Hohenlohe et al 2010
Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
Single Illumina GAII lane of RAD sequencing for SNP detection in two trout species, including 24 separately barcoded individuals.
The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to 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.  Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans, and will also provide flanking sequence for design of qPCR-based TaqMan® assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci.  This study demonstrates that it is now feasible to identify thousands of informative SNPs in non-model species quickly and at reasonable cost, even if no prior genomic information is available.