The reference genome of Atlantic salmon is ready
Work to map and systematize the salmon's genetic code has taken six years of interse effort.
– We now have a solid basis for applying genetic/genomic information to secure sustainable aquaculture, says Professor Sigbjørn Lien at the Norwegian University of Life Sciences (NMBU).
– The salmon genome assembly has a comparable quality to that of the human genome, and it is essential to have such a reference sequence in order to use modern genetics to further develop the Norwegian aquaculture salmon as well as ensure effective management of wild salmon.
Faster and better breeding
Even though Norway has been refining the salmon used in its aquaculture programs for 45 years, the job is by no means finished.
Refinement is a continuous process because fish with the best genetics for today are not necessarily the best adapted to new diseases, environmental conditions or future feeds.
The availability of the genetic sequence has already been put to good use in salmon breeding. The IPN-virus, which has been a serious problem in Norwegian salmon aquaculture for many years with mortality rates as high as 90% in affected farms, has inflicted great costs on the industry. Until scientists in AquaGen began working with the sequence of the salmon genome, the mechanism of disease resistance was unknown.
– We had known for a long time that there was a connection between genetics and IPN-resistance, but it was not until we got access to the most recent genome sequence that we could identify exactly which gene was responsible for making the fish resistant. Today, we can guard against IPN by ensuring that carriers of IPN-resistance are the only fish being used for further breeding, says Nina Santi, Administrative Director in AquaGen.
The new gene test has reduced the incidence of IPN-cases by 90%, from 223 (2009) to 19 (2015), and has thereby saved Norwegian salmon aquaculture billions of NOKs.
Preserving a national treasure
In addition to the importance of the salmon genome for securing the sustainable development of aquaculture, this resource will also play a central role in the conservation and management of a national treasure - the wild salmon. In two new large projects, Aqua Genome Project and QuantEscape, salmon genome sequencing is used to characterize genetic variation in the Norwegian salmon rivers. This work will allow researchers to accurately identify which salmon are escaped aquaculture salmon and which are wild salmon and to quantify how much the aquaculture salmon are affecting the wild populations.
The leader of the QuantEscape project, Kjetil Hindar, believes that information from the genome will be very important for protecting wild salmon:
– For the first time we can measure with great accuracy what effect escaped aquaculture salmon have on the genetics of wild salmon and subsequent effects on local adaptation. This underpins our ability to ensure sustainable co-existence between the aquaculture industry and wild salmon.
Back-up copy of the genes
In addition to its practical applications, publication of the Atlantic salmon genome sequence in this week's volume of Nature also provides new and important insight for basic research in evolutionary biology. 80 million years ago, the mother of all living salmon doubled its genetic material - instead of having 25, it suddenly had 50 chromosomes. Researcher Simen Rød Sandve at NMBU led part of the evolutionary analysis of salmon at NMBU:
– When the ancestral salmonid got a back-up copy of all of its genes, this meant that the extra copies could mutate and evolve into new functions. Many have speculated about whether some of the salmon's special qualities have evolved because of these new gene copies; for example, the salmon's red meat or its ability to live in freshwater as young fish and saltwater as adults (anadromous). These are exciting hypotheses that we are currently investigating further.
Many believe that the aquaculture industry will take over after the oil adventure declines, and now at least the genetic tool box is in place.