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
Affiliations
Hume Stroud
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
Bo Ding
Department of Plant Pathology, Ohio State University, Columbus, United States
Stacey A Simon
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, United States
Suhua Feng
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
Maria Bellizzi
Department of Plant Pathology, Ohio State University, Columbus, United States
Matteo Pellegrini
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
Guo-Liang Wang
Department of Plant Pathology, Ohio State University, Columbus, United States
Blake C Meyers
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, United States
Steven E Jacobsen
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
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.
