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

Plant Biotechnol J. 2016 Jan;14(1):51-60. doi: 10.1111/pbi.12348. Epub 2015 Feb 16.

Abstract

Genome-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.

Keywords: ethyl methanesulfonate; gamma rays; mutation; tomato (Solanum lycopersicum); whole-genome resequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Copy Number Variations / genetics
  • Ethyl Methanesulfonate
  • Gamma Rays*
  • Genes, Plant
  • Genome, Plant*
  • INDEL Mutation / genetics
  • Lycopersicon esculentum / genetics*
  • Lycopersicon esculentum / radiation effects*
  • Mutation / genetics*
  • Plants, Genetically Modified
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA
  • Surveys and Questionnaires*

Substances

  • Ethyl Methanesulfonate

Associated data

  • GENBANK/AEKE02023381
  • GENBANK/AEKE02026766
  • GENBANK/LA3911
  • GENBANK/LC003259
  • GENBANK/LC003260
  • GENBANK/TOMJPF00001
  • SRA/DRA002470