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Abstract
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10−7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
Highlights
The heavy-ion beam is an effective and unique mutagen that can induce mutations at a high rate and on a broad spectrum
Focusing on substitutions and small INDELs, we revealed the genomewide molecular profile and rate of mutations induced by carbon-ion beam (CIB) irradiation in A. thaliana
The Lab-WT A. thaliana seeds were exposed to CIB irradiation with the aim of constructing a comprehensive carbon-ion-induced mutation resource collection for A. thaliana
Summary
The heavy-ion beam is an effective and unique mutagen that can induce mutations at a high rate and on a broad spectrum. It has been widely used in the mutation breeding of plants and microbes because of their distinct physical and biological advantages. LET represents the energy deposition of ionizing radiations on their per unit track. The heavy-ion beam provides a higher relative biological effectiveness (RBE) than the low LET radiation (Tanaka et al, 2010; Kazama et al, 2011; Nagata et al, 2016; Zhou et al, 2016). Various mutant populations have been generated by heavy-ion beam irradiation: for instance, those of Arabidopsis thaliana (Tanaka et al, 1997, 2002), Lotus japonicus (Oka-Kira et al, 2005; Luo et al, 2016), Rice (Oryza sativa L.) (Ishikawa et al, 2012; Phanchaisri et al, 2012; Morita et al, 2017), Petunia (Petunia hybrid), Hase et al, 2010), Tricyrtis hirta (Nakano et al, 2010), Chrysanthemum (Matsumura et al, 2010), Wandering Jew (He et al, 2011), Geranium (Yu et al, 2016), and so on
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