A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

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 PC...

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Bibliographic Details
Main Authors: 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
Format: Article in Journal/Newspaper
Language:unknown
Published: The Royal Society 2016
Subjects:
amplicon sequencing
gadus morhua
genotyping by sequencing
next-generation sequencing
ssr
universal primer
single-nucleotide polymorphisms
cod gadus-morhua
population-structure
model selection
complete genome
snp discovery
homoplasy
loci
evolution
platform
Gadus morhua
Online Access:http://hdl.handle.net/10379/14279
https://doi.org/10.13025/25575
https://doi.org/10.1098/rsos.150565
Description
Summary: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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