Lake Erie Walleye Stock Discrimination Using Next-Generation RAD Sequencing

Recent advances in next-generation DNA sequencing technologies are allowing researchers to produce genetic data on a much larger scale than previously possible. The resulting genome-scale datasets could be especially valuable for detecting small but significant genetic differences between breeding stocks of harvested fish. Management of walleye (Sander vitreus) in Lake Erie could benefit greatly from the ability to reliably assign individuals to specific spawning stocks when the stocks are mixed outside of the breeding season. Towards this end, we have been using restriction-site associated DNA (RAD) sequencing to identify genetic markers that can be used to probabilistically assign individuals to 1 of 3 spawning locations in western Lake Erie (Sandusky River, Maumee River, and Ohio reef complex). To date, among 564 single nucleotide polymorphism (SNP) found in our study, 345 SNP loci can be genotyped for all individuals, and 23 out of 345 SNP loci were detected as differentiated loci among three spawning stocks based on a F_ST-outlier method. These F_ST-outlier loci have been further evaluated for the use in walleye stock discrimination and group membership analysis.