Next generation sequencing and bioinformatics procedures identify single nucleotide polymorphisms capable of differentiating cutthroat trout subspecies

Authors: Derek D. Houston, David B. Elzinga, Peter J. Maughan, Scott M. Smith, John S.K. Kauwe, R. Paul Evans, Ryan B. Stinger, Dennis K. Shiozawa

Year: 2012 (xliv)

Abstract

Considerable genetic information has been generated for model organisms, such as Drosophila, zebra fish, and white mice. Conversely, non model taxa have received significantly less genetic study. Salmonid fishes are non model organisms for which single nucleotide polymorphism (SNP) discovery has been actively pursued in recent years. But as a group they still warrant additional research. The cutthroat trout (Oncorhynchus clarkii), comprised of ten extant subspecies, have diagnostic SNPs identified. for only some subspecies. Cutthroat trout and rainbow trout (Oncorhynchus mykiss) have been widely stocked throughout western North America, historically with little regard for geographic variation among subspecies. Hybridization with introduced trout has placed the genetic integrity of native cutthroat trout populations at risk. As efforts to evaluate the genetic composition of cutthroat trout populations has increased, the need for additional genetic markers has also increased. We used genome reduction, MID barcoding, and next generation sequencing (454 pyrosequencing) to discover SNPs that differentiate cutthroat trout subspecies. These provide a rapid, cost effective method to evaluate cutthroat trout populations.