Data from: An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14,620 SNP loci including 2,336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11,728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to co-localize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth, and behavior. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.Genotypes for female consensus map formatted for LepMapThis file contains genotypes for haploid and diploid families used to create the female consensus linkage map. Description of data is in the ReadMe file.HapDipFemConsensus.linkageGenotypes for male diploid map formatted for LepMapDipMale.linkage contains the genotypes used to produce the diploid male map in McKinney et al. 2015. Description of data is in the ReadMe file.DipMale.linkageLocusNamingKeyLocusNamingKey.xlsx provides a lookup table to convert locus names used in HapDipFemConsensus.linkage and DipMale.linkage to the names presented in the linkage maps in McKinney et al. 2015