Comparative study of mutations induced by carbon-ion beams and gamma-ray irradiations in Arabidopsis thaliana at the genome-wide scale.

Abstract Mutation breeding induced by irradiation with highly energetic photons and ion beams is one of the important methods to improve plant varieties, but the mutagenic effects and molecular mechanisms are often not entirely clear. Traditional research is focused on phenotype screening, chromosome aberration tests and genetic variation analysis of specific genes. The whole genome sequencing technique provides a new method to understand and undertake the comprehensive identification of mutations caused by irradiations with different linear energy transfer (LET). In this study, ten Arabidopsis thaliana M3 lines induced by carbon-ion beams (CIB) and ten M3 lines induced by gamma-rays were re-sequenced by using the Illumina HiSeq sequencing platform, and the single base substitutions (SBSs) and small insertions or deletions (indels) were analysed comparatively. It was found that the ratio of SBSs to small indels for M3 lines induced by CIB was 2.57:1, whereas the ratio was 1.78:1 for gamma-rays. The ratios of deletions to insertions for carbon ions and gamma-rays were 4.8:1 and 2.8:1, respectively. The single-base indels were more prevalent than those equal to or greater than 2 bp in both CIB and gamma-ray induced M3 lines. Among the detected SBSs, the ratio of transitions to transversions induced by carbon-ion irradiation was 1.01 and 1.42 for gamma-rays; these values differ greatly from the 2.41 reported for spontaneous substitutions. This study provides novel data on molecular characteristics of CIB and gamma-ray induced mutations at the genome-wide scale. It can also provide valuable clues for explaining the potential mechanism of plant mutation breeding by irradiations with different LETs.