Real-time qRT-PCR analysis of genes encoding for enzymes involved in establishing and/or maintaining of DNA methylation.

<p>The steady-state transcript abundance of genes encoding three DNA methyltransferases, slMET1 (A), slCMT3 (B), and slDRM2 (C), two 5-methylcytosine DNA glycosylases, slDME (D) and slROS1 (E), and four proteins involved in the biogenesis of siRNAs participating in the RdDM pathway, slNRPDA (F), slAGO (G), slDRB (H), and slRDR (I) were analyzed by real-time qRT-PCR. All these genes were identified from the tomato genome (details are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061995#pone.0061995.s002" target="_blank">Table S1</a>). Reverse transcription was performed on three batches of independently isolated RNAs from young leaves of the seed-plant control (T), two independent hetero-grafted (tomato to eggplant) scion plants (eT1-2), and 12 and eight selfed progeny plants (S1) of each mother scion plant. A conserved <i>Solanaceae</i> actin gene (Genbank accession: U60481) was used as an internal control for RNA input and DNA contamination (on RNAs without reverse transcriptase). Asterisks denote statistical difference in the transcript abundance relative to that of the corresponding seed-plant control, based on t-test at <i>P</i> = 0.05 (*) and <i>P</i> = 0.01 (**) levels, respectively. Colors of asterisks refer to significant up- (blue) and down-regulation (red), respectively.