TY - JOUR TI - Plants regenerated from tissue culture contain stable epigenome changes in rice AU - Stroud, Hume AU - Ding, Bo AU - Simon, Stacey A AU - Feng, Suhua AU - Bellizzi, Maria AU - Pellegrini, Matteo AU - Wang, Guo-Liang AU - Meyers, Blake C AU - Jacobsen, Steven E A2 - Baulcombe, David VL - 2 PY - 2013 DA - 2013/03/19 SP - e00354 C1 - eLife 2013;2:e00354 DO - 10.7554/eLife.00354 UR - https://doi.org/10.7554/eLife.00354 AB - 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. KW - Rice KW - DNA methylation KW - tissue culture KW - small RNA KW - regeneration JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -