Abstract
Burbot populations in the Upper Kootenay watershed, transecting the US-Canada border, are subject to intense monitoring and management after severe declines beginning in the 1970s. Genetic monitoring is a high-priority goal for the East Kootenay Burbot Scientific Working Group, but managers do not currently have a genetic marker panel with enough resolution to understand genetic population structure and family structure in the Upper Kootenay burbot populations. Here, we detail the process of developing and optimizing a cost-effective GTseq panel to aid in the conservation of Upper Kootenay burbot. The final GTseq panel contains 331 markers with sufficient variation to accurately infer population structure and reconstruct pedigrees.
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Data availability
Primer sequences, input files for microhapWrap, and genotypes are available at https://github.com/ac-harris/upperKootenayBurbot.
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Acknowledgements
We extend great thanks to Angie Chia and Kelly Heindel at the Eagle Fish Genetics Laboratory for performing RADseq and GTseq genotyping. Funding for this work was provided by British Columbia Ministry of Forests and Montana Fish, Wildlife and Parks.
Funding
This work was supported by funding from British Columbia Ministry of Forests and Montana Fish, Wildlife, and Parks.
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MRC, HL, RPK, and JLD designed the study. ACH and DKC performed bioinformatic processing and analyzed RADseq data. ACH identified candidate markers and optimized the GTseq panel. ACH wrote the manuscript, and all authors provided feedback on manuscript drafts and approved the final manuscript.
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All samples were collected as part of a previous study, and fish were handled in accordance with the American Fisheries Society guidelines for fish collection and sampling.
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Harris, A.C., Coykendall, D.K., Lamson, H. et al. An improved genetic marker panel for conservation monitoring of upper Kootenay River burbot. Conservation Genet Resour (2024). https://doi.org/10.1007/s12686-024-01351-9
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DOI: https://doi.org/10.1007/s12686-024-01351-9