Yumin Huang, Yixing Zhang, Qing Zhang, Gui Hua Zhuang, Chunjia Li, Baiyu Wang, Ruiting Gao, Yi Xu, Yiying Qi, Xiuting Hua, Huihong Shi, Q. J. Xu, Wei Yao, Xinlong Liu, Yongwen Qi, Baoshan Chen, Muqing Zhang, Ray Ming, Haibao Tang, Jisen Zhang
The sugarcane genus Saccharum 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 Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 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 SaIRX10 and SaBAK5 . Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.