Open Access Highly Accessed Methodology article

Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing

Derek D Houston1*, David B Elzinga2, Peter J Maughan2, Scott M Smith2, John SK Kauwe1, R Paul Evans3, Ryan B Stinger1 and Dennis K Shiozawa14

Author affiliations

1 Department of Biology, Brigham Young University, Provo, UT, 84602, USA

2 Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, 84602, USA

3 Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA

4 Curator of Fishes, Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA

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Citation and License

BMC Genomics 2012, 13:724  doi:10.1186/1471-2164-13-724

Published: 23 December 2012



Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations.


Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses.


Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans.

Conservation genetics; Genetic admixture; Hybridization; KASPar; Oncorhynchus clarkii; Oncorhynchus mykiss; Population genomics; SNP; Rainbow trout