Plants regenerated from tissue culture contain stable epigenome changes in rice

Hume Stroud, Bo Ding, Stacey A. Simon, Suhua Feng, Maria Bellizzi, Matteo Pellegrini, Guo Liang Wang, Blake C. Meyers, Steven E. Jacobsen

Research output: Contribution to journalArticlepeer-review

188 Scopus citations


Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.

Original languageEnglish (US)
Article numbere00354
Issue number2
StatePublished - Mar 19 2013
Externally publishedYes

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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