Analysing 900,000 genetic markers from salmon at the same time

Samples from AquaGens breeding stock will be analysed on this board that contains what are called microarrays. Every one of the 96 microarrays has room for over 900,000 genetic markers. This means that 96 fish can be analysed for more than 900,000 genetic markers at the same time.

Samples from AquaGens breeding stock will be analysed on this board that contains what are called microarrays. Every one of the 96 microarrays has room for over 900,000 genetic markers. This means that 96 fish can be analysed for more than 900,000 genetic markers at the same time.

AquaGen has worked in co-operation with CIGENE and Affymetrix to develop and implement a new tool that analyses more than 900,000 genetic markers per sample from salmon.  This is the worlds largest genetic marker set for fish and is a major advance from the previously used set of 6,000 genetic markers.

Improvement in disease resistance and robustness

This new set will in the first instance be used to find other new genes and genetic markers that are associated with valuable traits in salmon. Making improvements against diseases and parasites will be central; CMS, salmon lice and Amoebic Gill Disease (AGD) have been given the highest immediate priority. This new genetic marker set also makes possible so-called genomic selection which is a further development and optimisation of the marker assisted selection that is used today for PD and IPN resistance.

“We are pleased to have been able to develop this ground-breaking genetic marker set for salmon in such a short time”, says Nina Santi, Research and development director at AquaGen. “AquaGen is always looking for new technologies that can meet the increasing demand for cost-effective and sustainable production of seafood.

This high-resolution gene marker set gives us entirely new opportunities for improving disease resistance and quality of farmed salmon. We are especially excited about the prospect of implementing genomic selection in our breeding programme. Marker sets will also make it easier to identify genetic variants that underlie complex traits, such as growth and feed efficiency whilst at the same time contributing greatly to the understanding of salmon biology”.

Increased precision and speed of genotyping

The development of genetic marker sets and automatic genotyping of Atlantic salmon is complicated because the salmon genome partly is comprised of four chromosome sets compared to the two we find in humans”, says Sigbjørn Lien, a professor at the University of life sciences (UMB) and the Centre for Integrative Genetics (CIGENE) “.  The good support from, and expertise of, the Affymetrix team of researchers in bioinformatics helped greatly in tackling these obstacles.”

“We are very pleased to have worked in partnership with AquaGen and CIGENE and offer them expertise in automatic genotyping using the Axiom® Genotyping Solution” says Andy Sist, Vice president for business unit for genetic analysis and clinical applications at Affymetrix.

“The Axiom® Genotyping Solution is the only platform that provides breeding companies and researchers with a powerful tool for genotyping and analysis, and cost-effective identification and validation of complex genetic traits. Using the Axiom Genotyping Solution® platform, scientific results can be rapidly developed and commercialised”.