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

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dc.contributor.authorVartia, Salla
dc.contributor.authorVillanueva-Cañas, José L.
dc.contributor.authorFinarelli, John
dc.contributor.authorFarrell, Edward D.
dc.contributor.authorCollins, Patrick C.
dc.contributor.authorHughes, Graham M.
dc.contributor.authorCarlsson, Jeanette E. L.
dc.contributor.authorGauthier, David T.
dc.contributor.authorMcGinnity, Philip
dc.contributor.authorCross, Thomas F.
dc.contributor.authorFitzGerald, Richard D.
dc.contributor.authorMirimin, Luca
dc.contributor.authorCrispie, Fiona
dc.contributor.authorCotter, Paul D.
dc.contributor.authorCarlsson, Jens
dc.contributor.funderMarine Instituteen
dc.contributor.funderEuropean Regional Development Funden
dc.contributor.funderMinisterio de Economía y Competitividaden
dc.contributor.funderIrish Research Councilen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderGovernment of Irelanden
dc.date.accessioned2019-11-01T07:50:23Z
dc.date.available2019-11-01T07:50:23Z
dc.date.issued2016-01-01
dc.description.abstractThis 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.en
dc.description.sponsorshipMarine Institute (Sea Change Strategy); European Regional Development Fund (Grant-Aid Agreement no. PBA/AF/07/004, EIRCOD); Spanish Ministerio de Economía y Competitividad (FPI BES-2010–038494 and EEBB-I-13–06270); Irish Research Council (Funding Agency Ref no. GOIPD/2013/320, Graduate Research Education Programme (GREP)); Government of Ireland (Beaufort Marine Research Award in Fish Population Genetics, Sea Change Programme, Marine Research Sub-programme of the National Development Plan 2007–2013)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid150565en
dc.identifier.citationVartia, 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.150565en
dc.identifier.doi10.1098/rsos.150565en
dc.identifier.eissn2054-5703
dc.identifier.endpage9en
dc.identifier.issued1en
dc.identifier.journaltitleRoyal Society Open Scienceen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/8936
dc.identifier.volume3en
dc.language.isoenen
dc.publisherThe Royal Societyen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Investigator Programme/12/IP/1308/IE/Taxonomy and connectivity of animal species at the Moytirra hydrothermal vent field: developing methods for assessing ecological impacts of mineral extraction in the deep-sea/en
dc.relation.urihttps://royalsocietypublishing.org/doi/10.1098/rsos.150565
dc.rights©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.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectGadus morhuaen
dc.subjectSSRen
dc.subjectNext-generation sequencingen
dc.subjectAmplicon sequencingen
dc.subjectGenotyping by sequencingen
dc.subjectUniversal primeren
dc.titleA novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcodingen
dc.typeArticle (peer-reviewed)en
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