Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world’s most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3MB of sequence was collected in a survey of variation in more than 131KB of unique genic regions, from more than 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5’ nuclease) assays, almost all from separate EST regions, which were validated in population samples from 5 major stocks of salmon from the three largest basins on the Pacific coast of the coterminous United States: the Sacramento, Klamath and C...