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.

An efficient regeneration system was established for an ethnomedicinal shrub Rhinacanthus nasutus from root-derived callus organogenesis. The root segments were cultured on MS medium supplemented with various concentrations of Kn (1.0-4.0 μM) alone or in combination with IBA (0.2-0.6 μM) or 2, 4-D (0.5-1.5 μM). The optimum frequency (94%) of callus induction was recorded on MS medium supplemented with 3.0 μM Kn and 0.4 μM IBA. For shoot regeneration from callus, MS medium supplemented with different concentrations (1.0-7.0 μM) of BA or TDZ alone or in combination with NAA (0.2-1.0 μm) was employed. The highest frequency of shoot regeneration (91%) and mean number of shoots (28.3) were observed on MS medium supplemented with 5.0 μM BA and 0.7 μM NAA. The shoots were excised and cultured on MS medium with 4.0 μM IBA produced 3.4 roots per shoot in 88% cultures. Of the 65 plants transferred to soil 54 survived (83%). The plants were transferred to field after successful hardening. RAPD analysis of the regenerated plants showed high similarity with the mother plant.

We studied the effects of different media for callus induction and differentiation, and pre-culture period of immature wheat embryo culture on biolistic transformation efficiency for including antifreeze gene KN2 and bar conferring resistance to the herbicide bialaphos. The percentage of plantlets generated from induction and differentiation media without Cu2+ was lower than those cultured on differentiation media with Cu2+ (71.15%) or induction media with Cu2+ (68.45%) and both induction and differentiation media with Cu2+ (52.17%). The combinations of Nor medium for callus induction and Cu2+ medium for regeneration, and Cu2+ medium for induction and R medium for regeneration were superior for biolistic transformation. The calli induced on Cu2+ medium and pre-cultured for 4 d before biolistic transformation, and cultured on R medium after biolistic transformation produced the highest percentage (65%) of transgenic plantlets with the KN2 gene. Overall, about 50% plantlets regenerated from calli pre-cultured 4d before bombardment carried the KN2 gene; 44.7% of the plantlets carried the bar gene, which was higher than for any other treatment, followed by pre-culture 1d with 31.43% transformation rate for the KN2 gene and 20% transformation rate for the bar gene.