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Background  Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants.    Results  A mutant ( C416 ) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in  Lotus japonicus  derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of  C416  was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that  C416  was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in  C416 , whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in  Lotus japonicus . The abscisic acid (ABA) signaling pathway is positively regulated in  C416 .    Conclusion  So far,  C416  might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in  Lotus japonicus , rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of  Lotus japonicus  from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in  C416 , and lays a foundation for candidate flower senescence gene identification in  Lotus japonicus . It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03283-0.

Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus