Abstract
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.DOI: http://dx.doi.org/10.7554/eLife.00354.001
Highlights
Rice is one of the world’s most important food crops, and genetic modifications are extensively used for various purposes such as to increase yield and tolerate harsh environments
We found that loss of DNA methylation occurred stochastically, affecting individual plants somewhat differently, was associated with loss of small RNAs, and changes were enriched at promoters of genes
When examining methylation levels of these samples at CG hypomethylation differentially methylated regions (DMRs) that were common in all regenerated plants, we found significant losses of DNA methylation at these sites in callus (Figure 5C,D), indicating that the methylation losses observed in callus were at largely the same sites as those observed in regenerated plants
Summary
Rice is one of the world’s most important food crops, and genetic modifications are extensively used for various purposes such as to increase yield and tolerate harsh environments. A previous study has reported that Arabidopsis cell suspension culture has a different epigenomic profile compared to wild-type plants, such that certain transposable elements (TEs) become hypomethylated and certain genes become hypermethylated (Tanurdzic et al, 2008). This raised the question of how tissue culture processes affect the epigenome of regenerated plants derived from tissue culture. Some evidence suggesting changes in the epigenome of regenerated plants have been reported at several specific loci or by methods such as methylation sensitive restrictive enzyme digestion (Neelakandan and Wang, 2012). The study of the model plant rice, may have practical implications for other crop species that are transformed using similar tissue culture methods
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