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Natural Sciences›Biology›genetics, evolutionary-biology

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

Yun HuangFujian Agriculture and Forestry University

Yixing ZhangGuangxi University

Qing ZhangGuangxi University

Gui Hua ZhuangGuangxi University

Chunjia LiYunnan Academy of Agricultural Sciences

Baiyu WangGuangxi University

Ruiting GaoGuangxi University

Yi XuGuangxi University

Yiying QiFujian Agriculture and Forestry University

Xiuting HuaGuangxi University

Science·February 5, 2026·1 citations

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Abstract

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.

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