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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2016
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ftnuigalway:oai:https://researchrepository.universityofgalway.ie:10379/14279 2024-09-30T14:35:15+00:00 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 2016-01-01 http://hdl.handle.net/10379/14279 https://doi.org/10.13025/25575 https://doi.org/10.1098/rsos.150565 unknown The Royal Society Royal Society Open Science 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 (2016). A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. Royal Society Open Science 3 (1), 2054-5703 http://hdl.handle.net/10379/14279 https://doi.org/10.13025/25575 doi:10.1098/rsos.150565 Attribution-NonCommercial-NoDerivs 3.0 Ireland https://creativecommons.org/licenses/by-nc-nd/3.0/ie/ 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 Article 2016 ftnuigalway https://doi.org/10.13025/2557510.1098/rsos.150565 2024-09-17T14:44:29Z 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. Article in Journal/Newspaper Gadus morhua National University of Ireland (NUI), Galway: ARAN |
institution |
Open Polar |
collection |
National University of Ireland (NUI), Galway: ARAN |
op_collection_id |
ftnuigalway |
language |
unknown |
topic |
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 |
spellingShingle |
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 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 A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
topic_facet |
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 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
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 |
author_facet |
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 |
author_sort |
Vartia, Salla |
title |
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
title_short |
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
title_full |
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
title_fullStr |
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
title_full_unstemmed |
A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
title_sort |
novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding |
publisher |
The Royal Society |
publishDate |
2016 |
url |
http://hdl.handle.net/10379/14279 https://doi.org/10.13025/25575 https://doi.org/10.1098/rsos.150565 |
genre |
Gadus morhua |
genre_facet |
Gadus morhua |
op_relation |
Royal Society Open Science 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 (2016). A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. Royal Society Open Science 3 (1), 2054-5703 http://hdl.handle.net/10379/14279 https://doi.org/10.13025/25575 doi:10.1098/rsos.150565 |
op_rights |
Attribution-NonCommercial-NoDerivs 3.0 Ireland https://creativecommons.org/licenses/by-nc-nd/3.0/ie/ |
op_doi |
https://doi.org/10.13025/2557510.1098/rsos.150565 |
_version_ |
1811638583484743680 |