Abstract
BackgroundAquaculture is a globally important and rapidly growing industry. It contributes positively to the economy and sustainability of coastal communities, but it is not without regulatory challenges. These challenges are diverse, and may include identification of fish discarded in an illegal manner, biological discharge from fish ensilage tanks, and partially destroyed or processed tissues. Robust genetic tools are required by management authorities to address these challenges. In this paper, we describe nine species-specific primer sets amplifying very short DNA fragments within the mitochondrial DNA cytochrome c oxidase (COI) gene, which were designed to permit diagnostic identification of degraded DNA from two of the most commonly farmed salmonids in Europe and North America.ResultsOf the nine designed primer sets, six were found to be species-specific (four Atlantic salmon, two rainbow trout), whereas the remaining three sets (two Atlantic salmon, one rainbow trout) also amplified a product from other, closely related, salmonid DNA templates. Screening of DNA templates from 11 other non-salmonid native fish species did not produce PCR products with any of the primer sets. Specific tests confirmed the ability of these markers to identify Atlantic salmon and rainbow trout tissues in treated food products, chemically treated ensilage waste and fillets left to degrade in saltwater for up to 31 days at 15°C. Importantly, these markers provided diagnostic identification in cases where other genetic methods failed because of degraded DNA quality.ConclusionsResults from this study demonstrate that amplification of very short DNA fragments using species-specific primers represents a robust and versatile method to create cheap and efficient genetic tests that can be implemented in a range of forensic applications. These markers will provide fishery, aquaculture and food regulatory authorities with a method to investigate and enforce regulations within these industries.
Highlights
Aquaculture is a globally important and rapidly growing industry
Aquaculture production of rainbow trout is based upon freshwater rearing or a mixture of freshwater and marine rearing, whereas production of Atlantic salmon almost exclusively involves a combination of juvenile rearing in freshwater and growing to market size in marine cages
This study reports the successful development of diagnostic markers for Atlantic salmon and rainbow trout, which permitted the amplification of severely degraded DNA obtained from canned fish products, ensilage and heavily decayed fish tissue
Summary
Aquaculture is a globally important and rapidly growing industry. It contributes positively to the economy and sustainability of coastal communities, but it is not without regulatory challenges. Aquaculture production of the Atlantic salmon (Salmo salar L.) was established in the 1960s, and in Europe this species represents the primary farmed fish in terms of both biomass and economic value. Norway has led this development, producing over 700,000 tons of Atlantic salmon and nearly 100,000 tons of rainbow trout in 2008 [3]. Challenges remain concerning the mitigation of the negative effects of aquaculture, including genetic interactions [4,5], pathogens [6] and fish-farm effluent discharge [7] Meeting such challenges involves, among other issues, the requirement to monitor the environmental effects and the ability to detect infringements of legislation. The latter often requires forensic investigation [8,9]
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