A Panax ginseng pangenome reveals two independent alleles underlying yellow berry color

Background Panax ginseng C. A. Meyer is a medicinally and economically important perennial herb valued for its diverse pharmacologically active compounds. However, the genetic basis of phenotypic variation in ginseng remains poorly understood because of its large, highly repetitive, and allotetraploid genome. Berry colour variation is a conspicuous trait in ginseng and may reflect differences in specialized metabolites such as flavonoids, yet its genetic basis has remained unclear. To investigate the genomic basis of this trait and capture broader genetic diversity, we constructed a chromosome-scale pangenome using sixteen diverse accessions, including cultivated varieties, wild-simulated ginseng, and approximately 50-year-old wild ginseng from Korea and Russia. Results We generated a chromosome-scale pangenome with multiple near telomere-to-telomere assemblies, providing highly contiguous and near-complete reference genomes for diverse ginseng accessions. Comparative analyses identified dihydroflavonol 4-reductase ( DFR ), a key enzyme in the anthocyanin biosynthesis pathway, as the major genetic determinant of berry colour. Two independent loss-of-function alleles were identified: a missense mutation (Gly17Arg) affecting a conserved NADPH-binding residue and a ~ 20 kb deletion removing the entire gene. Metabolite profiling and population-scale analyses further supported the central role of DFR in regulating flavonoid accumulation in ginseng berries. Conclusion Our findings demonstrate that pangenome analysis can effectively uncover structural variants underlying metabolic trait diversity in complex plant genomes. This study advances understanding of berry colour variation in ginseng and provides a valuable genomic framework for trait discovery and molecular breeding in this genetically and experimentally challenging medicinal crop.