Gene Mapping in Salmonids Using Sequenced RAD Tags

Linking specific genes to phenotypic and evolutionary traits of interest is an important component in understanding an organism’s biology and fitness.  One of the requirements for effective gene mapping is a dense genetic linkage map containing large numbers of markers.  In many non-model species, including many salmonids, one ongoing limitation of effective gene mapping is the lack of genetic markers and the expense of marker development.  RAD tag sequencing offers an effective solution, using the millions of reads produced by next-generation sequencing to identify and genotype thousands of tags in multiple individuals for relatively low cost.  Three families of sockeye salmon (Oncorhynchus nerka) from Hansen Creek, Alaska were created for the purpose of creating a genetic linkage map and association mapping of traits related to growth and heat tolerance.  RAD tag sequencing was carried out on the parents and 96 offspring from each family.  This resulted in discovery and genotyping of more than 4,000 SNPs.  These markers, as well as previously discovered EST based SNPs have been placed in a new SNP-based linkage map for sockeye salmon.  Using these linkage groups QTL loci for growth and heat tolerance were identified.  Application of these methods to additional species will greatly expand the available genetic resources for evolutionary and conservation efforts in salmonids.