Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean

Mung bean (Vigna radiata) is a globally important legume crop valued for its short growing cycle, nitrogen-fixing capacity and high nutritional value, particularly in developing countries. Here we report a comprehensive graph-based pan-genome assembled from 11 genetically diverse global accessions. The framework captures 75,268 gene families (50.86% core, 35.19% dispensable and 13.95% private) and 66,862 nonredundant structural variants. Integrating these structural variants and single nucleotide polymorphisms, genome-wide association studies across five environments identified candidate genes for 20 agronomic traits, underscoring the pivotal roles of these variants in driving mung bean domestication and improvement. Mechanistically, we demonstrate that a 68-bp promoter insertion in VrTIFY6B and a 136-bp promoter deletion in VrPGIP1 regulate flavonoid content and confer bruchid resistance, respectively. These genomic resources and actionable functional variants provide a powerful toolkit to accelerate mung bean improvement through marker-assisted breeding, genomic selection and genome editing to address global food security.