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.).

Jian Zhang,Qiling Liu,Libin Zhou,Zhiqiang Chen,Guili Yang,Ziai Peng,Wenjian Li,Tao Guo,Hui Wang

doi:10.3390/genes12091391

Abstract

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.

Highlights

Spontaneous mutations have been the primary drivers of evolution ever since life on Earth began [1]
We found that SBSs was the most frequent type of mutation induced by carbon ion beam (CIB)
More mutations have been detected with 40 Gy carbon ion beam(CIB) than 80 Gy at initial stage, this may due to the 80 Gy carbon ion beams caused serious damage and resulting the number of cells that can be used for sequencing is extremely small

Summary

Introduction

Spontaneous mutations have been the primary drivers of evolution ever since life on Earth began [1]. Almost all life relies on spontaneous mutations to create new genetic variation to adapt to the Earth’s environment, but these mutations occur very infrequently (7 × 10−9 in Arabidopsis thaliana) [2]. Several mutagens, both physical and chemical ones, such as X-rays [3], γ rays (GRs) [4], fast neutrons [5], ethylmethanesulfonate (EMS) [6], and heavy-ion beams (HIBs) [7], have been used for generating genetic variability and for plant mutation breeding. HIB irradiation has been recognized as a powerful mutagen and has been extensively utilized in plant breeding because it can generate new cultivars with desired traits without affecting other traits [8,9]. Based on many physical characteristics, such as high linear energy transfer (LET), mass and energy deposition, large damaged sections, and strong penetration ability, compared with conventional low-LET irradiation (such as X-rays and GRs), HIB irradiation produces single-strand breaks (SSBs) and causes double-strand breaks (DSBs), cluster damage, and other forms of DNA damage that are difficult to repair

Methods

Results

Discussion

Conclusion