Heritable epigenomic changes to the maize methylome resulting from tissue culture

Zhaoxue Han, Peter A. Crisp, Scott Stelpflug, Shawn M. Kaeppler, Qing Li, Nathan M. Springer

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ̴15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.

Original languageEnglish (US)
Pages (from-to)983-995
Number of pages13
Issue number4
StatePublished - Aug 2018

Bibliographical note

Funding Information:
We thank Peter Hermanson for sequence-capture library preparation, and technical support; Yaniv Brandvain for statistical advice; and Jackie Noshay, Sarah Anderson, and Peng Zhou for legendary computational assistance. This work was funded by a grant from the National Science Foundation (IOS-1237931) to N.M.S. Illumina sequencing was performed at the University of Minnesota Genomics Center. Computational support was provided by the Minnesota Supercomputing Institute and the Texas Advanced Computing Center.

Publisher Copyright:
© 2018 by the Genetics Society of America.


  • Bisulfite sequencing
  • DNA methylation
  • Epigenomics
  • Maize
  • Sequence capture
  • Somaclonal variation
  • Tissue culture


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