Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding

Roses are economically important ornamental plants, with widespread applications in the cut flowers, garden and cosmetics industries. The genomic evolution and diversity of the subgenus Rosa remain understudied, limiting exploitation of its diversity in breeding. Here we assembled genomes of 23 accessions, comprising 51 haplotypes that capture the subgenus's high genetic diversity. Extensive introgression across accessions from different sections highlights crossbreeding potential. Pangenome analysis revealed 1,801,537 structural variations, providing insights into the genetic basis and key regulators controlling key traits such as continuous flowering, petal number and discoloration. A key finding was the identification of a CCD4 homolog as the main regulator of petal discoloration. Additional subgenomic analysis of the allopolyploid Rosa gallica and the triploid Rosa hybrida 'La France', two important breeding materials of modern roses, revealed their hybrid origins. Overall, this study advances understanding of rose genomics and provides valuable resources for future breeding and trait improvement.