Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.).

Despite the large number of genes contributing to the immune response, wildlife immunogenetic studies have tended to focus mostly on the major histocompatibility complex-related genes. Here, we utilized previously published microarray and competitive RNA hybridization information to identify 3750 immune relevant Atlantic salmon (Salmo salar) expressed sequence tags. We then identified those expressed sequence tags containing microsatellites and subsequently designed 48 primer pairs and tested them for polymorphism in Atlantic salmon. Altogether, 16 polymorphic markers were characterized, with allele numbers ranging from two to 18, and these 16 loci were further tested in five other salmonid species.