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Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

Author

Listed:
  • Gen Xu

    (University of Nebraska-Lincoln
    University of Nebraska-Lincoln)

  • Jing Lyu

    (University of Nebraska-Lincoln
    University of Nebraska-Lincoln)

  • Qing Li

    (University of Minnesota
    Huazhong Agricultural University)

  • Han Liu

    (Chinese Academy of Sciences)

  • Dafang Wang

    (Delta State University)

  • Mei Zhang

    (Chinese Academy of Sciences)

  • Nathan M. Springer

    (University of Minnesota)

  • Jeffrey Ross-Ibarra

    (University of California)

  • Jinliang Yang

    (University of Nebraska-Lincoln
    University of Nebraska-Lincoln)

Abstract

DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

Suggested Citation

  • Gen Xu & Jing Lyu & Qing Li & Han Liu & Dafang Wang & Mei Zhang & Nathan M. Springer & Jeffrey Ross-Ibarra & Jinliang Yang, 2020. "Evolutionary and functional genomics of DNA methylation in maize domestication and improvement," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19333-4
    DOI: 10.1038/s41467-020-19333-4
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