The world is facing a serious food and energy crisis. Plant mutation breeding has played an important role in overcoming this crisis and maintaining world stability. New techniques are required to achieve faster and more effective breeding. At RIKEN, we have developed a unique technology for mutation induction by using heavy-ion beams from particle accelerators at the RI Beam Factory. This development was achieved through an efficient synergistic link between agricultural science and accelerator physics. The use of ion beams for mutagenesis has a number of advantages: the approach has low exposure levels and high survival rates with high mutation rates, and it creates a wide variety of different mutations. Because heavy-ion beams provide a very high amount of energy, even a single ion is enough to significantly damage a gene – in fact, the beams have enough energy to break the double strand of the DNA. The technique is also very useful in producing mutants that lack just a single gene; multiple propagation technology can be used to convert these mutants into new cultivars. Examples of such breeds include ‘Safinia Rose’ (petunia), ‘Temari Bright Pink’ (vervena) and ‘Olivia Pure White’ (dianthus). The development period for producing new varieties is only 2 years. Over last decade, molecular biology has made great advancements through technological innovation. We use high-throughput DNA sequencing techniques such as next-generation sequence instruments and microarray technologies for analysis of gene mutations. Mutants have become more and more useful and important in modern genetic studies, enabling the discovery of genes that control important traits, and revealing the functions and mechanisms underlying their operations. The discovery of genes using mutants may lead to the emergence of a new field in biology, ‘Mutagenomics’.