Genetics boost for cod farming

Scientists have developed a tool that makes it possible to advance 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. 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,” said Anne Kettunen, a scientist at Norwegian research institute Nofima.

Luqman Aslam, a senior scientist at Nofima, is a specialist in developing such tools and has done so together with Kettunen.

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 (single nucleotide polymorphism) array, or “snip chip”.

“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. But siblings aren’t identical, despite having an average of 50% of the gene variants in common. A cod can have significantly more or less than 50% in common with its siblings, just like people.

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, breeders can compare cod and calculate how related they are. They can then select siblings with the closest relationship to the cod that did best in the test, to become parents.

Genetic progress

This type of genomic selection provides higher accuracy and higher selection intensity, increasing genetic progress.

Such tools exist for breeding livestock, salmon and sea bass, and the tool developed by Aslam and Kettunen can be of great importance for efficient cod breeding.

The scientists used the Norwegian population of farmed cod and wild cod to create the SNP array, which has 21,000 markers for variations.

They can now use the array to find QTLs (quantitative trait loci). These are areas in the genome that strongly influence the desirable traits to improve cod breeding.

QTL for growth

“We have found QTL for growth. We can also use the SNP panel to find QTLs for different health traits and sexual maturation,” saif Kettunen.

An example of an important QTL is the one for resistance to the salmon disease called IPN (infectious salmon necrosis), discovered by the Roslin Institute in Scotland in 2008. The QTL could be used to weed out salmon predisposed to IPN, and since its arrival, IPN has decreased drastically in salmon farming.

The SNP array for cod will enable producers to genotype their own cod to calculate relationships between fish or look for beneficial gene variants.

“You don’t become a good carpenter simply by buying a good hammer. To benefit from the tool, you need expertise and good material in the population to breed from,” said Kettunen.

Kettunen and Aslam will use the SNP array themselves in research projects. For example, they will study resistance to the bacterial disease francisellosis in the new ‘Frantic’ project and use the tool in routine selection in the cod breeding programme.

The research is funded by MABIT, an R&D programme within marine biotechnology in Northern Norway.