Issues

The salmon louse, Lepeophtheirus salmonis, is a common parasite of the skin of farmed and wild salmon throughout the northern hemisphere (Fig 1). In farming, the parasite is important because of production losses and significant costs of treatment (total est. cost $0.50/kg; $35M/yr in Canada). Furthermore, the salmon louse is notable for the perception that disease is transmitted between farmed and iconic wild salmon populations. Recent studies have provided correlative evidence that sea lice from salmon farms are detrimental to pink salmon populations in the Broughton Archipelago and other locations on the British Columbia coast¹. The smaller wild Pacific salmon emerging from rivers into ocean inlets containing fish farms appear to be particularly vulnerable to louse infestation. Pink salmon for example, migrate to the sea immediately after emerging from spawning grounds and seem to be more affected than other Pacific salmon, which spend more time and grow larger in rivers and streams before migrating to the sea². The central question is whether sea lice infections result in higher wild salmon mortality. The issue however, is complicated because sea lice are commonly and naturally associated with wild salmon and there are documented historical outbreaks of lice on salmon long before farming began in BC. Furthermore, salmon populations as well as louse populations naturally vary quite dramatically and determining causes for these fluctuations is very difficult. Fish farms change the natural equation by having large numbers of salmon at a few locations, year round. Currently chemotherapeutics are used to control lice on farms but because of the large numbers of fish, it is not clear to what extent these farms act as louse reservoirs and what affect they have on wild populations³. Limited scientific knowledge and a polarized, entrenched and historically rooted debate make it difficult to assure both a sustainable and effective aquaculture industry and the protection of our wild fish stocks.

Genomics in Lice and Salmon (GiLS) has four primary objectives :

1. To understand Pacific and Atlantic salmon genetic responses following laboratory exposures to salmon lice, Lepeophtheirus salmonis, using existing and a newly developed 28k salmon microarray technology in order to understand and develop effective host responses.

2. To understand parasite genetic responses hosts in order to develop effective parasite treatment targets. We will obtain a comprehensive list of the genes of L. salmonis and Caligus spp. and build a gene chip to examine gene expression patterns of susceptible and refractory species as well as the effects of temperature, salinity, chemical and biological agents.

3. To confirm and define the newly identified Pacific population of L. salmonis. We will mine the L. salmonis EST database for microsatellite markers and single nucleotide polymorphisms (SNPs) and use these molecular markers to examine the amount of genetic variation and its distribution in Pacific populations of sea lice.

4. To analyze the potential for effective use of science in understanding, and ultimately moving towards the resolution of the sea lice/salmon controversy. This will done through analysis of the history of scientific study of sea lice and their interactions with salmon, the science communication strategies employed, throughout and the evolution of the relationship between science and management practices for the BC salmon aquaculture industry.

     GiLS will develop salmon louse gene chips to be used together with cGRASP salmon gene arrays to define and control the battle/conflict parameters during louse infestation. The objectives outlined above will enable us to understand the differential response of susceptible and resistant salmon species to lice, louse responses to different environments and salmonid species, to develop vaccine targets and prophylactic measures, and to better understand how the utility of these tools might be effectively deployed.

     GiLS builds on existing strengths in salmon genomics (cGRASP), GenomeBC technology platforms, expertise in parasitiology, and a major wild and aquaculture fishery.

     With one of the longest coastlines in the world, Canada and BC in particular has an enormous opportunity for economic development in ocean systems, as well as a major responsibility to manage development in an environmentally sustainable manner. In GenomeBCs assessment of the Fisheries Sector in BC, three of the four applied research priorities for health and disease are; i) to understand host pathogen interactions, ii) vaccine development, and ii) pathogen monitoring tools and strategies. These three priorities are addressed by GiLS. Sea lice in particular is specifically singled out as a priority issue. Fisheries and Oceans Canada has already demonstrated a commitment to the application of genome sciences technologies⁴ to predict and assess the fitness of wild stocks, assess potential impacts of aquaculture and hatchery stocks on wild stocks, assess disease in wild and aquaculture stocks and address health and environmental issues that are directly relevant to sustainable fisheries management. These technologies lead to direct economic benefits by aiding in the development of strategies to minimize impacts where the conservation needs of stocks and species must be considered. Aquaculture and biotechnology companies are also beginning to pursue genomic tools to; a) increase productivity, b) decrease the impact of disease, and c) reduce the impact on wild fisheries. Both federal and provincial governments are concerned with supporting economic development in a sustainable way and genomics tools provide way to incorporate genetics into existing ecological, physiological and environmental strategies. To address government, industrial and public concerns, GilLS has created a Business Advisory Council specifically to insure that interested groups have input into experimental directions and are aware of potential opportunities.

     In addition, because of the persistent conflict surrounding aquaculture and fisheries, we need to not only better communicate scientific results but also examine the structures, processes and historical contextual realities that influence the capacity of the genomics sciences to serve as a basis for movment towards ecological and social sustainability. A specific research area of GiLS will be to examine mechanisms used by various interest groups to contextualize scientific research and to identify better ways of presenting results and implications of genomic data.

Scientific Summary

Fig 2. Chip Sandwich - GiLS chip on chip

GiLS is one of very few projects that will examine gene expression patterns of both the host and the parasite. The concept is straight-forward, the host salmon skin (the fin cross section is shown in the lower part of the micrograph, Fig 2) is the sight of both a defense response and an aggressive attack response (shown in green arrows). Similarly the louse has a defense and attack response (shown in red arrows near the funnel mouth area of the chalimus [upper figure in the micrograph]). The feeding region is the primary area of interaction, though several other organ systems are active in generating the various responses. Using high density microarrays for both the host salmon (28K) and the parasite louse (proposed 12-15k) we can identify genes which undergo significant transcriptional changes when different species of lice (Lepeophtheirus and Caligus) come into contact with various host species, or when they are exposed to different environmental conditions (salinity, temperature, etc) or when they are exposed to various biological or chemical therapeutic agents. Similarly gene expression patterns in the various hosts can be monitored under normal conditions and when parameters are manipulated. Similarly, identification of commonalities (and differences) between the responses of two louse genera will help focus subsequent therapeutic targets. Understanding how environmental, chemical or biological parameters alter the success of defense and attack responses of both the host and parasite will provide an important understanding of host-parasite interactions as well as provide important measures to control those interactions.

Extensive genomic resources are available for salmonids (cGRASP), but few are available for lice. GiLS will incorporate the salmonid resources and further identify thousands of salmon louse genes and develop louse microarrays to monitor gene responses. In the process of identifying louse genes, many polymorphic genetic markers will become available. GiLS will use these markers to examine population characteristics such as migration, inbreeding coefficients, selection and mutation. These tools may provide important information about mixing of lice among salmon species, across oceans and between farmed and wild salmon stocks.

GiLS has nine specific activities; (1) Gene Identification in L. salmonis, (2) Gene ID in Caligus spp., (3) Microarray construction, (4) Identification of genetic markers, (5) Meta-population analysis of L. salmonis from the Pacific and Atlantic, (6) Genetic structure of L. salmonis populations in British Columbia, (7) Microarray – coincident salmon and louse responses, (8) Microarray – responses of salmon and lice to environmental stimuli, and (9) historical analysis of the trajectory of the sea-lice/salmon controversy.

GiLS is an ambitious project that explores the use of genomics tools not only in an area of fundamental scientific interest but also in an area with many commercial applications. GiLS does not aim to be comprehensive in all areas but to build core resources and provide pilot studies demonstrating the use of these fundamental new approaches for the broader scientific and industrial community. In doing so, GiLS will examine louse populations and characterize various host and louse responses to species (host and parasite), environmental parameters, biological and chemical therapeutic strategies, and communication and education strategies.

GiLS original Proposal pdf, (large file)