Genetic Fingerprinting Techniques Harnessed to Track Wild Salmon Stocks

The Irish Marine Institute, the National University of Ireland Cork, and BioTrove in the United States, will be collaborating to identify individual Atlantic salmon stocks using a new, high-throughput system for detecting candidate Single Nucleotide Polymorphisms (SNPs) in large populations.

This innovative project will attempt to adapt and evolve recent breakthroughs in human genetics for fisheries related applications. These could include: quantitative genetic research, tools for managing fish stocks, improving and developing new aquaculture techniques, and ensuring the safety of marine food products.

In recent years Microsatellites have been the molecular marker of choice for population biological applications. However, since the completion of the human genome project there has been increasing interest in the use of Single Nucleotide Polymorphisms (pronounced  SNiPs), which are essentially point mutations or permanent changes in the nuclear genome. SNPs provide a new and very exact way of genetic fingerprinting micro-organisms, animal or plant life.  The greatest advantage of SNPs, is that they lend themselves more readily to automation, increasing the speed of processing by at least an order of magnitude. 

"Currently genetic analysis of large fish populations, such as mixed salmon stocks, is constrained by our inability to accurately process large sample numbers. The Institute is very excited by this initial pilot study which, if successful, could provide a new and innovative tool for fisheries research," Said Dr. Peter Heffernan, CEO of the Marine Institute.

Microsatellites have had extensive use in fisheries and aquaculture genetics. In comparison, validation of SNPs is relatively new to the industry. This pilot project compares SNP screening technology with microsatellites in Atlantic salmon populations. Researchers will be using data from the ground-breaking River Moy genetic study in Ireland (a collaboration between the Marine Institute and NUI Cork) to demonstrate the advantages of SNP OpenArray ™ technology.

"The Marine Institute's commitment to an expansive salmon tracking program makes them an excellent partner for BioTrove's OpenArray™ technology. The OpenArray™ platform provides an accurate, affordable solution for high throughput, PCR-based SNP analysis against thousands of salmon samples," said Alan Carter, Chief of Commercial Operations at Biotrove.Marine survival of Atlantic salmon is of major concern to nations such as the United States, Canada, Russia, Norway, and the countries of the European Union bordering the Northeast Atlantic Ocean. The North Atlantic Salmon Conservation Organization's (NASCO) International Atlantic Salmon Research Board recently launched the SALSEA (Salmon at Sea) initiative to determine the reasons behind the serious decline of North Atlantic salmon stocks ( ). Genetic fingerprinting will play a major role in this initiative.

This pilot study will assess the feasibility of using SNPs to identify and track individual salmon stocks at sea. "Ireland is a world leader in Atlantic salmon molecular ecology and it is seen as vital to maintain a competitive edge in the research and application of novel gene probes," said Professor Tom Cross of the Zoology Department at NUI Cork.

Currently, a bottleneck exists in terms of the ability to quickly analyse thousands of salmon DNA samples, extracted from scales or adipose fins. Validated SNP identification panels, which will require testing of large numbers of salmon to create, are crucial to continuing with ongoing population studies. The industry needs a method to accurately test large numbers of salmon in a way that is reproducible from lab to lab. The importance of providing this information in a timely manner is high, as it could affect strategic decisions on salmon management in Ireland's homewaters.