RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays

Molecular Ecology Resources
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Abstract

Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single-nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here, we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and nonhybridized individuals. This technique shows promise as a very low-cost, reliable and relatively rapid method for developing and testing SNP markers for nonmodel organisms with limited genomic resources.

Additional publication details

Publication type Article
Publication Subtype Journal Article
Title RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Series title Molecular Ecology Resources
DOI 10.1111/j.1755-0998.2012.03157.x
Volume 12
Issue 4
Year Published 2012
Language English
Publisher Blackwell Science
Publisher location Oxford, England
Contributing office(s) Northern Rocky Mountain Science Center
Description 8 p.
First page 653
Last page 660
Online Only (Y/N) N
Additional Online Files (Y/N) N
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