A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding
Vartia, Salla; Villanueva-Cañas, José L.; Finarelli, John; Farrell, Edward D.; Collins, Patrick C.; Hughes, Graham M.; Carlsson, Jeanette E. L.; Gauthier, David T.; McGinnity, Philip; Cross, Thomas F.; FitzGerald, Richard D.; Mirimin, Luca; Crispie, Fiona; Cotter, Paul D.; Carlsson, Jens
Date:
2016-01-01
Copyright:
©2016 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ , which permits unrestricted use, provided the original author and source are credited.
Citation:
Vartia, S., Villanueva-Cañas, J. L., Finarelli, J., Farrell, E. D., Collins, P. C., Hughes, G. M., Carlsson, J. E. L., Gauthier, D. T., McGinnity, P., Cross, T. F., FitzGerald, R. D., Mirimin, L., Crispie, F., Cotter, P. D. and Carlsson, J. (2016) 'A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding', Royal Society Open Science, 3(1), 150565. (9pp.) DOI: 10.1098/rsos.150565
Abstract:
This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
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