A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Abstract

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping‐in‐thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye ( Sander vitreus ) from the Great Lakes region of North America. High genome‐coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave‐one‐out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false‐positive rates of parent‐offspring and full‐sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline

“…Microhaplotypes have shown promise in several fisheries‐related studies including pedigree inference and population assignment. Inclusion of microhaplotype data can increase power for identifying kin relationships (Baetscher et al., 2018; Delomas & Campbell, 2022; Euclide et al., 2022) and fewer microhaplotypes are necessary to obtain equivalent levels of accuracy with parentage analysis relative to bi‐allelic SNPs (May et al., 2020). Similarly, added variability associated with microhaplotypes has the potential to differentiate closely‐related populations, resulting in increased accuracy in GSI assignments (Euclide et al., 2021; McKinney et al., 2020).…”

Population Genetic Differentiation of Walleye (Sander vitreus) across the Eastern Highlands of the United States

“…Using microsatellite DNA markers, Stepien et al [10,11] showed differentiation among populations of Walleye from watersheds across the Laurentian Great Lakes, Lake Winnipeg (MB, Canada), upper Mississippi River, Ohio River, and Mobile Bay drainage. Using SNP markers, Euclide et al [12] showed differentiation among Walleye populations in the Great Lakes region.…”