Mitigating the effects of escaped farmed salmon: combining SNPs, lipid acid profiling and statistical methods to trace escapees to origin

Recently DNA microsatellites have been successfully used to identify individual farmed escaped salmon back to cage of origin. In some cases, however, the information drawn from DNA based markers must be followed with supplementary information from other markers, such as lipid acid profiles. Microsatellites are subject to inter-laboratory calibration problems and are technically demanding. The statistical power of a microsatellite locus is typically 4-10 times higher than for a SNP (single nucleotide po lymorphism) locus, but the ability to screen a large number of SNP loci simultaneously, in combination with the opportunity to analyse a large number of loci to find those that are diagnostic, far outweighs the advantage of microsatellites. Recently, the Centre for Integrated Genetics (CIGENE) in Norway started production of a genome wide genotyping chip interrogating a large number of SNPs for the Atlantic salmon. The main objective of the four work packages in the project is to improve the precision in methods for identification of origin of farmed salmon escaping from sea cages and smolt farms, by a combination of SNP markers and lipid acid profiles. SNP markers on the Illumina and Sequenom platforms, and the 15 microsatellites currently in use fo r tracing farmed escapees, will be screened in order to compare the diagnostic power of both marker types.