Abstract
Genotyping-by-sequencing (GBS) is a method to discover and genotype simultaneous genome-wide high-throughput single nucleotide polymorphisms (SNPs). GBS is based on reducing genome complexity with restriction enzymes. Here we describe a method developed by Elshire et al. for constructing simplified GBS libraries and recent bioinformatic approaches developed to analyze the large volume of polymorphism data generated by this method. GBS approach is suitable for population studies, taxonomic and phylogenic studies, germplasm characterization, and breeding and trait mapping for a wide range of organisms, including plants with complex genomes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mamanova L, Coffey AJ, Scott CE et al (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111–118
Miller MR, Dunham JP, Amores A et al (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248
Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Catchen J, Hohenlohe PA, Bassham S et al (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
Campa A, Ferreira JJ (2018) Genetic diversity assessed by genotyping by sequencing (GBS) and for phenological traits in blueberry cultivars. PLoS One 13:e0206361
Pavan S, Curci PL, Zuluaga DL et al (2018) Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon. PLoS One 13:e0205988
Poland J, Endelman J, Dawson J et al (2012) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113
Taranto F, D’Agostino N, Greco B et al (2016) Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genomics 17:943
Taitano N, Bernau V, Jardón-Barbolla L et al (2019) Genome-wide genotyping of a novel Mexican Chile pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication. Evol Appl 12:78–92
Nimmakayala P, Abburi VL, Saminathan T et al (2016) Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms. Front Plant Sci 7:1646
Nimmakayala P, Abburi VL, Saminathan T et al (2016) Genome-wide diversity and association mapping for Capsaicinoids and fruit weight in Capsicum annuum L. Sci Rep 6:38081
Salgon S, Raynal M, Lebon S et al (2018) Genotyping by sequencing highlights a polygenic resistance to Ralstonia pseudosolanacearum in eggplant (Solanum melongena L.). Int J Mol Sci 19:357
Gabay G, Dahan Y, Izhaki Y et al (2018) High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time. BMC Plant Biol 18:175
Gonda I, Ashrafi H, Lyon DA et al (2019) Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection. Plant Genome 12:1–14
Scheben A, Batley J, Edwards D (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149–161
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Paradis E (2010) Pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26:419–420
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Favre, F., Jourda, C., Besse, P., Charron, C. (2021). Genotyping-by-Sequencing Technology in Plant Taxonomy and Phylogeny. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_10
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0997-2_10
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0996-5
Online ISBN: 978-1-0716-0997-2
eBook Packages: Springer Protocols