Genomic evaluation of native Walleye in the Appalachian Region and the effects of stocking

Objective: Create a quicker and more accurate genetic assignment tool for Walleye Sander vitreus broodstock in the Eastern Highlands region and to quantify genetic diversity of four Walleye populations using next-generation sequencing.Methods: To determine the impacts of stocking nonnative Great Lakes strain Walleye on local populations, three Appalachian populations were sampled: two native populations (Rockcastle River, Kentucky, and New River, Virginia) and one population founded from the Great Lakes strain (Tygart Lake, West Virginia). Walleye from Lake Erie were used as a reference for the Great Lakes strain. Utilization of a genotype-by-sequencing approach supported genome-wide estimates of genetic diversity, population structure, and creation of two single-nucleotide polymorphism assays that can be used to rapidly identify Great Lakes-strain, native Eastern Highland-strain, and F-1 hybrid Walleye.Result: Results indicate that the four populations we evaluated were genetically distinct from one another and that each population contains varying degrees of genetic differentiation relative to its source population. The stocked Tygart Lake population displayed lower genetic diversity in metrics such as nucleotide diversity (0.172 vs. 0.184), private alleles (4057 vs. 7623), and observed heterozygosity (0.163 vs. 0.204), likely indicative of genetic drift stemming from a founder effect. The two native populations displayed varying levels of genetic diversity. The New River population was found to have a higher ancestry of the Great Lakes strain in their genome than the Rockcastle River population, reflecting the known admixture of New River Walleye following historic stocking of Great Lakes-derived Walleye. Our results also identified a pure native Eastern Highlands strain population that can be used for future augmentation and restoration of Eastern Highlands Walleye.Conclusion: Our results provide a diagnostic single-nucleotide polymorphism assay to quickly identify Great Lake strain, Eastern Highland strain, and their F-1 hybrid for future management efforts and provide key population genetic insights to managers to enhance best management practices.