Whole Genome Resequencing in Rainbow Trout

We performed high coverage whole genome resequencing of 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples from the US added to 12 samples that we previously used for SNP discovery from AquaGen (Norway). Of the 49 US samples, 11 were from the Washington State University double-haploid lines and 38 represented wild and hatchery populations with divergent migratory phenotypes. The sequence data was used for SNP discovery and the resulting SNP database provides an important resource for a new high density SNP array design and other SNP genotyping platforms used in various genetic and genomics studies of this iconic salmonid fish species.