Isolation and characterization of novel salmon microsatellite loci: Cross-species amplification and population genetic applications

Twenty-two variable number of tandem repeat microsatellite dinucleotide repeat ([GA](n) and [CA](n)) loci were cloned from sockeye salmon (Oncorhynchus nerka) partial genomic libraries. Characteristics and optimal polymerase chain reaction (PCR) conditions were defined for each locus. The degree of conservation of sequences flanking microsatellite repeat motifs and the utility of heterologous PCR primers for analyses in closely related taxa was tested using 10 salmonid species from four genera. Nearly all microsatellite primers produce amplification products in multiple species, suggesting broad application in salmonid research. The utility of these loci for population genetic studies was tested using individuals (N = 83) from three spawning populations of chinook salmon (Oncorhynchus tshawytscha) from the Yukon River, Yukon Territories. Twelve of 16 loci screened were polymorphic (mean heterozygosity = 0.254). Genetic distance estimates between populations were concordant with results from a previous allozyme survey of these same populations. Discussions of the utility of microsatellite markers in salmonid population genetic research are presented in light of recently described statistical methodologies based on mutational properties and interallelic differences in repeat score.