The first salmon genome — of a female fish named Sally — will be fully sequenced by the end of 2013 and researchers from around the world are already exploring ways to use this reference genome to address challenges in salmon farming and production.
“The expectations are that this will make aquaculture better, more directed and more sustainable,” explains Steinar Bergseth, chair of the International Collaboration to Sequence the Salmon Genome and advisor for the Research Council of Norway. “We can tap into the genes and understand how these are regulated with regard to diseases, food uptake, treatment of the animal and environmental adaptations.”
The sequencing of the salmon genome began in 2009 after research funding bodies from Norway, Canada and Chile pumped millions of dollars into the project. The genome sequence was supposed to be completed this spring, but the complexity of the sequencing meant timelines had to be pushed back.
“It’s not a very straightforward genome to sequence,” Bergseth says.
Whereas the genetic information of most organisms is encoded in two strands of DNA, most of the salmon’s genetic material is stored in four strands: two each from the mother and father. And these strands are very long and repetitive, which makes it difficult for scientists to break up strands of DNA into workable pieces, figure out what gene sequences are on those strands and then stitch the DNA back together.
Once this is done, scientists will see where all gene sequences are – the first step towards figuring out what the gene sequences do.
“Sequencing the genes, understanding where they are, doesn’t necessarily mean you know the function of the proteins that those genes encode,” cautions Unni Grimholt from the Centre for Ecological and Evolutionary Synthesis at University of Oslo. She was among those who sequenced the cod genome, which was completed in 2011.
“We don’t know everything about salmon once we see the genome,” she says. “This is not the end of the journey, we’re still half-way.”
But already that journey is moving forward. Given the importance of salmon aquaculture for the Norwegian economy – the country is one of the world’s leading producers of farmed salmon and accounted for a third of global production in 2008 – the Research Council of Norway in January invested the equivalent of almost €5.5 million into three projects that will use the sequenced genome to tackle specific hurdles to aquaculture.
One such project, headed by Anna Troedsson Wargelius, a scientist with the Institute of Marine Research in Bergen, will attempt to locate where genes are that code for puberty and which ones are associated with late maturation.
From a fisheries perspective, fish that reach sexual maturity later in life are more desirable than those that mature earlier because later maturation gives them a chance to get larger, Wargelius says.
Fisheries used to selectively breed fish that matured later in life, but this strategy fell out of practice once breeders discovered they could delay sexual maturation by exposing fish to continuous light. But now, warming waters are starting to promote early puberty and continuous light may not be enough to effectively delay this.
“It’s getting to be an increasing problem,” Wargelius says.
She and her research team will identify genes for sexual maturation by mapping the genome of fish in populations known to mature after one year and then comparing these to genomes of fish from populations that mature after three or more years. This is possible because the team will be using the soon-to-be-completed reference genome as a template.
But the task is still a formidable one.
“The trick is to be able to see which of these millions of differences are really showing something that’s related to puberty,” Wargelius says.
When this has been achieved, a chip can be developed that reads a small region of a salmon’s genome to determine if the fish has gene sequences that make it likely to mature later. Breeders would then be able to use this information when choosing fish to breed.
Other funded projects are looking for genes that code for resistance to sea lice and good meat texture. Many of the researchers on these projects may join Bergseth and his colleagues next spring when they plan to share the findings from the genome sequencing at an international conference.