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.