Salmon genome fully sequenced

The detailed overview of the salmon’s genetic material provides the framework for new research and development that may solve many longstanding riddles.

“We now have the complete sequence of the Atlantic salmon genome, every letter and code,” says Steinar Bergseth, Special Adviser at the Research Council of Norway.

“This is a powerful tool for understanding the connection between the salmon’s genetic codes and its biology,” he says.

As chair of the international project, Bergseth made the genetic code public at a scientific conference in Vancouver, Canada, on 10 June 2014.

Help streamline the industry 

The new knowledge will be useful in efforts to develop new salmon vaccines, improve feeding and understand more about what happens when escaped farmed fish mix with their wild counterparts. Selective breeding of salmon will be more targeted and efficient.

In the longer term, the genomic knowledge will help to streamline the aquaculture industry while providing consumers with healthier farmed salmon, produced with as little environmental impact as possible.

Petter Arnesen, Breeding Director at the fish farming company Marine Harvest, agrees that this is a milestone for anyone involved in aquaculture. Marine Harvest is one of the industrial partners in the genome project and has contributed to its funding.

“The sequence will make it possible to develop new, more effective selective breeding tools that will make us even better at choosing parent fish with desired traits for the next generation of salmon,” says Arnesen.

“Enhanced knowledge about the genetic material allows us to utilise more of the genetic variation from within the stocks that farmed salmon are produced from. Furthermore, the sequence opens up new prospects for studying biological and physiological processes.”

Healthier fish

Arnesen emphasises that selective breeding practices in no way involve gene modification, but rather are a means to finding the right individuals to select as parent fish – individuals that naturally have desired traits that producers want to pass on to coming generations of production salmon.

He is convinced that the salmon genome sequence will help to promote a healthier aquaculture industry.

“We are seeking to produce fish that are as healthy as possible,” says Arnesen,

“Salmon lice are currently our biggest challenge, along with other parasites and viruses.”

Solving environmental challenges

Using the salmon genome as a tool, salmon producers hope to raise fish that grow faster, which means less time spent at sea. 

The sequence is also going to play a major role in solving our environmental challenges, according to Arnesen.

“If we can, for instance, select for individuals that are more resistant to disease and parasites and that can adapt well to new feed types. For many consumers, environmental soundness is an integral part of product quality. The conscientious consumer will not buy salmon if its production is harmful to the environment.”

Fighting disease

Improved vaccines have eliminated most of the bacterial diseases that were causing substantial losses at fish farms into the 1990s. These vaccines, however, are not effective against viruses – so one solution is selecting parent fish with virus-resistant traits to use as broodstock for salmon egg production.

AquaGen is another industrial partner in the genome project that is looking forward to utilising the sequenced genome. As a major supplier of salmon eggs, the company invests heavily in research and development.

One project that AquaGen started up in 2005, was to make a precise map of the genetic markers that make certain salmon individuals resistant to the IPN (infectious pancreatic necrosis) virus.

A collaboration with the Centre for Integrative Genetics (CIGENE), at the Norwegian University of Life Sciences, and the Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima). 

Only the first step

Over the years this virus has been the cause of major disease outbreaks at fish farms around the world. The research project has paid off.

“The IPN project has been a huge success,” says Nina Santi, head of R&D at AquaGen.

“Since we started using eggs from fish with the desired traits, the number of IPN outbreaks in Norway has dropped from 200 per year to 50.”

The project also illustrates the progress to be gained from knowing the complete salmon genome.

“After the IPN markers were identified in 2007, we have been working for seven years on mapping the mechanism for resistance to the IPN virus. Had we had access to the genome sequence now being made public, it would have saved us several years,” says Santi.

She stresses that the sequence is only the first step.

“Now we know the genome of one individual, which the scientists named Sally, but we are more interested in understanding the variations between individuals.”

The researchers' next step is to sequence different generations of fish in order to find out, for example, which of them is most resistant to disease and exhibits good growth and red fillet colour.

Benefit the entire aquaculture industry

Researchers and industry involved with other salmonids such as rainbow trout, char and Pacific salmon will also find useful applications for this new tool.

“This will strengthen salmon-related research in many fields, from physiology and genetics to nutrition and reproduction,” says Kjell Maroni of the Norwegian Seafood Research Fund (FHF).

“It will also open up more possibilities for international cooperation, which will benefit the entire aquaculture industry,” he says.

Extraordinary potential to create value

Survival rates just a few percent higher translate into major earnings for the Norwegian aquaculture industry, where the annual turnover is NOK 45 billion (approximately 5,6 billion Euro/7,6 billion Dollars), according to Odd Magne Rødseth, Chairman of the Board at AquaGen.

“In the past 15 to 20 years, viruses have been the primary cause of mortality. What we are seeing now is the result of better selective breeding programmes focused on disease resistance,” Rødseth explains.

Mortality has dropped four to five percent for the latest year-class of salmon. This is due to what is in effect the elimination of IPN, thanks to practical application of new knowledge about the salmon genome. This increase in survival means an additional profit of NOK 2.6 billion (approximately 320 million Euro/440 million Dollars).

Rødseth is certain that it will become cheaper and faster to find other significant genes in the future, now that the entire salmon genome has been sequenced and made available.

“In the next three to five years, we will probably be hearing more success stories,” Rødseth predicts.

Must be used

Bergseth emphasises how crucial it is to use the sequence now that it has been obtained:

“Now we have a new textbook at our disposal, but it won’t help if we don’t consult it. Salmon is Norway’s most important production animal, and we have invested a great deal in the genome project. Now we need to continue to invest in R&D to translate that knowledge into products of value,” Bergseth concludes.

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Read the Norwegian version of this article at forskning.no

Translated by: Carol B. Eckmann

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