Multiscale pangenome graphs empower the genomic dissection of mixed-ploidy sugarcane species

The sugarcane genus <i>Saccharum</i> is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph-based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy <i>Saccharum</i> accessions, revealing convergent selection and identifying the Andropogoneae <i>TB1</i> homolog linked to tillering as a promising gene-editing target to boost cane yield. Additionally, the pangenome supports dosage-informed genome-wide association study, improving heritability estimates and identification of sugar or leaf-angle-associated loci, including <i>SaIRX10</i> and <i>SaBAK5</i>. Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.