Identification of SNP Markers for Parentage Based Tagging of Burbot Lota Lota Using Restriction-Site-Associated DNA Sequencing

The trans-boundary population of Burbot native to the Kootenai River basin once provide a popular sport and commercial fishery, and is culturally significant to the Kootenai Tribe of Idaho. However, the population has experienced significant declines over the last 30 years, due primarily to habitat loss and alteration. By the late 1990’s, the population was considered functionally extinct, prompting an on-going international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to re-build the population. While supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. In order to monitor genetic diversity and potential inbreeding in the broodstock and to provide Parentage Based Tagging of supplementation offspring, we developed a set (N = 93) of highly variable Single Nucleotide Polymorphic (SNP) genetic markers. We demonstrated the accuracy of our SNP set for parentage by running a known parent/offspring dataset (N = 344/313, respectively). All 313 offspring accurately assigned to the correct parent pair. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track growth, post-release survival and movement of released individuals.