An Improved Linkage Map Reveals Candidate Genes for Adaptive Variation in Chinook Salmon

A fundamental goal in genomics studies is to find genes involved in natural selection and local adaptation.  RAD loci have become the marker of choice for many genome-scale studies.  However, linkage maps built from these markers often contain no annotation information, allowing identification of genomic regions, but not genes, involved in adaptation and differentiation.  The wealth of genomic resources for salmonids presents an opportunity to combine datasets across multiple studies and enhance our ability to make genetic inferences.  We utilized resources from five previous studies to demonstrate the gains achieved by leveraging multiple smaller datasets to enhance inference.  We generated an improved linkage map for Chinook salmon, greatly increasing the number of mapped markers relative to previous studies.  We also provided resources for gene annotation by placing Atlantic salmon genome and Chinook salmon EST sequence onto this map.  Finally, we applied this new map to a re-examination of existing QTL and population genetic datasets to identify candidate genes associated with adaptive traits and population differentiation.  Using this second generation map, we identified strong candidates for adaptive genes within previously detected QTL.  We also detected genes with likely roles in adaptive processes in multiple genomic regions of divergence between populations.