title: Scanning the effects of ethyl methanesulfonate on the whole genome of Lotus japonicus using second-generation sequencing analysis.
abstract: Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two individually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes; however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.
authors: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
authors: Nur Fatihah
authors: NF
authors: Mohd-Yusoff
authors: Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors: Pradeep
authors: P
authors: Ruperao
authors: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia.
authors: Nurain Emylia
authors: NE
authors: Tomoyoshi
authors: Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia.
authors: David
authors: D
authors: Edwards
authors: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia p.gresshoff@uq.edu.au.
authors: Peter M
authors: PM
authors: Gresshoff
authors: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia.
authors: Bandana
authors: B
authors: Biswas
authors: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia.
authors: Jacqueline
authors: J
authors: Batley
mesh_terms: D000477:Alkylating Agents / Q000737:chemistry*; D020029:Base Pairing; D018744:DNA, Plant / Q000032:analysis / Q000737:chemistry; D005020:Ethyl Methanesulfonate / Q000737:chemistry*; D005787:Gene Frequency; D056426:Genetic Loci; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D000070116:Lotus / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D000477:Alkylating Agents; D018744:DNA, Plant; D005020:Ethyl Methanesulfonate
keywords: Lotus japonicus; SNP; abscisic acid; mutagenesis; second-generation sequencing