Abstract
Ethyl methanesulfonate (EMS) is a chemical mutagen believed to mainly induce G/C to A/T transitions randomly in plant genomes. However, mutant screening for phenotypes often gets multiple alleles for one gene but no mutant for other genes. We investigated the potential EMS mutagenesis bias and the possible correlations with sequence context and chromatin structure using the whole genome resequencing data collected from 52 rice EMS mutants. We defined the EMS-induced single nucleotide polymorphic sites (SNPs) and explored the genomic factors associated with EMS mutagenesis bias. Compared with natural SNPs presented in the Rice3K project, EMS showed a preference on G/C sites with flanking sequences also higher in GC contents. The composition of local dinucleotides and trinucleotides was also associated with the efficiency of EMS mutagenesis. The biased distribution of EMS-induced SNPs was positively correlated with CpG numbers, transposable element contents, and repressive epigenetic markers but negatively with gene expression, the euchromatin marker DNase I hypersensitive sites, and active epigenetic markers, suggesting that sequence context and chromatin structure might correlate with the efficiency of EMS mutagenesis. Exploring the genome-wide features of EMS mutagenesis and correlations with epigenetic modifications will help in the understanding of DNA repair mechanism.
Highlights
Mutation breeding is an efficient way to obtain desirable traits in crop plants (Pathirana, 2011; Sikora et al, 2011)
When estimating the distributions of these single nucleotide polymorphic sites (SNPs) with a 100-kb window size, we found that ∼96.71% of 100-kb bins harbored at least one SNP, indicating that these SNPs were sufficient for analyzing the features of Ethyl methanesulfonate (EMS) mutagenesis in rice genome
These natural SNPs represent the diversity of rice genomes and provide a good background reference for comparative analysis of general features associated with EMS-induced SNPs
Summary
Mutation breeding is an efficient way to obtain desirable traits in crop plants (Pathirana, 2011; Sikora et al, 2011). With the development of various mutagenesis technologies and tools to explore genomic changes, many databases have been established for the collection of induced mutant plants of various species (Beale et al, 2002; Zhang et al, 2006; Saito et al, 2011; Li et al, 2017; Lu et al, 2017). These databases play a significant role in advancing the research and development of plant science and crop breeding. Among the mutants collected in MVD that were induced by chemical mutagens, more than 80% of them were induced by alkylation agents
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