Steadily depleting wild fish stocks and growing consumer demand for fish products mean that the aquaculture of marine species could become an increasingly important food source and economic activity within the European Union. The potential expansion of the aquaculture sector is recognized and supported by the European Parliament (Guillot, 2010), however any such development must be sustainable and regulated with respect to biosafety, including possible risks to the environment (European Commission, 2009). One aspect of environmental risk associated with marine fish aquaculture is the potential impact of releasing farmed fish into the wild, through accidental escape (Bekevold et al., 2006; Svasand et al., 2007) or deliberate restocking (Bell et al., 2008). Such releases raise issues relating to the spread of disease, ecological disruption and changes to the genetic make-up of wild stocks. In contrast to the large investment in management of farmed fish, including research and technology development (RTD), little information is available on the fate of escapees, in terms of their fitness, breeding success or distribution. Knowledge about the fate of farm escapees is however crucial as interbreeding with individuals from wild populations leads to genetic introgression, the introduction of gene alleles from farmed animals into wild populations, a process implying considerable risks.

The major risks, loss of genetic diversity within populations; loss of genetic diversity among populations; loss of fitness, although known for several decades, are difficult to predict. A rule of thumb is that if farmed escapees comprise more than 10% of successful spawners, overall effective population size will not be much larger than the effective size of the captive broodstock. Moreover, while in the past typically low levels of genetic divergence in many marine fish were assumed, several recent studies show strong evidence for local adaptations of marine species,  including mobile and highly fecund fishes like Atlantic cod (Harald et al., 2010). Escape of farmed fish thus poses a significant threat to locally adapted populations, even on local scales.

To manage and mitigate risks, and to assess the impact of releases, it is important to be able to characterize, distinguish and identify farmed and wild individuals. The ability to trace-back fish to a farmed origin also has applications to product label authentication. Escapes of fish from sea-cages have been reported for almost all species presently cultured across Europe, including Atlantic salmon, Atlantic cod, rainbow trout, Arctic charr, halibut, sea bream, sea bass and meagre. In comparison to Atlantic salmon, knowledge of the extent and effect of escapes of Atlantic cod is very limited. Also for other culture species, like sea bream, sea bass and meagre, knowledge regarding identification of escaped fish and how escapes might affect to local fisheries is virtually non-existent (Moe et al., 2007). The use of DNA technology to identify the origin of fish is now widely implemented (Ogden, 2008) but its application to the issue of farmed origin has to date been mainly limited to salmonids (Glover et al., 2008). With an increasing range of marine fish now subject to aquaculture operations, there is a need to evaluate methods for the genetic assignment of fish to either a farmed or wild source and, where possible, to determine the precise genetic population of origin.