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Abstract
A high-density microsatellite genetic map for rainbow trout Oncorhynchus mykiss is needed for the identification of quantitative trait loci affecting traits of economic interest to the aquaculture industry. These markers are also useful for evolutionary and population genetic studies. The candidate marker sequences that are identifed must be characterized with respect to their uniqueness, polymorphism, heterozygosity, ploidy, and usefulness as comparative mapping markers within the family Salmonidae. Ninety-seven microsatellite markers were developed and characterized in this study. Twenty-eight of these markers have been identified as duplicated in the rainbow trout genome based on the observation of more than one allele in at least one homozygous individual from clonal (doubled haploid) lines and more than two alleles in diploid fish. All of the 69 single-copy markers were polymorphic in the rainbow trout sampled, with an average heterozygosity of 58%.