario, Genome Québec and Genome Prairie.

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Authors and Affiliations

  1. Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave., Windsor, N9B 3P4, Canada

    C. A. D. Semeniuk, K. Keeshig & D. D. Heath

  2. Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, MB, R3T 2N2, Canada

    K. M. Jeffries

  3. Department of Food, Agricultural and Resource Economics, University of Guelph, 50 Stone Rd E., Guelph, ON, N1G 2W1, Canada

    T. Li

  4. Hatfield Consultants, #200-850 Harbourside Drive, North Vancouver, BC, V7P 0AP, Canada

    C. M. Bettles

  5. Pisces Scientific Group, 1303 Steeple Drive, Coquitlam, BC, V3E 1K3, Canada

    C. M. Bettles

  6. Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada

    S. J. Cooke

  7. LEA Consulting Ltd., 625 Cochrane Drive, 9th Floor, Markham, ON, L3R 9R9, Canada

    B. A. Dufour

  8. Nova Scotia Salmon Association, Middle Sackville, 163 McCabe Lake Drive, Mount Uniacke, NS, B4E 0M9, Canada

    E. A. Halfyard

  9. Yellow Island Aquaculture Ltd., Heriot Bay, BC, V0P 1H0, Canada

    J. W. Heath

  10. Member of Chippewas of Nawash, Unceded First Nation, Manitoulin, ON, Canada

    K. Keeshig

  11. Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada

    N. E. Mandrak

  12. Great Lakes Fishery Commission, 2200 Commonwealth Blvd Suite #100, Ann Arbor, MI, 48105, USA

    A. J. Muir

  13. Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada

    L. Postma

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  1. C. A. D. Semeniuk
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  3. T. Li
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Contributions

Authors CADS and DDH were responsible for conceptualization of the review. All authors contributed to manuscript writing, and commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to C. A. D. Semeniuk.

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Semeniuk, C.A.D., Jeffries, K.M., Li, T. et al. Innovating transcriptomics for practitioners in freshwater fish management and conservation: best practices across diverse resource-sector users. Rev Fish Biol Fisheries 32, 921–939 (2022). https://doi.org/10.1007/s11160-022-09715-w

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