Characterization of 22 novel single nucleotide polymorphism markers in steelhead and rainbow trout

Thirty-two individuals representing coastal and inland populations of steelhead and rainbow trout (Oncorhynchus mykiss) were sequenced at 18 expressed sequence tags and nine microsatellite loci to identify single nucleotide polymorphisms. A total of 98 polymorphisms were discovered during the screen and 22 were developed into 5' exonuclease assays (Taqman assays). Genotypes from TaqMan assays were compared to sequence data from individuals in the ascertainment panel to confirm proper allele designations. A larger number of samples (n = 192) from six regions were tested with the validated assays. Per-locus F-ST values ranged from 0.001 to 0.414.