Studies focused on the responses of plants to ionizing radiation are becoming more important due to the increased need for radiation-induced mutations, post-harvest or phytosanitary irradiation treatment of plants, and environmental monitoring of radioactive sites. To elucidate the influence of ionizing radiation on genome-wide transcription in plants, we performed integrated analysis of diverse transcriptomic data from different Arabidopsis samples and at various time points after γ irradiation or H2O2 treatment. The expression levels of most of the differentially expressed genes (DEGs) that were induced or repressed after γ irradiation returned to baseline levels of transcription within 12h, while some of these genes showed prolonged transcriptional changes. Expression of the DEGs did not correlate with genomic DNA methylation; however, there were substantial differences in DEG levels between the wild type and the cmt3-11 mutant, which has a defect in non-CG DNA methylation. Moreover, the proportion of the DEGs in common between 2 independent experiments using different batches of samples was only 12-18%. These results suggest that there is a diversity or randomness in radiation-induced physiological or phenotypic alterations. However, the results also indicated that 47 DEGs maintained a transcriptional change until 48h, and 7 of them, until 16d. Forty-five additional DEGs were found to be sustainably induced or repressed until 24h after γ irradiation regardless of sample-to-sample variation or genotype, and 4 or 2 of them, until 5d or 16d, respectively. Therefore, we suggest that the 4 γ-ray-responsive genes that showed sustainable transcriptional changes until day 5 would be reliable and reproducible genetic markers when evaluating the responsiveness of plants to γ-rays.
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