Aqua Gen salmon eggs. (Photo Credit: Aqua Gen)
World gets first high-density view of Atlantic salmon marker patterns
Friday, March 22, 2013, 00:50 (GMT + 9)
Aqua Gen, a member of the Erich Wesjohann (EW) Group GmBH and Centre for Integrative Genomics (CIGENE) at the Norwegian University of Life Sciences (UMB) in collaboration with Affymetrix, Inc 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 leader in selective breeding, manages a large scale selective breeding programme 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.
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 programmes, as well as for a wide variety of applications in genetics and ecology.
“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,” said Dr Nina Santi, Director, Research and Development at Aqua Gen.
“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 programme. 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, UMB and CIGENE. “The unparalleled design support and expertise from Affymetrix’ team of bioinformatics scientists helped tremendously to cope with these obstacles.”
“The automated genotype calling in non-diploid species offers the unique advantage of accelerating data analysis by greater than 90 per cent, to about an hour regardless of the number of SNPs, making it easier to meet tight breeding deadlines whilst also improving accuracy,” said Dr Andy Last, Executive Vice President of Genetic Analysis and Clinical Applications Business Unit at Affymetrix.