Identification of Novel Single-nucleotide Polymorphisms in Chinook Salmon and Variation Among Life History Types
Single-nucleotide polymorphisms (SNPs) are simple base substitutions of small indels in otherwise conserved regions of nuclear or mitochondrial DNA. Assays detecting these genetic markers have been a powerful tool for conserving and managing fish populations. In nonmodel species, however, available DNA sequence data are limited and inventive techniques must be employed in screening for SNPs. In this study, we used expressed sequence tags from Rainbow Trout Oncorhynchus mykiss) to design primers for amplification of genomic DNA fragments from Chinook Salmon O. tchawytscha. The regions flanking the repeat sequence of published microsatellite loci in Chinook Salmon were also chosen to examine nucleotide variation. Thirty-two individuals representing the majority of the species’ range from Russia to California were sequenced at 19 loci to identify SNPs. We discovered 58 polymorphisms during the screen and chose 13 for development into 5′ exonuclease assays (TaqMan assays). The genotypes from the TaqMan assays were compared with sequence data from individuals from the ascertainment panel to confirm proper allele designations. To evaluate the power of these markers to differentiate populations and life history types, we typed 91 individuals representing the major lineages of Chinook Salmon with 11 validated assays. Significant allele frequency differences were observed among life history types of Chinook Salmon at seven SNP loci, demonstrating the power of these markers to differentiate lineages.
Campbell, N.R., and S.R. Narum. 2008. Identification of novel single-nucleotide polymorphisms in Chinook Salmon and variation among life history types. Transactions of the American Fisheries Society 137(1):96-106. Online at https://doi.org/10.1577/T07-011.1.