Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

Authors

  • Meredith V. Everett,

    1. School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
    Current affiliation:
    1. Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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  • James E. Seeb

    Corresponding author
    1. School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
    • Correspondence

      James E. Seeb, School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195-5020, USA.

      Tel.: +1 206 685 2097;

      fax: +1 206 685 7471;

      e-mail: jseeb@uw.edu

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Abstract

Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome.

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