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Skim-Based Genotyping by Sequencing

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Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1245))

Abstract

Genotyping by sequencing (GBS) is a relatively new method used to determine the differences in the genetic makeup of individuals. Its novelty stems from a combination of two already available methods: genotyping and next-generation sequencing. Depending on the individual study design GBS protocols can take multiple forms, however most share a sequence of core steps that have to be undertaken. These include: sequencing of the DNA from the individuals of interest (usually two parents of a mapping population and their progeny), mapping of the sequencing reads to the reference sequence, SNP calling and filtering, SNP genotyping and imputation, followed by haplotype identification and downstream analysis. GBS has a range of applications from general marker discovery, haplotype identification, and recombination characterization to quantitative trait locus (QTL) analysis, genome-wide association studies (GWAS), and genomic selection (GS). It has already been applied to a range of plant species including: rice, maize, artichoke, and Arabidopsis thaliana. It is a promising approach which is likely to provide new and important insights into plant biology.

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Authors and Affiliations

  1. School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia

    Agnieszka A. Golicz, Philipp E. Bayer & David Edwards

  2. Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia

    Agnieszka A. Golicz, Philipp E. Bayer & David Edwards

  3. School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    David Edwards

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  1. Agnieszka A. Golicz
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  2. Philipp E. Bayer
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  3. David Edwards
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Correspondence to David Edwards .

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  1. School of Plant Biology, The University of Western Australia, Crawley, West Australia, Australia

    Jacqueline Batley

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Golicz, A.A., Bayer, P.E., Edwards, D. (2015). Skim-Based Genotyping by Sequencing. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_19

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  • DOI: https://doi.org/10.1007/978-1-4939-1966-6_19

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