TY - JOUR
T1 - Multiscale pangenome graphs empower the genomic dissection of mixed-ploidy sugarcane species
AU - Huang, Yumin
AU - Zhang, Yixing
AU - Zhang, Qing
AU - Zhuang, Gui
AU - Li, Chunjia
AU - Wang, Baiyu
AU - Gao, Ruiting
AU - Xu, Yi
AU - Qi, Yiying
AU - Hua, Xiuting
AU - Shi, Huihong
AU - Xu, Qiutao
AU - Yao, Wei
AU - Liu, Xinlong
AU - Qi, Yongwen
AU - Chen, Baoshan
AU - Zhang, Muqing
AU - Ming, Ray
AU - Tang, Haibao
AU - Zhang, Jisen
N1 - We thank Q. Lian (South China Agricultural University) for the A. thaliana pangenome variants datasets sharing and Z. Bao (Max Planck Institute for Biology Tübingen) for his instructive discussions and advices. This work was supported by the National Key Research and Development Program (grant 2024YFF1000800), the Guangxi Science and Technology Major Program (grants AA24206023 to J.Z. and AA24206006 to Q.Z.), and the National Natural Science Foundation of China (grants 32272196 and U24A20387 to J.Z., 32500548 to Y.H., and 32201794 to Q.Z.)
We thank Q. Lian (South China Agricultural University) for the A. thaliana pangenome variants datasets sharing and Z. Bao (Max Planck Institute for Biology Tübingen) for his instructive discussions and advices. Funding: This work was supported by the National Key Research and Development Program (grant 2024YFF1000800), the Guangxi Science and Technology Major Program (grants AA24206023 to J.Z. and AA24206006 to Q.Z.), and the National Natural Science Foundation of China (grants 32272196 and U24A20387 to J.Z., 32500548 to Y.H., and 32201794 to Q.Z.). Author contributions: H.T. and J.Z. conceived and designed the project.Y.H., Q.Z., C.L.,Y.X.,X.H.,W.Y.,Yo.Q., R.M.,X.L., B.C., M.Z., and J.Z. collected and generated sugarcane materials. G.Z. and H.S. performed the experiments. C.L. and X.L. conducted the gene editing for TB1.Y.H.,Y.Z., B.W., Q.Z., R.G., and Yi.Q. performed the bioinformatic analysis.Y.H., H.T., and J.Z. wrote the manuscript.Y.H,Y.Z., Q.Z., Q.X., H.T., and J.Z. further revised the manuscript. Competing interests: The authors declare that they have no competing interests. Data, code, and materials availability: All data are available in the main text or the supplementary materials or are deposited as follows:
PY - 2026/2
Y1 - 2026/2
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/105030165049
UR - https://www.scopus.com/pages/publications/105030165049#tab=citedBy
U2 - 10.1126/science.adx1616
DO - 10.1126/science.adx1616
M3 - Article
C2 - 41643009
AN - SCOPUS:105030165049
SN - 0036-8075
VL - 391
SP - 11
JO - Science
JF - Science
IS - 6785
M1 - eadx1616
ER -