Development and Application of Single‐Nucleotide Polymorphism (SNP) Genetic Markers for Conservation Monitoring of Burbot Populations

Abstract

The transboundary (Idaho, USA; and British Columbia, Canada) population of Burbot Lota lota native to the Kootenai River basin once provided a popular sport and commercial fishery and has been culturally significant to the Kootenai Tribe of Idaho for millennia. However, the population has experienced significant declines over the last 30 years, due primarily to habitat loss and alteration caused by water storage and diversion. By the late 1990s, the population was considered functionally extinct, with estimates of fewer than 50 Burbot in the wild and little to no recruitment, prompting an ongoing international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to rebuild the population and support future tribal subsistence harvest and recreational fisheries. Although supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. To monitor genetic diversity and potential inbreeding in the broodstock and to provide parentage-based tagging of supplementation offspring, we developed a set (N = 96) of highly variable single-nucleotide polymorphism (SNP) genetic markers. The subset of 96 SNP markers was developed from a larger suite of 6,517 SNPs that were discovered by using restriction site-associated DNA sequencing. This cost-efficient technology allows for the rapid discovery of thousands of SNP markers in species that have not been extensively studied previously or for which there are little existing DNA sequence data. We demonstrated high accuracy (>99%) of our SNP set for parentage and individual identification through simulated and empirical tests. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track the growth, survival, and movement of released individuals.

A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

“…The development of high density genome-wide single nucleotide polymorphism (SNP) marker resources is key to a number of downstream applications of interest to the forestry industry [4]. Early prediction of genomic breeding values [5], particularly for traits with late expression in long-lived forest tree species [6, 7], monitoring of relatedness within breeding programmes [8, 9] and pedigree reconstruction in open-pollinated trials [10], are but a few of the possible applications. We have chosen to develop a genome-wide marker panel suitable for several downstream applications requiring anywhere from several hundred, to up to many thousands of markers, and to test the efficacy initially in pedigree reconstruction.…”

Parentage-based tagging improves escapement estimates for ESA-listed adult Chinook salmon and steelhead in the Snake River basin

“…The application of PBT to identify source of origin for individuals lacking marks or tags is not unique, and there are several examples of such use in both resident (Dehaan et al 2008;Campbell et al 2019) and anadromous freshwater fishes (Hauser et al 2006;Seamons et al 2012). For example, recovery efforts for endangered Pallid Sturgeon in the Missouri River include the use of a captive breeding program to compensate for low or non-existent levels of natural recruitment (Dehaan et al 2008).…”

A New Estimator to Correct for Bias from Tag Rate Expansion on Natural‐Origin Fish Attributes in Mixed‐Stock Analysis Using Parentage‐Based Tagging

“…Monitoring of Coho Salmon O. kisutch and Chinook Salmon in British Columbia by PBT was deemed capable of replacing the current coded wire tag program (Beacham et al 2017, 2018, 2019). Beyond Pacific salmon, PBT has been used to monitor Burbot Lota lota in the Kootenai River basin (Campbell et al 2019) and has been proposed for monitoring populations of Blueback Herring Alosa aestivalis (Evans et al 2018) and Sauger Sander canadensis (Bingham et al 2018). These examples demonstrate the widespread applicability of PBT to monitoring coexisting hatchery‐ and natural‐origin populations.…”