24andmore: Using genome-wide SNPS to investigate the genetic diversity of Iowa walleye (\u3cem\u3eSander vitreous\u3c/em\u3e) broodstock

The stocking of Sander vitreus in Iowa waterbodies is one of the primary tools used by the Iowa Department of Natural Resources (DNR) to ensure healthy populations for enjoyable fishing experiences. A substantial amount of time and money goes into this effort, so stocking efficiency is vital. Knowledge of genetic diversity contained in the broodstock increases this efficiency by having a better understanding of which strain will survive and contribute to the fishery in certain environments. The objective of this study is to investigate the genetic diversity of Iowa S. vitreus broodstock to identify genetic ancestry and quantify the genetic diversity of each strain contained in the broodstock. From this information, the creation of a strain-specific identification marker was explored. Rathbun Fish Hatchery’s captive walleye broodstock contains two genetic strains: the lake-strain and the river-strain. Sampling of the 2019 captive broodstock at the Rathbun Fish Hatchery in Moravia, IA was conducted to genotype individuals and generate genome-wide single nucleotide polymorphism (SNP) datasets. Three datasets were generated; one to infer genetic variation between strain, the combined LR dataset, and two to infer genetic variation within strain, lake-only and river-only datasets. In total, 69 individuals were sampled and 11,764 SNPs were analyzed for the combined LR dataset. The datasets demonstrated the ability to detect fine-scale structure both between and within strains. The results of the analyses support a genetic differentiation between the two Iowa walleye strains; however, this variation is complex and subtle. Multiple genetic markers significantly associated with both lake- and river-strain were identified. The variation identified when the loci were compared between strains was not enough to differentiate the strains and, therefore, create a stock identification tool. Based on these results, a simple strain-identification tool is not recommended. Instead, genotyping and generating more SNP datasets would not only allow for the unknown samples to be evaluated alongside the known individuals of this study, revealing genetic strain, but also would give further insight into the ancestry of Iowa walleye by revealing admixture and wild types that were not included in the present broodstock individuals