Genomics of Hybridization in Westslope Cutthroat Trout

The increased numbers of genetic markers produced by genomic techniques will help localize chromosomal regions responding to selection and influencing introgression.  We used RAD sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (O. clarkii lewisi).  We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions.  We identified 2,923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labeled individuals.  Ongoing genome sequencing of rainbow trout allows physical mapping of SNP loci for genome-wide scans, and provides flanking sequence for design of qPCR-based TaqMan® assays for high-throughput, low-cost genome wide scans using a subset of 200-400 SNP loci.  We demonstrate the feasibility of identifying thousands of informative SNPs in non-model species quickly with no prior genomic information.  We are applying RADs and TaqMan® SNP genotyping to test for natural selection and to identify “invasive” RBT chromosomal regions that spread rapidly to high frequency among populations.