Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants

Guili Yang; Wenlong Luo; Jian Zhang; Xiancheng Yan; Yan Du; Libin Zhou; Wenjian Li; Hui Wang; Zhiqiang Chen; Tao Guo

doi:10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants

Front Plant Sci. 2019 Nov 28:10:1514. doi: 10.3389/fpls.2019.01514. eCollection 2019.

Authors

Guili Yang¹, Wenlong Luo¹, Jian Zhang¹, Xiancheng Yan¹, Yan Du², Libin Zhou², Wenjian Li², Hui Wang¹, Zhiqiang Chen¹, Tao Guo¹

Affiliations

¹ National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China.
² Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.

Abstract

Physical mutagens, such as carbon-ion beams (CIBs) and gamma rays (GRs), induce mutations with high frequency at a relatively low dose and are more user-friendly and environment-friendly in mutation breeding. Previous studies showed that CIBs induced large sized deletions and insertions, and chromosomal rearrangements, whereas GRs induce shorter deletions and insertions, and more frequent base substitutions. However, the difference on the genomic level between CIB- and GR-induced mutations remains to be clarified. In the present study, we re-sequence six mutagenized lines derived from CIB irradiation and four mutagenized lines derived from GRs. A total of 283 and 381 variations are induced in these mutants by CIBs and GRs, respectively, including single base substitutions (SBSs), small insertion and deletions (InDels), multiple nucleotide variants (MNVs). SBSs are the most abundant type of mutation and single base transition is the main form for SBSs. CIB-induced InDels accounted for 25.44% of the total variations, while GR-induced InDels accounted for 17.85%. On the contrary, the frequency of MNVs induced by GRs was approximately 2.19 times that induced by CIBs, which indicates CIBs induced increased InDels, whereas GRs induced increased MNVs. Notably, multiple base deletions (≥5 bp) were induced at a much higher frequency by CIBs than by GRs. We also find mutations induced by CIBs and GRs are unevenly distributed on chromosomes. Unusual high-frequency (HF) and low-frequency (LF) mutation regions are discovered by analyzing mutations per 1Mb along the genome. The mutation frequency within the HF regions were significantly higher than the LF regions (P < 0.05). A large majority of SBSs, InDels, and MNVs induced by CIBs and GRs occurred in upstream and downstream regions. Our study compares difference of mutation profiles induced by the CIB irradiation and GR on rice genomes, and give some clues for understanding the mutagenesis mechanism of physical radiation and improving the mutagenesis efficiency.

Keywords: InDels; Oryza sativa L.; carbon-ion beams (CIBs) irradiation; gamma rays (GRs); multiple nucleotide variant (MNV); resequencing; single base substitution (SBS); structural variant (SV).