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

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

doi:10.3389/fpls.2019.01514

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.

Highlights

Creating phenotypic variation through spontaneous or artificially induced mutations and excavating mutant genes have been an important topic in plant genomic studies for decades
Phenotypic screening for visible mutant candidates in the M2 or M3 population was throughout the whole growth period, and six lines (H633, H634, H635, H636, H639, H640) induced by carbon-ion beams (CIBs) irradiation and four M6 lines (H404, H409, H410, and H411) induced by gamma rays (GRs) were used for sequencing in the end
We found 36 multiple nucleotide variants (MNVs) induced by CIBs and 54 MNVs induced by GRs

Summary

Introduction

Creating phenotypic variation through spontaneous or artificially induced mutations and excavating mutant genes have been an important topic in plant genomic studies for decades. Through artificial mutagenesis treatment, the mutation frequency can be increased by tens to hundreds of times. Artificial mutations have greatly contributed to the advancement of plant breeding (Ishikawa et al, 2012; Li et al, 2017; Kamolsukyeunyong et al, 2019). EMS predominantly induces point mutations throughout the genome, mainly G/C-to-A/T transitions, with high frequency (Uchida et al, 2011); EMS treatment of tissues or plantlets is time consuming because of its weak penetration capability (Kazama et al, 2011). The irradiation times required with physical mutagens are short; only a few seconds of irradiation are needed for imbibed seeds, tissues, and plantlets, and a few minutes are needed for dry seeds (Kazama et al, 2011)

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