Plants regenerated from tissue culture contain stable epigenome changes in rice

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 transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed 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. Overall design: Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA). Whole genome expression maps of rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).