New technologies enable scientists to identify the genes that control disease resistance. They also open possibilities for rapid and accurate genetic improvement using this knowledge. But efforts also need to focus on how such technologies can be most effectively implemented considering the biology of the organisms involved and the practical constraints of established aquaculture industries.
Large research initiatives such as CrispResist (funded by the Norwegian Seafood Research Fund FHF) are generating groundbreaking knowledge about the natural genetic and cellular response to sea lice infection in species such as coho salmon. Coho salmon kill and reject lice when they are at the early attached (chalimus) stage of development, before the lice present severe welfare problems for the fish.
If we could effectively implement this knowledge about coho biology in a way that makes Atlantic salmon more coho-like in their response to sea lice, we could greatly improve the welfare of farmed Atlantic salmon and transform the sector by reducing the need for delousing.
The CrispResist project has used the latest in comparative genomics technologies to map the response of genes in time, space and cell type after infection with sea lice in salmon species of interest. All salmon species contain basically the same tens-of-thousands of genes, but how each of these genes responds to infection can differ between species. From these complex data sets we have identified many of the genes likely to be involved in giving coho this natural response against the lice.
The genes we have identified are ones that enhance the immune response of coho, and these are particularly active within the area, which is less than the size of a pin head, where the louse attaches and anchors itself to the host’s skin. Many of these genes are involved in directing and activating immune cells in the area where the lice attach. But in Atlantic salmon these same genes do not respond at the lice attachment site in the skin and other genes are activated. Sea lice are somehow able to suppress the gene response of Atlantic salmon.
Molecular scissors
One of the most effective ways of further testing and verifying the function of these genes and their involvement in the response against sea lice is to use gene editing or “molecular scissors”. CRISPR-Cas9 gene-editing is a 2020 Nobel Prize winning technology discovered by Emmanuelle Charpentier and Jennifer Doudna which can be used to make precise changes to the series of bases in the DNA molecule that makes up the genetic code. CRISPR can be used to “knock out” the function of undesirable genes or to achieve “gain-of-functionality” for desirable ones.
In our CrispResist project we are using gene editing with molecular scissors to test whether the genes implicated in cohos’ response against sea lice affect sea lice infection when these genes are either edited to become more functional or are knocked out (turned off) in Atlantic salmon. Because coho and Atlantic salmon share basically the same set of genes, it is not necessary to introduce any new genes to Atlantic salmon to test gene functionality. The gene edited fish we have created for the project are reared and tested in our secure research facilities. None of them are used for production purposes.
© Nofima
Utilising knowledge about coho’s natural defences
Now that we are gathering this ground-breaking knowledge about the genetic and cellular mechanisms involved in providing natural host-resistance against sea lice, there are several potential pathways that can be taken for implementing such knowledge to make Atlantic salmon more “coho-like” in their response to sea lice. These pathways include the implementation of new breeding methods, vaccination, use of feed additives and potentially the use of CRISPR molecular scissors to create lice-resistant lines of fish. But all these pathways for implementing this knowledge have challenges, and further testing is needed to develop, and thoroughly evaluate, the efficacy and risk-benefits of each pathway.
Under current legislation, gene editing cannot be used in the EU or Norway to produce fish for human consumption. But, given the knowledge we currently have, how effective could gene editing be for improving Atlantic salmon welfare and reducing the need for delousing in the future?
© Nofima
How can we achieve enduring benefits?
We know that sea lice, like other parasitic species, are engaged in an evolutionary “arms race” against their hosts, and also against preventative measures and treatments that humans introduce. We haven’t seen that sea lice are capable of counter-evolving to overcome the natural coho salmon immune response. But might they be able to adapt to overcome future efforts if we were to use molecular scissors to edit genes. And, if so, how could we slow or prevent this adaptation so that these molecular scissor treatments would be effective over the long-term?
In a paper published and featured as the “editor’s pick” in the journal Evolutionary Applications, Dr Andrew Coates and co-authors Tim Dempster, Ben Phillips and myself, describe how effective gene-editing could be at controlling sea lice and how it would be best implemented to decrease the possibility of the lice counter-evolving to adapt to host-genetic changes.
We believe it is unlikely that very simple evolutionary genetic changes to the louse will enable the parasite to re-activate or re-supress a gene that we have edited with molecular scissors. But lice might evolve in a way that allows them to suppress an alternative genetic pathway and evade the impact of our “snips” with the molecular scissors. So, in the paper we considered worst case scenarios where one or two very simple genetic changes in the louse might lead to an ability to re-suppress the host immune response.
We also considered whether the way that the gene edited fish were distributed among farms could affect the ability of lice to counter-evolve to adapt against the changes made to the host genes. Lice grow, mature and reproduce on the skin of salmon, with free floating copepodid stage lice released into the water column, spreading by prevailing currents to salmon on other farms.
We used available spatial models that have been developed in Norway by the Institute of Marine Research which account for how lice copepodids drift and distribute over the seasons, tides and currents. We also incorporated the location of existing Atlantic salmon farms along the coast. We adapted the model so that we could simulate the creation and dispersal of new lice genetic variants over time.
We could then see how the creation and dispersal of these lice variants would be affected by the introduction of gene edited salmon into farms. We were also able to show what effects could be expected on the rate of delousing needed in different areas along the coast over time with evolution of the lice.
We could expect that if molecular scissors were effective, that the welfare of both gene edited and non-gene edited fish could be improved, as not only will gene edited fish be exposed to fewer lice, but they will also act to supress the successful propagation of lice through the farming environment to other salmon (a bit like a vaccine’s “herd-effect”). The model showed that a strategy in which we stock some non-gene edited fish in key areas along the Norwegian coast to create “refugia” where the parasites are not exposed to the full force of the salmon immune response could suppress the evolution of the lice and their ability to counter-evolve to overcome the changes to the salmon.
Could molecular scissors cut lice?
Overall, we found that if non-edited Atlantic salmon were used to create refugia in key areas, and if more than one gene was edited using the molecular scissors, that counter-evolution by the lice would be suppressed, lice infestation would be lessened and the need for delousing could be substantially reduced, resulting in welfare benefits for the salmon and cost savings for the industry. Our work highlights that careful consideration needs to be made about how new technologies can be most effectively implemented to give Atlantic salmon an enduring coho-like response in the battle against sea lice.
Sea lice have been an intractable problem for Atlantic salmon aquaculture. Infection and treatment have severe effects on fish welfare. Knowledge about the natural defences deployed against sea lice by Pacific salmon species such as coho could provide lasting solutions. There are different ways that we could potentially make Atlantic salmon more coho-like in their response to sea lice. But our study highlights that we need to carefully consider how to best implement these solutions and how to most effectively deploy the fish so that we can achieve enduring effects that will benefit both fish and farmers and satisfy sustainability and ethical concerns.
CrispResist partners and funders
CrispResist is led by Nick Robinson of Nofima and funded by the Norwegian Seafood Research Fund FHF with research partners from Curtin University, Deakin University, Institute of Marine Research, The University of Edinburgh, The University of Price Edward Island, Stirling University, Bigelow Laboratory for Ocean Sciences, University of Bergen, University of Gothenburg and Rothamsted Research. The industry partners are Benchmark Genetics, Mowi and Salmar.
The full journal publication discussed in this article can be found here.
