title: A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding.
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.
authors.affiliation: Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland; Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Republic of Ireland.
authors.forename: Salla
authors.identifier: 0000-0001-5704-2883
authors.initials: S
authors.lastname: Vartia
authors.affiliation: Evolutionary Genomics Group , Research Programme on Biomedical Informatics (GRIB) , Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
authors.forename: José L
authors.initials: JL
authors.lastname: Villanueva-Cañas
authors.affiliation: School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.
authors.forename: John
authors.initials: J
authors.lastname: Finarelli
authors.affiliation: Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.
authors.forename: Edward D
authors.initials: ED
authors.lastname: Farrell
authors.affiliation: School of Biological Sciences , Queen's University Belfast , Medical Biology Centre, Lisburn Road, Belfast, UK.
authors.forename: Patrick C
authors.initials: PC
authors.lastname: Collins
authors.affiliation: School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.
authors.forename: Graham M
authors.initials: GM
authors.lastname: Hughes
authors.affiliation: Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.
authors.forename: Jeanette E L
authors.initials: JE
authors.lastname: Carlsson
authors.affiliation: Department of Biological Sciences , Old Dominion University , Norfolk, VA, USA.
authors.forename: David T
authors.initials: DT
authors.lastname: Gauthier
authors.affiliation: Beaufort Fish Genetics Programme , School of Biological , Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland.
authors.forename: Philip
authors.initials: P
authors.lastname: McGinnity
authors.affiliation: Beaufort Fish Genetics Programme , School of Biological , Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Cross
authors.affiliation: Carna Research Station, Ryan Institute , National University of Ireland , Galway, Carna, Connemara, Republic of Ireland.
authors.forename: Richard D
authors.initials: RD
authors.lastname: FitzGerald
authors.affiliation: Marine and Freshwater Research Centre , Galway-Mayo Institute of Technology , Dublin Road, Galway, Republic of Ireland.
authors.forename: Luca
authors.initials: L
authors.lastname: Mirimin
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland; Alimentary Pharmabiotic Centre, Cork, Republic of Ireland.
authors.forename: Fiona
authors.initials: F
authors.lastname: Crispie
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland; Alimentary Pharmabiotic Centre, Cork, Republic of Ireland.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
authors.affiliation: Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.
authors.forename: Jens
authors.initials: J
authors.lastname: Carlsson
keywords: Gadus morhua; amplicon sequencing; genotyping by sequencing; next-generation sequencing; ssr; universal primer