Application of Genotyping-by-Sequencing (GBS) in Atlantic Salmon (Salmo salar)

Advances in next generation sequencing technology have made genotyping-by-sequencing (GBS) a viable and cost effective alternative to more traditional methods for studies of genetic diversity, parentage assignment and genomic selection in livestock and aquaculture species.

High-throughput GBS methodology produces SNP genotypes that are supported by varying depth of sequence reads. The cost effectiveness of the method is determined by the number of samples and proportion of the genome assayed within a lane of sequencing. Selecting the most appropriate combination to sequence will depend on the read depth required to validate the SNP genotypes for use in the intended downstream application.

Here we present results from Atlantic Salmon (Salmo salar) using GBS with the restriction enzymes ApeKI and PstI and the subsequent use of PstI for genetic diversity, parentage assignment and genomic selection studies. This work demonstrates how this approach can be implemented at low cost in a non-traditional species that contains a partially duplicated genome.