Scientists at the Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima) have developed a tool that makes it possible to lift cod breeding from family selection to individual selection, thereby increasing genetic gain.
"We have now tailored a genomic tool for cod, that is, we can breed based on the good traits of individuals," said Nofima scientist Anne Kettunen. "The tool is openly available and well timed seeing that cod farming is on the rise again. It can contribute to more efficient seafood production."
Nofima senior scientist Luqman Aslam is a specialist in developing such tools and has done so together with Kettunen.
From family breeding to individual breeding
Although siblings inherit half of their genes from their mother and half from their father, siblings are often very different from each other. These differences are the starting point for the new SNP panel tool (SNP is pronounced "snip" and stands for "single nucleotide polymorphism.").
"This is probably the first medium density SNP panel suitable for both research and commercial use in cod breeding programmes," said Aslam.
Nofima's cod breeding programme currently uses family selection based on relationships, i.e., they breed from siblings of cod that have been tested for selected traits and passed. However, siblings can be very different, despite them having an average of 50 per cent of the gene variants in common.
Like humans, a cod can have significantly more or less than 50 per cent in common with its siblings.
So-called genomic tools now allow cod breeding programmes to consider that siblings inherit different gene variants from their parents. In the same way that DNA samples from traces and suspects are compared in criminal cases, it is now possible to compare cod and calculate how related they are.
Scientists can then select siblings with the closest relationship to the cod that did best in the test, to become parents. The process then transitions from family breeding to individual breeding, including those traits that cannot be measured on the breeding candidate itself.
This type of selection is called genomic selection. It provides higher accuracy and higher selection intensity.
Such tools exist for breeding livestock, salmon and sea bass, and Nofima said the tool developed by Aslam and Kettunen can be applied in efficient cod breeding
How the tool was developed
Aslam and Kettunen have used the Norwegian population of farmed cod and wild cod to create this SNP panel.
The work has involved finding variation in the Norwegian cod population genome. This information is in the SNP panel, with a total of 21,000 markers.
The scientists can now use the SNP panel to find QTLs (Quantitative Trait Loci). These are areas in the genome that strongly influence the traits one is interested in improving in cod breeding.
"We have found QTL for growth," said Kettunen. "We can also use the SNP panel to find QTLs for different health traits and sexual maturation."
An example of an important QTL is the one for the salmon disease called IPN. QTL could be used to weed out salmon predisposed to IPN, and since its arrival, IPN has decreased drastically in salmon farming.
Useful for cod farmers and breeding companies
Nofima said the SNP panel is useful for industry because it provides more accurate selection, QTLs can be found in cod, and it can reduce the use of trial fish.
The scientists have thus developed a tool that everyone is free to use. One can genotype one's own cod to calculate relationships between fish or look for beneficial gene variants.
"To benefit from the tool, you need expertise and good material in the population to breed from", advises Kettunen.
Kettunen and Aslam will use the tool themselves in research projects. For example, they will study resistance to the bacterial disease francisellosis in a separate project and use the tool in routine selection in the cod breeding programme.
The research is funded by MABIT, an R&D program within marine biotechnology in northern Norway.
