DNA test to trace escaped salmon back to their farm of origin

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DNA test to trace escaped salmon back to their farm of origin

NORWEGIAN scientists have developed a new and efficient DNA test to trace escaped salmon back to their farm of origin. Testing of the system on a pilot scale demonstrates virtually 100% accuracy, and simulation of data that has so far been done on an industrial scale is promising, according to the researchers from the food research institute Nofima. In order to follow the gene trail from an escaped fish to the responsible owner, the scientists need to record the genotypes of the parents of all the farmed salmon. This is achieved by cutting off their adipose fins and analysing the DNA.
The parents of the farmed salmon may be found at the breeding company's roe producers, where a male salmon is crossed with one or more female salmon. The offspring of each specific set of parents has a unique DNA profile, and by sending all fertilised eggs from one set of parents or parental group to a smolt producer along with a certificate of traceability, all fish from each smolt producer can receive a unique DNA profile. This will follow the fish when it is later transferred to a sea cage. The DNA profile will be stored in a national database so that the fish in the cage do not need to be tested in the event of suspicion of escaping.
DNA analysis of an escaped salmon will therefore match the gene profile of only one responsible company.
This system means that fish at sea do not need to be tested in order to be matched with escaped fish because their parents were tested before the production fish were hatched. "The advantage of this tracing system is that only the parents of the production fish need to be tested, which is around 30-40,000 fish at the roe producers," says Celeste Jacq at Nofima. Jacq has developed and validated the new DNA test together with fellow Nofima scientist Matthew Baranski. A goal was to have a DNA test of equivalent utility value as the test used in forensic medical studies.
By taking samples of the parent fish, the scientists obtain an overview of the DNA profile of 350 million farmed salmon, which is the number of salmon currently in Norwegian cages. By allowing a certificate of traceability to accompany the roe via the hatchery to the sea-based fish farm, the scientists also have a complete overview of where the offspring grow up. When an escaped farmed salmon is found in the river, only a DNA analysis of this salmon is required in order to find out which fish farm it comes from. In order to find the DNA profile, the scientists have selected microsatellite markers from the genome of the salmon. This is the salmon's DNA fingerprint. Every fish has a unique DNA fingerprint, and by using the marker set the scientists can link an offspring back to the parent fish.
Nofima has used the set of markers in several blind tests of farmed fish with known pedigree, and have confirmed with a high degree of probability that they have found the correct parents of each individual farmed fish. They have also taken blind tests of wild fish in collaboration with scientist Sten Karlsson from the Norwegian Institute for Nature Research (NINA), and these tests have confirmed that the results did not match the DNA of the parents of the farmed fish.
DNA markers have been used for several years to trace escaped farmed salmon to sea cages in the area where escaping occurred, but one advantage of this DNA test is that the fish may be traced far away in terms of both time and space (e.g. minor escapes that have occurred over a period of time). The set of markers may also be used to avoid crossbreeding of siblings in stock enhancement programmes in rivers in order to minimize inbreeding.
Vidar Lund from Salmar has a background in tracing of tilapia at Genomar, and is well acquainted with the technical aspects of this traceability project. "This is a very useful tool because the set of markers is a prerequisite for being able to trace fish. The technology is already there and the method functions with a high level of precision. There are practical challenges involved in implementing the system, particularly with respect to logistics, but in the end whether the system shall be used is a political decision," says Lund.
In 2012 the Norwegian Seafood Research Fund (FHF) implemented six research projects with different possible methods for making and tracing farmed salmon. Several methods have proven to be relevant, including DNA tracing.
Jacq believes DNA tracing must be used in combination with marking that is physically visible such as adipose fin clipping of all production fish. This would enable someone to distinguish a farmed fish from a wild fish on the riverbank before any DNA test is taken. Jacq and Baranski expect the final results from the simulations of the industrial scale will be ready in the winter. It is in the up-scaling for industry that the challenges may lie. The logistics involved in tracing of eggs from the roe producer through to the fish farmer are just as important as the laboratory procedures. The aquaculture industry needs to continue working on both aspects.
The Norwegian School of Veterinary Science, in collaboration with the research centre Cigene, Biobank AS and AquaGen, is now running a parallel traceability project that involves some joint components with Nofima's project. Both projects are financed by FHF, and they have a joint steering committee. The laboratory equipment is easy to use in sampling conditions and minimizes the risk of incorrect recording by the samplers.

With this test, it will not be possible to blame errors on the tests if you are uncomfortable with the test result, says Project Manager Matthew Baranski at Nofima. The laboratory equipment is easy to use in sampling conditions and minimizes the risk of incorrect recording by the samplers. With this test, it will not be possible to blame errors on the tests if you are uncomfortable with the test result, says Project Manager Matthew Baranski at Nofima.

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