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

Citation

Clemento, Anthony J.; Abadía-Cardoso, Alicia; Starks, Hilary A.; Garza, John C. (2010), Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha, Dryad, Dataset, https://doi.org/10.5061/dryad.8108

Abstract

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 Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3 to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean FST estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.

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