Abstract
Microsatellites have been a staple of population genetics research for over three decades, and many large datasets have been generated with these markers. Microsatellites have been used, for example, to conduct genetic monitoring and construct large multigeneration pedigrees as well as genotype thousands of individuals from a given species to create high-resolution baselines of spatial genetic structure. However, the capillary electrophoresis (CE) approach used to genotype microsatellites is inefficient compared to newer genotyping-by-sequencing (GBS) approaches, and researchers have begun transitioning away from CE. Backward compatibility between GBS and CE would facilitate a seamless transition to a more efficient chemistry, while ensuring that research based on CE panels could continue. Here, we explore the feasibility of converting a legacy panel of 15 microsatellites developed for muskellunge (Esox masquinongy) from CE to GBS chemistry. Muskellunge are an important sportfish in the Great Lakes region, and the existing microsatellite panel has been used to genotype thousands of samples to develop a region-wide baseline of genetic structure. We successfully converted all 15 microsatellites to GBS chemistry. GBS produced high genotyping rates (98%) and had high concordance with CE microsatellite genotypes (99%). Conversion to GBS required redesign of some primers and pairs to shorten amplicon length and adjust melting temperatures, optimization of primer concentrations, and comparisons with CE genotypes to optimize GBS genotyping parameters; however, none of these steps were especially onerous. Our results demonstrate that it is highly feasible to convert legacy CE panels to GBS, ensuring seamless continuation of important, often long-term research.
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Data availability
The datasets generated and analyzed during the current study will be made available in the Dryad repository, pending publication.
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Acknowledgements
We thank biologists for the Wisconsin and Michigan Departments of Natural Resources for collecting samples used in this project. Funding was provided by the Sport Fish Restoration Program and the Wisconsin Department of Natural Resources. We would also like to thank Dr. Gregory Sass of the Wisconsin Department of Natural Resources for his support and helping to facilitate this research as well as Dr. Loren Miller and an anonymous reviewer for helpful commentary on the manuscript. Any use of trade, product, or company name is for descriptive purposes only and does not imply endorsement by the U.S. Government.
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This study was funded by the Sport Fish Restoration Program and the Wisconsin Department of Natural Resources.
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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by KG and WL. The first draft of the manuscript was written in full collaboration by KG and WL. Both authors read and approved the final manuscript.
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Gruenthal, K.M., Larson, W.A. Efficient genotyping with backwards compatibility: converting a legacy microsatellite panel for muskellunge (Esox masquinongy) to genotyping-by-sequencing chemistry. Conservation Genet Resour 13, 151–159 (2021). https://doi.org/10.1007/s12686-020-01185-1
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DOI: https://doi.org/10.1007/s12686-020-01185-1