Genome‐wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

Abstract

SummaryGenome‐wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro‐Tom genome were identified by a whole‐genome shotgun sequencing analysis to estimate the spectrum and distribution of whole‐genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired‐end reads for four EMS‐induced mutants and three gamma‐ray‐irradiated lines as well as a wild‐type line were obtained by next‐generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma‐ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1 140 687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild‐type Micro‐Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild‐type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse‐genetic approaches.

The glycerol-3-phosphate acyltransferase GPAT6 from tomato plays a central role in fruit cutin biosynthesis

“…Indeed, the mutagenesis-induced SNPs are later used as polymorphic markers to map the causal mutation. It has been reported that a typical cv Micro-Tom EMS mutant plant typically carries 2,000 to 4,000 SNPs (Shirasawa et al, 2016).…”

The Analysis of Physiological Variations in M2 Generation of Solanum melongena L. Mutagenized by Ethyl Methane Sulfonate

“…Inducing mutations by chemical and physical methods is a highly efficient approach to increase genetic diversity (Shirasawa et al, 2016). Mutants are also potential materials for breeding new cultivar (Takagi et al, 2015).…”

“…The types of EMS-induced mutation include SNV (base transition, base insertion, and base deletion), CNV, and indel section. The C/G to T/A transitions are the predominant mutations in EMS mutants (Uchida et al, 2011; Henry et al, 2014; Tsuda et al, 2015; Shirasawa et al, 2016). These mutations affect the protein synthesis or structure, thereby leading to phenotypic change.…”

Mutant Resources and Mutagenomics in crop plants

“…Henry et al (2014) analyzed mutations in EMS-derived mutant progenies of rice and wheat by using multiplexed global exome capture and sequencing coupled with bioinformatics tools and detected ~18,000 induced mutations. In EMS induced and gamma ray induced mutants of tomato, whole-genome shotgun sequencing analysis was used to calculate the spectrum and distribution of DNA mutations at genome level in the Micro-Tom genome (Shirasawa et al, 2016). The authors found that major mutations in the EMS mutants were C/G to T/A transitions type, while in the gamma-ray mutants, mutations were C/G to T/A transitions, A/T to T/A transversions and A/T to G/C transitions.…”