Development of a high-throughput single nucleotide polymorphism panel for genetic stock identification of Striped Bass

ABSTRACT Objective The Striped Bass Morone saxatilis is an anadromous fish that has experienced population declines and recoveries throughout its range from the 1960s to the present day. While many United States fisheries have reopened since the most recent declines, ongoing monitoring is required to ensure that numbers remain stable in the long term. Central to this is the need to determine the extent to which major spawning locations contribute to coastal stocks. While next-generation genomic sequencing can discriminate among closely related breeding aggregations within the Striped Bass native range, the cost per sample of next-generation sequencing methods currently used is too high to be applied to large-scale and long-term projects moving forward. Methods We developed, optimized, and evaluated a GT-Seq panel—a small panel of highly informative single nucleotide polymorphisms—capable of assigning large numbers of Striped Bass to six genetically distinct regions across the Striped Bass spawning range at much lower cost than the previous next-generation sequencing methods. Results The final panel of 233 loci was able to assign 95% of reference individuals to region of origin and had <5% error across all simulations when estimating the mixing proportion of any stock. Conclusions This panel is being used in ongoing characterizations of Striped Bass along the Massachusetts coast and the eastern coast of Nova Scotia. For researchers tracking the migration of Striped Bass throughout their native range, this panel provides a low-cost method of genetically characterizing stocks at specific locations and times that can be easily modified or updated as additional, new genetic data become available.