Genome-wide analysis of mutations in a dwarf soybean mutant induced by fast neutron bombardment

Abstract

Fast neutron (FN) bombardment is a powerful mutagen that can be effectively employed for functional genomics studies in the post-genome era. In soybean, dwarfism is a desirable agricultural characteristic that improves lodging resistance. In the present study, we selected a dwarf mutant soybean among approximately 10,000 M4 progeny lines derived from FN-irradiated seeds of cultivar Williams 82. This dwarf mutant exhibited reduced plant height, only approximately 20 % of wild type. Using mutant plants homozygous for this dwarf phenotype, we performed whole genome sequencing by Illumina HiSeq to identify the deletion site responsible for the dwarfism. Comparative sequence analysis by mapping the mutant reads to the soybean reference genome sequence (wild type) predicted 13 large deletion regions. Among these, three loci (designated del1–3, del2–3, and del3–15) were validated by two complementary PCRs using two allele-specific reverse primers, respectively. We found that the del1–3 and del2–3 loci are positioned in non-coding regions of chromosome 3. In del3–15, the mutated allele has an 803-bp deletion including the first partial exon of Glyma15g05831 (peroxidase superfamily protein) on chromosome 15, resulting in the loss of a start codon. Reverse transcription-PCR analysis revealed that the expression of the gene Glyma15g05831 was completely abolished in the dwarf mutant. A lack of peroxidase (which catalyzes the generation of reactive oxygen species) coupled with indole-3-acetic acid oxidation may be responsible for the dwarfing of this mutant.