The origin and domestication of modern cultivated Chrysanthemum × morifolium

The modern cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a globally important ornamental plant, ranking as the second-largest cut flower after roses. Here, to unravel its complex origin and domestication history, we achieved 6 haplotypes of the elite hexaploidy cut chrysanthemum cultivar 'Jinba' (2n = 6x = 54). By constructing a genome-wide variant map across 147 core accessions, we classified current Chrysanthemum varieties into 4 wild and 4 cultivated groups. We observed extensive, intricate gene flow among these groups, demonstrating that wild germplasms from both China and Japan contribute substantially to the formation of modern cultivars. We constructed a global dispersal map for cultivated chrysanthemum and confirmed Chrysanthemum indicum as one of the key ancestral taxa. In addition, we identified candidate loci and genes associated with the development of important agronomic traits, including plant architecture, flower type and flower colour. This study provides crucial insights into the evolutionary history of cultivated chrysanthemums and establishes a robust genomic resource for advancing molecular breeding.