Heritability of the Run-Timing Trait and Association Mapping Using Admixture Linkage Disequilibrium in Chinook Salmon

Admixed populations of humans and other species have long been exploited for purposes of association mapping of traits such as disease resistance.  This strategy is an ideal approach for non-model organisms such as Chinook salmon (Oncorhynchus tshawytscha), because long generation times complicate alternative strategies that require genetic crosses using inbred lines. However, association studies that employ admixed populations require a rare set of conditions including distinct pairs of lineages living in sympatry and interbreeding, as well as a measurable heritable trait that differs between lineages.  In the Columbia River Basin, this rare set of conditions exists in the Hood River where two Chinook salmon lineages, a reintroduced population from the Interior stream-type lineage and a group of colonizers from the Lower Columbia lineage, have been interbreeding for several years.  In addition, the two lineages are distinguished by run-timing.  This admixed population was discovered through an 18 year long pedigree study which has set the foundation for this current study.  In the pedigree study, approximately 7,700 Chinook salmon were genotyped using 15 microsatellite loci, and parent-offspring matches were identified to test heritability (h²) of run-timing.  For the Lower Columbia versus Interior stream-type parental matings, run-timing was found to have high heritability in offspring suggesting a genetic basis for this trait.  As a first step to investigate the genetic basis of run-timing, we genotyped 140 single nucleotide polymorphism (SNP) loci for 332 individuals from the Hood River that were identified as early- and late-run-timing admixed fish.  These loci were then analyzed for associations between run-timing category and lineage using software that implements mapping by admixture linkage disequilibrium methodology.  As a second phase, we will employ Restriction site Associated DNA (RAD) sequencing to genotype thousands of loci on the same individuals for a more in depth association analysis.  We expect this ideal set of conditions discovered in the Hood River can be used to greatly advance our understanding of genes underpinning the run-timing trait in Chinook salmon.