Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic study of salmonids

We have cloned 76 microsatellite sequences from rainbow trout (Oncorhynchus mykiss), each consisting of tandemly repeated arrays of either (GT)(n) or (GA)(n). To summarize patterns of genetic structure, each microsatellite was characterized according to the length and complexity of the repetitive sequences. Two microsatellites were developed for use as genetic markers in O. mykiss. The locus PuPuPy contained >100 repeats of a trinucleotide motif of the general form purine-purine-pyrimidine. The locus Omy77 contained similar to 18-40 repeats of the dinucleotide GA. Length polymorphisms were identified through polymerase chain reaction (PCR) analysis, and each locus displayed at least 8-9 alleles. Primers designed from the O. mykiss sequence were employed to PCR-amplify and clone fragments from Oncorhynchus clarki, Oncorhynchus keta, Oncorhynchus kisutch, Oncorhynchus tshawytscha, Salmo salar, and Salvelinus fontinalis. The Omy77 primers failed to amplify Salvelinus fontinalis DNA. Sequencing of clones confirmed that the PCR-amplified fragments were derived from homologous loci. Both loci appear to be polymorphic in most species examined, suggesting that microsatellite markers isolated from one species of salmonid are likely to also be useful in genetic studies of other salmonid species.