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

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 non-model
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 that 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 was 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.