Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean ( Glycine max (L.) Merr.)

• Published in: International journal of molecular sciences 2023-05, Vol.24 (10), p.8825
• Main Authors: Feng, Zhuo, Du, Yan, Chen, Jingmin, Chen, Xia, Ren, Weibin, Wang, Lulu, Zhou, Libin
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Biological effects; Carbon; carbon-ion beam; Crops; Fertility; Gamma Rays; Gene deletion; Genomes; Genomics; Genotypes; Germplasm; Glycine max; Glycine max - genetics; Ion beams; Ions; Irradiation; Linear energy transfer (LET); Missense mutation; Mutagenesis; Mutagens; Mutants; Mutation; mutation screening; Phenotype; Phenotypes; Plant breeding; Proteins; Radiation; Relative biological effectiveness (RBE); Rice; Seeds; soybean; Soybeans; structural variation; whole-genome sequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24108825

Soybean ( (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M generation, their stability was verified, and the genome mutation spectrum of M was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion-deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6