RNA Sequencing-Based Transcriptome Analysis in Response to Different Types and Doses of Ionizing Radiation in Rice

Ionizing radiation (IR) is regarded as an abiotic stressor for plants because it causes oxidative stress and changes the expression of genes. We investigated RNA sequencing-based global transcriptome changes induced by three different types of IR (gamma rays (GR), ion beams (IB), and proton beams (PB)) at different doses in rice. On average, 489 upregulated and 234 downregulated differentially expressed genes (DEGs) were found per sample. The union of the DEGs for each IR type was collected to simplify the comparison of effects among the different IR treatments. This resulted to a total of 1,558 DEGs after GR irradiation, 1,865 DEGs after IB irradiation, and 1,347 DEGs after PB irradiation. The gene ontology (GO) enrichment analysis of the union DEG sets revealed 69 and 12 commonly enriched GO terms for up- and downregulated DEGs, respectively, many of which were closely related to oxidative stress responses. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping and enrichment analysis of the union DEG sets also showed that most of the DEGs fell into common pathways related to oxidative stress, stress signaling, and redox reactions. A total of 137 transcription factor (TF) genes were differentially expressed, and many belong to families associated with stress responses. Our results suggest that different types and doses of IR can induce universal gene expression changes in response to oxidative stress. This study contributes to our understanding of the molecular response mechanisms to IR in plants.