Feature – Genetics in mariculture and beyond

In the third feature article in our series, we look at the field of genetics and genomics in wild and farmed fish and related issues such as interbreeding, escapement, and conservation.
Published: 1 July 2015

​​By Gary Carvalho​ (Bangor University, UK) and Dorte Bekkevold​ (Technical University of Denmark): current and past Chair of ICES Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM).

​Mariculture for working group

At a time when many pressures on natural fisheries stocks continue to escalate, it is especially pertinent that the role of genetics in mariculture is considered. Mariculture, a sub-component of aquaculture production, which includes freshwater taxa, involves the cultivation of marine organisms for food or stock enhancement and other products (such ​as fish meal, nutrient agar, and cosmetics), reared in either seawater enclosures or tanks. Mariculture species can encompass disparate organisms, including fish, shellfish and algae, though they all share the common characteristics of being reared in captivity and initially established from wild broodstock.

A concern about effects of mariculture on the productivity and sustainability of wild stocks stems from the effects of captive individuals with artificially selected traits interbreeding with wild members of the same species (conspecifics). Indeed, it is not fortuitous that the origins of the Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM) derive from the rapid growth of mariculture in marine food production back in the early 1990s and the need for sustainable practices without jeopardizing local fisheries. While the overall objective of the WGAGFM is to consider specific knowledge revealed by genetics and genomics to identify, trace, restore and manage finfish and shellfish. It draws on the evidence base indicating that sustainability depends upon genetic differences in such traits as growth, maturation and reproductive capacity amongst populations. Such biological diversity provides the raw material for adaptation to changing environments and likely affects the ability for collapsed stocks to recover and persist. As such, there is a focus within the group in the context of mariculture to provide evaluation and advice on tools and methods for assessing and mitigating the impact of genetic and ecological changes driven by domestication, stock enhancement and escapees. More widely, since genetic resources are the foundation for adaptation and resilience, the WGAGFM focuses on optimal strategies for their conservation in the face of environmental change, captive breeding, and exploitation. ​​​​

​A surge in aquaculture

In 2012, global fish production from capture fisheries was 91.3 million tonnes, while aquaculture production attained an all-time high of 90.4 million tonnes, of which 66.6 million tonnes constituted fish products for human consumption. Aquaculture is the fastest-growing food production sector, with mariculture being a major driver. Indeed, five of the seven top aquaculture species produced in the EU, for example, are marine: mussels, Atlantic salmon, Pacific oyster, sea bream and sea bass. Continued global investment in mariculture necessitates an appropriate management framework to maximise profit and sustainability while minimizing detrimental effects. The advent of genomics in particular, in combination with traditional practices, offers new opportunities to attain such goals. Foremost amongst these include captive broodstock management, traceability of escapees, selective breeding and monitoring the impact of escapees on native populations. Here, we explain the role of genetics and genomics in advancing our ability to provide advice for broodstock management and assessing the impact of escapees. 

Genetics and genomics: from application to advice​​

Advice for broodstock management aims to minimize the impacts of domestication and inbreeding in the long-term, which demands knowledge of the levels of natural diversification in wild stocks, as well as pedigree information on genetic similarity among breeding pairs. While the links between specific genetic and ecological traits are often complex, a precautionary approach is to retain where possible, natural levels of locally adaptive variation. DNA methods such as microsatellite variation (short and highly variable repeat DNA sequences scattered within the genome), or single nucleotide polymorphisms (SNPs, variation in a single DNA building block) that differs amongst members of a species, are especially informative for characterising natural patterns of genetic diversity. For example, a recent study of Atlantic cod from the Baltic using > 10,000 SNPs showed significant differentiation amongst eastern and western populations, necessitating corresponding distinction in broodstock for maximising yield and retention of locally adapted traits. ​

Escaping the net

In parallel with trends in mariculture growth have been corresponding concerns about the impact of escapees on native populations. Amongst global efforts is the European Commission-funded consortium AquaTrace (a project that includes several WGAGFM members), which aims to develop tools for tracing and evaluating the genetic impact of fish from aquaculture. Targeted species include Atlantic salmon, brown trout, European sea bass, gilthead sea bream, and turbot. Evidence indicates the generally detrimental genetic impacts of interbreeding between formerly captive fish and native populations, including a breakdown of local adaptation that may compromise recruitment and persistence in changing environments. Escape events are a common occurrence. For example, in 2013 the Norwegian Fisheries Directorate received reports of 198 000 Atlantic salmon escaping from commercial farms throughout Norway; in 2014, the Scottish Government received reports of over 184 500 escapees; while in Ireland, 230 000 salmon escaped during a single event .  ​

Effective risk assessment and mitigation demands tools that allow both the tracing of individuals back to farms of origin and the clarification of potential impacts on performance of "hybrid" offspring produced by crosses between wild and farmed parents. AquaTrace addresses both issues, and includes advanced genomic approaches for characterising SNP-based signatures of wild and farmed individuals, as well as common garden experiments to compare growth and survival of offspring reared under controlled conditions from farmed, wild, and farmed-wild crosses. Information to date indicates that the impact of escapees will depend critically on both the genetic and ecological characteristics of origin and recipient populations. An especially insightful and effective system based on genetic considerations is the monitoring and management of Atlantic salmon escapees in Norway. Kevin Glover and colleagues from the Norwegian Institute of Marine Research (IMR)​ have developed a real-time system for rapid detection and identification of escapees from specific farms or regions, which is already resulting in improved governance and deterrence. Clearly, this type of approach is also an extremely valuable element in the risk assessment of the environmental impact of mariculture. ​

Genetics and the ecosystem

The WGAGFM functions within the ICES science priority areas, and in particular aims to implement scientific evidence and advice within the context of ecosystem-based approaches. Mariculture and related activities are no exception. We know that single-species approaches, while necessarily dependent upon the dynamics of species, benefit from a consideration of ecosystem-wide processes, including considerations on many levels - from species and biodiversity within species, over communities, trophic and competitive interactions, to linkages to socio-economic constraints and opportunities. An ecosystem approach promotes the sustainable development, equity,​ and resilience of interlinked social and ecological systems in the long-term. The ability to identify and monitor the genetic impact of escapees and restocked fish into wild populations provides a baseline for conservation of ecosystem diversity, with links to sustainability through risk assessment and mitigation. Moreover, understanding the interactions between captive breeding and the environment is a critical step towards securing an adequate regulatory framework. Forensically validated tools and ecosystem-based strategies are a prerequisite for growth and sustainability because mariculture and aquaculture relies strongly on a high-quality rearing environment and the demands of the market. Indeed, the WGAGFM is coordinating a session​ at ICES Annual Science Conference this year to examine the opportunities to develop an ecosystem approach for marine management and conservation through the application of genetic and genomic approaches.

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Caught salmon on riverbank

​A 7kg WILD salmon from the river Dale in western Norway. This is a river that has a seen many escapees over the years, an issue which poses a threat to the integrity of healthy wild populations. ​Photo: Kevin Glover​​​​​

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Feature – Genetics in mariculture and beyond

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