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Discovering new genetic mutations is vital for expanding genetic resources for exploring the functions and breeding applications of genes. In this study, we created new mutant populations of rice and evaluated its effectiveness by using a chemical mutagen diepoxybutane (DEB) with the expectation of manageably causing small-scale deletions that induce knock-out mutations. Compared with the more common mutagen, ethyl methanesulfonate (EMS), DEB exhibited approximately 160 times the adverse impact on the early growth of rice. At 0.3 mM, which was 1/160 the concentration of EMS in the control population, the heading date in the DEB-mutated population showed dispersion, albeit with a small standard deviation. Therefore, similar to EMS, DEB has been shown to induce DNA mutations. According to the screening of waxy mutants using the Targeting Induced Local Lesions in Genomes (TILLING) method, DEB-mutated populations had nearly similar mutation frequencies to those of EMS-mutated populations. Therefore, we successfully isolated five mutant lines from the DEB-mutated population. Some of these mutants exhibited a low-amylose phenotype, which is applicable to breeding leading to enhanced taste evaluation. To utilize these mutated alleles, we developed co-dominant DNA markers. In this study, EMS induced transition mutations, as previously reported. In contrast, DEB specifically induced transversion mutations rather than small-scale deletions contrary to our initial expectations. These results demonstrate that DEB has a novel point of action for mutation and is useful for expanding genetic resources for crops.

Soybean (Glycine max) oil normally contains 2%–4% stearic acid. Increased saturated fatty acid levels elevate the melting point of soybean oil and improve oxidative stability. Using X-ray irradiation, we isolated six high stearic acid mutants and investigated mutations in the gene encoding Δ9-stearoyl-ACP-desaturase (SACPD). Our analyses of the KK2 mutant revealed an approximately 155-kbp deletion in the GmSACPD-B region. We also identified a frameshift mutation in the KK24 mutant, corresponding with a base-pair deletion in the GmSACPD-C coding region. The other four mutants M2, M18, MM106, and MS827 also had 2.2–21.8-kbp deletions in the GmSACPD-C region. Thus, we designed co-dominant marker sets for KK2 and KK24 mutant alleles using multiplex polymerase chain reactions and the CEL I mismatch detection method, respectively. In addition, we quantified the degradation of GmSACPD-C mRNA with a single base-pair deletion and related it to nonsense-mediated mRNA decay and simultaneous reductions in GmSACPD-A and -B mRNA levels. This molecular mechanism may be exploited to introduce silent mutations in duplicate genes of soybean plants and other organisms.