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

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.

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.)

“…Overall, under 40 Gy or 80 Gy, single-base substitutions (SBSs) were the main mutation types induced by CIB irradiation. Moreover, CIB irradiation also induced a number of InDels, and short ones (<5 bp) were more prevalent than large ones, which is in accordance with the findings of previous studies [ 15 , 16 ]. Among CIB irradiation-induced SBSs, we detected a bias towards C:T and A:G transitions and observed a higher overall frequency of CIB irradiation-induced transversions versus transitions ( Figure 3 ).…”

“…Those authors suggested that mutation frequency may be a good indicator for sequencing-based determination of the optimal irradiation conditions for inducing mutations. Using whole-genome resequencing, researchers conducting two recent independent studies compared and characterized mutations induced by CIB irradiation and GRs in rice ( Oryza sativa L.) [ 15 , 16 ]. Both studies showed that SBSs were the most abundant type of mutation induced by the two mutagens.…”

AFLP-Based Analysis of Variation and Population Structure in Mutagenesis Induced Faba Bean

“…These results agree with the sequencing data for 1504 rice mutants, in which a wide range of mutations was observed across the mutant plants [42]. Moreover, genome-wide comparisons using resequencing was performed by Yang et al [43], to compare four mutant rice plants induced by 250 Gy gamma radiation. The results showed that the individual mutants had different total numbers of mutations and proportions of mutation types.…”

Genetic Variation and Unintended Risk in the Context of Old and New Breeding Techniques

“…Furthermore, high-LET irradiation also typically leads to larger deletions and more complex DNA rearrangements than low-LET irradiation, which may derive, at least in part, through the action of an alternative end-joining repair pathway in these instances (Hirano et al, 2015). In rice, tens up to hundreds of thousands of SNVs and indels, along with 0 to approximately 11,000 structural variations (SVs), have been observed per mutant plant following treatment with ionizing radiation (Table 1; e.g., Cheng et al, 2014;Zhenga et al, 2017;Li, Shimizu, et al, 2019;Yang et al, 2019;Hwang et al, 2020).…”