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Epigenetic Approaches in Non-Model Plants

  • M. Teresa Boquete
  • Niels C. A. M. Wagemaker
  • Philippine Vergeer
  • Jeannie Mounger
  • Christina L. RichardsEmail author
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Part of the Methods in Molecular Biology book series (MIMB, volume 2093)

Abstract

Reduced representation bisulfite sequencing is an emerging methodology for evolutionary and ecological genomics and epigenomics research because it provides a cost-effective, high-resolution tool for exploration and comparative analysis of DNA methylation and genetic variation. Here we describe how digestion of genomic plant DNA with restriction enzymes, subsequent bisulfite conversion of unmethylated cytosines, and final DNA sequencing allow for the examination of genome-wide genetic and epigenetic variation in plants without the need for a reference genome. We explain how the use of several combinations of barcoded adapters for the creation of highly multiplexed libraries allows the inclusion of up to 144 different samples/individuals in only one sequencing lane.

Key words

Epigenetics DNA methylation Bisulfite treatment epiGBS Next-generation sequencing Restriction enzymes Multiplexing Reduced representation sequencing 

Notes

Acknowledgments

This work was supported by funding from the National Science Foundation (U.S.A.) IOS-1556820 (to C.L.R.), and through the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska Curie grant agreement No. 704141 (to M.T.B.).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • M. Teresa Boquete
    • 1
    • 2
  • Niels C. A. M. Wagemaker
    • 3
  • Philippine Vergeer
    • 3
    • 4
  • Jeannie Mounger
    • 2
  • Christina L. Richards
    • 2
    Email author
  1. 1.Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC)SevillaSpain
  2. 2.Department of Integrative BiologyUniversity of South FloridaTampaUSA
  3. 3.Institute of Water and Wetland Research, Radboud University NijmegenNijmegenThe Netherlands
  4. 4.Plant Ecology and Nature Conservation GroupWageningen University and ResearchWageningenThe Netherlands

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