Milestone in salmon research: 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.

This is a powerful tool for understanding the connection between the salmon's genetic codes and its biology," says Steinar Bergseth, Special Adviser at the Research Council of Norway.

As chair of the international project, Dr 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 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 10 June 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.

Better breeding tools

"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 Mr 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

Mr 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," continues Mr Arnesen, "and among other traits that entails better disease resistance. 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, he asserts, "is also going to play a major role in solving our environmental challenges, 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. A major supplier of salmon eggs, the company invests heavily in research and development.

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

Success

Over the years this virus has been the cause of major disease outbreaks at fish farms around the world, leading to significant economic losses. 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."

Could have saved years of work

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

First step

"After the IPN markers were identified in 2007," continues Dr Santi, "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."

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

Extraordinary potential to create value

Survival rates just a few per cent 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," Dr Rødseth explains, "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. Mortality has dropped four to five per cent 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) ."

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

"In the next three to five years," he predicts, "we will probably be hearing more success stories like the IPN achievement."

Complex genetic material

The international genome project has revealed the salmon's genetic material as very complex.

Whereas most species (including humans) have two copies of each chromosome, salmon have four, which posed special challenges during the already painstaking work of sequencing.

The five-year project is the largest research collaboration ever carried out between the salmon-producing countries of Canada, Chile and Norway. The sequence is now being made available to the global research community and industry alike.

"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."

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

Continued international work

Participants at the 10 June conference in Canada will be discussing possibilities for continued international collaboration based on the reference sequence.

Countries other than Norway, Canada and Chile are also invited to take part.

"These efforts, if successful, will yield great returns in the form of future understanding of salmonids and their environment," says Dr Bergseth, emphasising 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.