Single‐Nucleotide Polymorphisms Associated with Allozyme Differences between Inland and Coastal Rainbow Trout

Native inland populations of rainbow trout Oncorhynchus mykiss gairdneri, particularly resident populations, often hybridize with introduced populations of the widely cultured coastal form of the species, O. m. irideus. The inland and coastal subspecies differ genetically from each other by allozyme polymorphisms at the lactate dehydrogenase (LDH‐B2*) and superoxide dismutase loci (sSOD‐1*) that can be detected using protein electrophoresis. Fewer laboratories, however, are now using allozyme technology, and most genetic studies from wild organisms are now being conducted using DNA rather than protein analyses. We have identified the single‐nucleotide polymorphism (SNP) differences responsible for the protein variations by sequencing the complementary DNA for the LDH‐B2* and sSOD‐1* genes in a large number of individuals whose genotypes were also determined by protein electrophoresis. The genetic differences causing the allozyme polymorphisms have been converted into SNP allelic discrimination assays. This should allow simple, efficient tests to be conducted in a large number of laboratories as an aid to assessing the level of hybridization between inland and coastal rainbow trout. It should also allow DNA studies to be more directly related to previous allozyme studies. High variability was also found at other sites in the superoxide dismutase gene.