Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis

Abstract

Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.

The Mutational, Epigenetic, and Transcriptional Effects Between Mixed High-Energy Particle Field (CR) and 7Li-Ion Beams (LR) Radiation in Wheat M1 Seedlings

“…Similarly, Weng et al (2019) found that spontaneous mutation profile in Arabidopsis do not occur evenly across the genome: they are biased toward G: C to A: T transitions ( Weng et al, 2019 ). Similar results were observed in the gamma rays, carbon-ion beams, LR, and proton beams induced mutations ( Guo et al, 2019 ; Li et al, 2019 ; Xiong et al, 2019 ; Yang et al, 2019 ; Oono et al, 2020 ; Choi et al, 2021 ; Lee et al, 2021 ), which is also consistent with the present study. Therefore, the uneven distribution of IR induced mutations may be related to mutational bias.…”

“…In Arabidopsis , mutation rates induced by gamma rays (M 2 –M 6 ) and carbon-ion irradiation (M 2 ) were 1.4–2.2 × 10 –7 and 0.9–1.2 × 10 –7 /bp ( Hase et al, 2020 ). However, the mutation rates obtained in the present study were higher than those estimated by these previous studies ( Li et al, 2019 ; Yang et al, 2019 ; Hase et al, 2020 ; Oono et al, 2020 ; Lee et al, 2021 ). The present study demonstrates that LR and CR radiation are all effective for mutation induction in wheat, suggesting that CR and LR could be good mutagens for plant mutation breeding in the future.…”

“…While the carbon-ion beams induced mutation frequencies reported by Yang et al (2019) and Oono et al (2020) were average 2.4 × 10 –7 /bp (M 2 ) and 2.7 × 10 –7 /bp (M 2 and M 3 ), respectively. More recently, proton beams and gamma rays induced mutation frequencies of M 2 mutants in rice were estimated ∼5.0 × 10 –7 and ∼7.0 × 10 –7 /bp, respectively ( Lee et al, 2021 ). In Arabidopsis , mutation rates induced by gamma rays (M 2 –M 6 ) and carbon-ion irradiation (M 2 ) were 1.4–2.2 × 10 –7 and 0.9–1.2 × 10 –7 /bp ( Hase et al, 2020 ).…”

Ionizing Radiation: Effective Physical Agents for Economic Crop Seed Priming and the Underlying Physiological Mechanisms

“…As a dense IR, it has higher linear energy transfer (LET), which is defined as the energy per unit track length, and it shows a higher relative biological effectiveness in lethality and mutation [ 58 , 90 ]. Based on these, heavy-ion beams show many outstanding advantages, for instance, a lower damage rate, a higher mutation rate, and a wider mutational spectrum, which generate the unique variations which are different from those induced by electromagnetic radiation [ 91 , 92 ]. Further, ROS generated by ionizing the water molecules in cells during heavy-ion beam irradiation show a biphasic dose response, and on the one hand, it activates a variety of positive physiological and metabolic behaviors, such as breaking dormancy, accelerating germination, and enhancing the antioxidant capacity at low doses, while on the other hand, it causes negative oxidative stress and exerts inhibitory effects on organisms at high doses [ 25 , 93 ].…”

Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

“…Studies aimed at understanding the molecular effects of the physical mutagens at whole-genome level is increasingly being pursued with the advent of rapid technological developments in the eld of genomics such as the nextgeneration sequencing (NGS). NGS has been used to unravel the molecular effects of spontaneous mutations (Weng et al 2019) as well as those induced by various physical mutagens like gamma-rays (Hase et al 2020), X-rays (Nath et al 2020), ion-beams (Hase et al 2018;Kazama et al 2017), proton beams (Lee et al 2021), andneutrons (Bel eld et al 2012). This coupled with superior bioinformatic algorithms provide a holistic approach in novel understanding of the mutagenic effects of various physical mutagens in different genomic backgrounds.…”