Tapping into the salmon genome

Photo: GT Nergaard/Salmar

New research into the genetic diversity of farmed fish species is paving the way for improved population management and farming practices.


“It will be a tremendous source of information for the aquaculture industry and aquaculture research,” says principal investigator Kjetil Jakobsen from the University of Oslo’s Centre for Ecological and Evolutionary Synthesis.

Together with collaborators in Canada, Sweden, Iceland and Switzerland, he is sequencing the genomes of 1,000 Atlantic cod and 1,000 Atlantic salmon to build a database detailing the genetic diversity of these species, which are economically important for Norway and the partner nations.
The project, dubbed Aqua Genome, builds on work done by scientists who sequenced the genomes of these fish. A Norwegian research group sequenced the cod genome in 2011 and the sequencing of the salmon genome is on track to be completed this winter.

The sequencing of a single reference genome allows researchers to know where genes of interest are located on a species’ chromosome, but doesn’t give a sense of the genetic variation within the species.

That’s what this research team is now working to accomplish.

“Once you’ve done it the first time, then you can go back and sequence many, many more related and unrelated fish so that you can do the really interesting stuff,” explains Ken Dewar, project collaborator and associate professor of bioinformatics and genomics at McGill University in Montreal, Canada.

The interesting stuff, in Dewar’s view, involves comparing and contrasting the genomes of different fish from the same species to see how genes differ and how those differences correspond to variation in physical properties and behaviour.

This will be done over the next four years as scientists involved in the project sequence and compare the genomes of fish from populations around the world. Genetic diversity of populations can then be monitored over time, which is important given that the amount of genetic variation in populations indicates how well they can adapt to environmental changes.

This is because even if population sizes remains constant, a decrease in genetic variation can put populations in danger since there is a greater risk of all individuals being wiped out if a new disease emerges or if there are significant changes to water chemistry or temperatures. In populations with high genetic diversity, there is a better chance of some individuals having the traits necessary to survive these new conditions.

A database of genetic variation also has commercial applications since it will outline variation in genes for desirable traits, including disease resistance, delayed maturation and good muscle texture.

With a database of genes and a knowledge of which ones produce healthier, better-tasting fish, farmers might soon be able to use simple and cheap technologies to identify whether advantageous genes exist in their animals, researchers say. For example, breeders could send away fin samples of fish for DNA analysis that would determine whether desirable genes exist at key locations in the genome. Such technology is already being used in salmon farming to identify whether the fish are susceptible to a pancreatic virus.

And as more research is done to unlock the secrets of fish genomes, these technologies could soon offer more information and allow breeders to make more informed choices about the fish they breed. It’s a reality that can prove hugely beneficial for nations such as Norway where demand for aquaculture products is only increasing.