The world’s first high-density view of the marker patterns in the Atlantic salmon – Fishfarmer Magazine

The world’s first high-density view of the marker patterns in the Atlantic salmon19 March, 2013 –

A genetic, biotechnical and breeding partnership have announced that they are the first to genotype more than 900,000 markers per sample from the Atlantic salmon (Salmo salar), thereby achieving the capability to implement genomic selection and improve their salmon breeding programme at Aqua Gen.

Aqua Gen, a member of the Erich Wesjohann (EW) Group GmBH and a leader in selective breeding, manages a large scale selective breeding program for Atlantic salmon, a major contributor to the world’s aquaculture production. Aqua Gen has also been pioneering the use of marker-assisted selection in aquaculture breeding through their highly successful QTL-innOva products.

Center for Integrative Genomics (CIGENE), located at the Norwegian University of Life Sciences, maintains research programmes that contribute to the understanding of the biology of aquaculture and plant production, focusing in particular on the genetics of complex traits of economic and ecological significance. Aqua Gen and CIGENE partnered with Affymetrix to develop the salmon genotyping screening array which consists of 923,627 SNP (Single Nucleotide Polymorphism) markers and includes both diploid and tetraploid sequence variants.

The goal of the ongoing study is to identify relevant and polymorphic high resolution markers that can be used downstream for marker trait association studies, genomic selection programs, as well as for a wide variety of applications in genetics and ecology.

“We are thrilled to have access to this first of its kind and groundbreaking marker map of the Atlantic salmon in such a short time,” said Dr. Nina Santi, Director, Research and Development at Aqua Gen.

“Aqua Gen is always looking for new technologies that can assist in the development of genetic material to meet the increasing demand for cost-effective and sustainable seafood production. This high-density SNP array gives us entirely new possibilities for improving the disease resistance and robustness of farmed Atlantic salmon. In particular, we are enthusiastic about the prospects of implementing so-called genomic selection in our breeding program. This array will also facilitate the identification of causal genetic variants underlying complex traits, thus contributing greatly to our understanding of salmonid biology.”

“Development of SNP arrays and automated genotyping in Atlantic salmon is complicated by the autotetraploid whole genome duplication that occurred in the common ancestor of extant salmonids.” said Dr. Sigbjørn Lien, Professor and Assistant Director, Norwegian University of Life Sciences (UMB) and Centre for Integrative Genetics (CIGENE). “The unparalleled design support and expertise from Affymetrix’ team of bioinformatics scientists helped tremendously to cope with these obstacles.”

“We are very pleased to partner with Aqua Gen and CIGENE and offer them our expertise in automated genotyping using the Axiom® Genotyping Solution”, said Dr. Andy Last, Executive Vice President of Genetic Analysis and Clinical Applications Business Unit at Affymetrix. “The automated genotype calling in non-diploid species offers the unique advantage of accelerating data analysis by greater than 90%, to about an hour regardless of the number of SNPs, making it easier to meet tight breeding deadlines whilst also improving accuracy”.

Axiom Genotyping Solution is the only platform that provides breeders and researchers with a powerful set of genotyping tools and analysis software to cost effectively identify, validate, and screen complex genetic traits.

As scientists make progress in decoding genomes of various human disease states, plant, and animals using next generation sequencing platforms, they can advance their research and commercial objectives by translating those discoveries to routine applications on the Axiom Genotyping Solution platform.

Aqua Gen AS (Trondheim, Norway) is a selective breeding company which develops, produces and delivers genetic material to the global sea-farming industry.

The Centre for Integrative Genetics (CIGENE) was formally established in 2003 at the Norwegian University of Life Sciences at campus Aas 30 km southeast of Oslo. Over the last decade, CIGENE has become Norway’s foremost SNP genotyping facility and has gained comprehensive experience in analyzing sequencing data and developing SNP genotyping resources in a wide range of species.

Affymetrix technologies are used by the world’s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government, and nonprofit research institutes. More than 2,300 microarray systems have been shipped around the world and more than 48,000 peer-reviewed papers have been published citing its technologies.