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

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 3 Mb of sequence was collected in a survey of variation in almost 132 kb of unique genic regions, from 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate ESTs, which were validated in population samples from five major stocks of salmon from the three largest basins on the Pacific coast of the contiguous 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 F(ST) 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.

Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current large marine ecosystem

“…Estimates of The genetic baseline described here was designed primarily to identify fi sh caught in PFMC ocean fi sheries and in ecological investigations in the southern portion of the California Current ecosystem and its associated tributary rivers and streams. We have shown that it performs well in this area but, because of an ascertainment strategy during SNP discovery that included individuals from the Columbia River and British Columbia (Clemento et al, 2011), the baseline also has suffi cient statistical power to identify the source of some fi sh from elsewhere in the North American range of this species. We observed high rates of self-assignment to reporting unit for all regions represented in the baseline, although some reporting units clearly were composed of populations with minimal differentiation from each other.…”

“…We compiled a list of 192 TaqMan (Life Technologies Corp., Carlsbad, CA), or 5'-nuclease, SNP genotyping assays from previously published discovery studies (Smith et al, 2005a(Smith et al, , 2005bCampbell and Narum, 2008;Narum et al, 2008;Clemento et al, 2011) to test their scorability and power for GSI. TaqMan technology combines standard PCR primers that target the genomic region around a SNP with 2 different fl uorescent probes that identify the 2 nucleotide bases present at the SNP.…”

“…The first genetic markers widely used for identification in salmon were electrophoretically detectable protein polymorphisms known as allozymes (Milner et al, 1985;Shaklee and Phelps, 1990;Tessier et al, 1995;Allendorf and Seeb, 2000). With the advent of polymerase chain reaction (PCR), many more types of genetic markers became available to discriminate salmon populations, including mitochondrial DNA polymorphisms (Cronin et al, 1993), minisatellites Miller et al, 1996), microsatellites Moran et al, 2013), amplifi ed-fragment length polymorphisms (Flannery et al, 2007) and, most recently, single nucleotide polymorphisms (SNPs; Smith et al, 2005aSmith et al, , 2005bAguilar and Garza, 2008;Narum et al 2008;Abadía-Cardoso et al, 2011;Clemento et al, 2011).…”

The invasion of an Atlantic Ocean river basin in Patagonia by Chinook salmon: new insights from SNPs

“…For example, SNP data is used on a regular basis to predict the stock composition of the world's largest salmon fishery, for sockeye salmon (O. nerka) migrating into Bristol Bay (Habicht et al 2010). The ability of GSI with SNPs to resolve both broad-and fine-scale population structure for ChS across its native range (Clemento et al 2011;Hess et al 2011;Templin et al 2011), as well as to identify the composition of ocean mixtures (Habicht et al 2010;Larson et al 2012;Satterthwaite et al 2014), has been well documented. In this paper, we use GSI to identify the origin of ChS spawning in the Santa Cruz River Basin in Argentina.…”

An Evaluation of Otolith Thermal Marking at the Feather River Hatchery, California

“…Though genetic stock identification techniques based on allele frequencies would not be sufficient to accurately identify the run type and origin of individuals at the FRH (Banks et al 2000;Williamson and May 2005;Garza and Pearse 2008), recent work with single nucleotide polymorphisms (SNPs) has demonstrated the possibility of using a genetics-based method to determine the origin and run type of FRH-produced fish (Clemento et al 2011). Parentage-based tagging using SNPs is a method that requires not only genotyping of the parent broodstock, but also the genotyping and parentage analysis of returning offspring (Anderson and Garza 2006).…”