Salmon genome opens door to better farm fish, without genetic engineering

Scientists have successfully mapped the whole genome sequence of the Atlantic salmon, a breakthrough that should accelerate selective breeding programs for farmed salmon and reduce the aquaculture industry’s impact on wild salmon stocks.

“This has the potential to improve the sustainability of aquaculture, to reduce feed demand and increase feed efficiency and it might lead to reduced susceptibility to disease in fish farms,” said Brian Riddell, president and CEO of the Pacific Salmon Foundation, a non-governmental conservation organization. “If we can improve the performance of aquaculture it will translate into less risk for the Pacific salmon.”

An international consortium of scientists and funding bodies — including Genome BC — based in Norway, Canada and Chile spent four-and-a-half years and $10 million to map the entire DNA sequence of about 3 billion characters, essentially the genetic instruction set required to grow and operate an Atlantic salmon. The sequence will be made available at no charge to researchers.

The announcement is to be made Tuesday at the International Conference on Integrative Salmonid Biology in Vancouver.

Understanding and targeting heritable traits in the genome will help speed breeding programs for Atlantic salmon aimed at improving resistance to viruses and sea lice, problems that have created considerable controversy for the aquaculture industry in B.C. and in Norway, according to Steinar Bergseth, Chair of the International Steering Committee for the consortium.

“Eliminating the sea lice problem in net pens would eliminate the risk of transfer between wild and farmed salmon,” he said.

Even without the luxury of a full genome to work from, a Norwegian firm has produced Atlantic salmon resistant to a pathogen that once plagued salmon farms in that country.

“One company in Norway has already identified a family of Atlantic salmon that is resistant to the bacteria that causes Infectious Pancreatic Necrosis. These eggs reduce IPN infections by 90 or 95 per cent in Norway,” Bergseth said.

Scientists can now begin use the genome to identify families of Atlantic salmon that resist other pathogens, grow faster or even synthesize omega-3 fatty acids on a plant-based diet, reducing the amount of wild fish that is required to feed farmed fish, he said.

The success of the dairy industry’s use of genomic tools to guide breeding for disease resistance, increased milk production and even altering the protein and fat content of the milk, presents a template for the aquaculture industry, said salmonid geneticist William Davidson of Simon Fraser University.

The ability to identify desirable traits in families of Atlantic salmon using the full genome as a reference will diminish the need to employ genetic engineering as a means to improve the commercial viability of farmed fish, according to Davidson, who chairs the executive scientific committee of the salmon genome consortium.

The American biotech firm AquaBounty has applied for permission in Canada and the United States to market a fast-growing genetically engineered Atlantic salmon, but the company has faced opposition from environmental groups and a number of grocery store chains have said they will not sell GE fish.

Researchers faced significant technical hurdles in their effort to decode the salmon genome.

While human cells contain two copies of the genetic sequence, salmon cells contain four copies. In addition, there are very long strings of repeating code, which has no apparent meaning.

“The strings of repeating code are so long that the available methods could not read through all these repetitions,” said Bergseth. “We can tell where they start and where they end it is really hard to understand how things fit together.”

To recreate the entire genome sequence, the DNA is chopped up into pieces, translated into short strings of characters and then reassembled in the correct order.

“It was a really big challenge and we had to create new mathematical algorithms and computer programs to get it all together in the right order,” he said.

(Source: VancouverSun)

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