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

Authors

  • STEPHEN J. AMISH,

    1. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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  • PAUL A. HOHENLOHE,

    1. Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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  • SALLY PAINTER,

    1. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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  • ROBB F. LEARY,

    1. Montana Fish, Wildlife & Parks, University of Montana, Missoula, MT 59812, USA
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  • CLINT MUHLFELD,

    1. U.S. Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, MT 59936, USA
    2. Flathead Lake Biological Station, University of Montana, Polson, MT 59860, USA
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  • FRED W. ALLENDORF,

    1. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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  • GORDON LUIKART

    1. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
    2. Flathead Lake Biological Station, University of Montana, Polson, MT 59860, USA
    3. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
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Steve Amish, Fax: 406-243-4384; E-mail: stephen.amish@umontana.edu

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.

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