title: Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map.
abstract: Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett). wlarson1@uw.edu.
authors.forename: Wesley A
authors.initials: WA
authors.lastname: Larson
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
authors.forename: Garrett J
authors.initials: GJ
authors.lastname: McKinney
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
authors.forename: Morten T
authors.initials: MT
authors.lastname: Limborg
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
authors.forename: Meredith V
authors.initials: MV
authors.lastname: Everett
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Seeb
authors.affiliation: From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005260:Female; D008040:Genetic Linkage; D005838:Genotype; D008297:Male; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012474:Salmon / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: RAD; condition factor; genotyping by sequencing; linkage map; quantitative trait loci; size; sockeye salmon; thermotolerance