Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the replication and repair pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.

Automated summary

In this study, the dynamic changes caused by carbon ion beam (CIB) irradiation on rice seeds were comprehensively characterized using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques. The analysis revealed that the highest number of differentially expressed genes (DEGs) was observed at 48 hours post-irradiation, with the replication and repair pathway being enriched at this time point. These results suggest that DNA damage response (DDR) and DNA repair mechanisms are quickly activated within the initial stage (48 hours) after irradiation.