Functional Genomics

photo: RNA labSockeye salmon Migration Physiology revealed through gene expression profiling

For over a decade, Fraser River sockeye salmon that normally return to the river to spawn in the fall have entered the river up to 6 weeks early and migrated through water temperatures that are 3-5 oC higher than they would normally encounter. Unprecedented large (up to 90%) and variable levels of mortalities in the river have resulted, both en route to spawning grounds and prior to spawning. Through a multidisciplinary collaboration between physiologists and ecologists at University of BC (Farrell and Hinch) and Carleton (Cooke), fisheries managers at the Pacific Salmon Commission (LaPointe), field biologists/researchers at DFO (Patterson), LGL (English) and Kintama Research (Welch), the MEGA group, led by Dr. Kristi Miller, has been applying cDNA microarray technology to issues surrounding the unusual early river entry timing of Late-run Fraser River sockeye. The microarray experiments have revealed dramatic physiological shifts occurring in brain, gill and muscle tissue during ocean migration and migration into the FW environment. Non-lethal sampling of gill and muscle tissue from radio-tagged fish allowed an assessment of physiology associated with behaviour and fate in river. This analysis revealed a strong association between transcriptional profiles in gill tissue and both river entry-timing and in-river fate. Importantly, these physiological signals were present in fish as far as 800 km from the mouth of the Fraser River. The ultimate goal of this research is the development of predictive biomarkers that can be used to aid in the management of sockeye salmon fisheries. The research program highlights the first large scale application of microarray technology to address questions in wild ecological genomics, and has included the analysis of over 750 arrays.

Funded by

  • DFO Genomics Research and Development Initiative
  • Pacific Salmon Commission Southern Endowment Fund

Collaborator Links

Kristina M. Miller, Angela D. Schulze, Norma Ginther, Shaorong Li, David A. Patterson, Anthony P. Farrell, Scott G. Hinch, Salmon Spawning Migration: Metabolic Shifts and Environmental Triggers, Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, In Press, Accepted Manuscript, Available online

Cooke, S.J., S.G. Hinch, A.P. Farrell, D.A. Patterson K. Miller-Saunders, D.W. Welch, M.R. Donaldson K.C. Hanson, G.T. Crossin, M.T. Mathes et al. 2008. Developing a mechanistic understanding of fish migrations by linking telemetry with physiology, behaviour, genomics and experimental biology: an interdisciplinary case study on adult Fraser River sockeye salmon. Fisheries 33(7) 321-338.

Miller, KM, K Kaukinen, S Li, AP Farrell, and DA Patterson. 2007. Expression profiling of Fraser River late-run sockeye salmon: Migration physiology uncovered using cDNA microarray technology. Amer. Fish. Soc Symp 54: 101-103.

Genomic Tools for Fisheries Management (FishManOmics)

photo: FishManOmicsThere are many distinct challenges that salmon face in each of the environments within which they live. In freshwater, salmon can be physiologically challenged by varying water flows, temperatures, pollutants, and sedimentation. In the marine environment, shifting climatic regimes not only affect prevailing ocean temperatures, but also affect the abundance, timing and quality of prey and the numbers of predators, all factors that influence whether salmon will thrive upon entry into the ocean. In BC, global climate change has already impacted the environments in which salmon live, increasing river flows in the spring but deceasing water levels in the fall, increasing peak temperatures in the ocean, rivers and lakes in the summer, and these changes have been felt by our BC salmon stocks. In this era of change, the next generation of management models not only need to account for shifting environmental conditions, but must also consider how salmon will adapt and respond both physiologically and behaviourally to these changes. This is the goal of the FishManOmics project, which is co-funded by Genome BC, DFO, NSERC and the Pacific Salmon Commission.

The FishManOmics project focuses on conditional states that diminish performance and survivorship as salmon transition between fresh water and salt water both in adult spawning migration and smolt out-migration. Through the use of the cGRASP 32K salmonid microarrays, we will perform large scale wild ecological genomics research to identify novel expressed biomarkers that can stage osmotic, growth, metabolic, energy, and disease states. These will be used in models to predict the overall health of migrating stocks and to estimate survivorship under different environmental conditions.

Research on adult spawning migration will be expanded from earlier studies to include stock-specific temperature responses and effects on physiology of capture-release fisheries, as well as continued study on physiological associations with fate.

Novel research on wild smolts will include elucidation of the spatial and temporal patterns of physiological change (and their molecular control) from pre-smolts to smolts over wintering their first 6 months in the ocean, and testing of specific hypotheses on the physiological factors controlling smolt survivorship in the ocean.

Guided by stakeholder feedback, our research will provide managers with the first generation of models that integrate fish physiological condition, environmental variables, and traditional stock assessment data. These mechanistic and predictive models will assess the impacts of physiological condition on growth, metabolism, migratory cueing, and survivorship. Ultimately, this research will lead to greater predictive accuracy in escapement estimation and in support of sustainable fisheries management.

Funded by:
  • Genome BC
  • DFO Genomics Research and Development Initiative
  • NSERC
  • Pacific Salmon Commission

Collaborators

Relationship between susceptibility and host response to the Infectious Hematopoietic Necrosis (IHN) virus in salmon.

This research was undertaken to gain a better understanding of the molecular controls of salmon susceptibility to the IHN virus. Time-series post-exposure cDNA microarray experiments were run on five species of salmon known to have different susceptibilities to disease caused by the virus. The most susceptible species responded most vigorously, using multiple innate pathways of defence, and culminating in a strong cellular immune response. Since no up-regulation of the intracellular-mediated response was observed in the least susceptible species, it appeared that differences in susceptibility were likely related to the efficiency of the viral receptor. A number of genes potentially co-opted by the virus were uncovered, as were pathways associated with better disease outcomes. This research will be applied to vaccine development to help control outbreaks of the virus in aquaculture fish.

Miller, K.M, G Traxler, KH Kaukinen, S Li, J Richard and N Ginther. A cDNA microarray study of Atlantic salmon (Salmo salar) response to Infectious Hematopoietic Necrosis (IHN) virus. Aquaculture: In Press 2007.

Funded by:
  • BC Innovation Council BC Aquaculture Research and Development Committee (BCARDC)
  • DFO Genomics Research and Development Initiative
  • Physiological response to density stress in salmon aquaculture

Physiological response to density stress in salmon aquaculture

The aim of this project is the elucidation of stress biomarkers associated with rearing density at multiple stages in the ocean culture of Atlantic salmon. The GRASP 32K cDNA microarrays will be used to compare the physiology of fish reared at three stocking densities at multiple sample points over 1.5 years of ocean culture. Standard measures of stress, growth and survivorship will also be taken. Density stress biomarkers may, in future, be used by industry to assess appropriate stocking densities under different environmental conditions and in additional species.

Funded by:
  • DFO Aquaculture Research and Development Program
  • Marine Harvest Ltd.
Key collaborator:
  • BC Centre for Aquaculture Health Sciences (CAHS: Val Funk)