Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

Authors

  • PAUL A. HOHENLOHE,

    1. Center for Ecology and Evolutionary Biology, 5289 University of Oregon, Eugene, OR 97403-5289, USA
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  • STEPHEN J. AMISH,

    1. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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  • JULIAN M. CATCHEN,

    1. Center for Ecology and Evolutionary Biology, 5289 University of Oregon, Eugene, OR 97403-5289, 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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Paul Hohenlohe, Fax: 541 346 2364; E-mail: hohenlo@uoregon.edu

Abstract

The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy–Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan® assays for high-throughput, low-cost hybrid identification using a subset of 50–100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.

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