The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

Jisen Zhang; Yiying Qi; Xiuting Hua; Yongjun Wang; Baiyu Wang; Yongwen Qi; Yumin Huang; Zehuai Yu; Ruiting Gao; Yixing Zhang; Tianyou Wang; Yuhao Wang; Jing Mei; Qing Zhang; Gang Wang; Haoran Pan; Zhen Li; Shuangyu Li; Jia Liu; Nameng Qi; Xiaoxi Feng; Mingxing Wu; Shuqi Chen; Cuicui Du; Yihan Li; Yi Xu; Yaxue Fang; Panpan Ma; Qingyun Li; Yuanchang Sun; Xiaomin Feng; Wei Yao; Muqing Zhang; Baoshan Chen; Xinlong Liu; Ray Ming; Jianping Wang; Zuhu Deng; Haibao Tang

doi:10.1038/s41588-024-02033-w

The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

Nat Genet. 2025 Jan 3. doi: 10.1038/s41588-024-02033-w. Online ahead of print.

Authors

Jisen Zhang^#¹, Yiying Qi^#², Xiuting Hua^#³, Yongjun Wang^#², Baiyu Wang^#³, Yongwen Qi^#⁴, Yumin Huang^#⁵, Zehuai Yu^#³, Ruiting Gao^#³, Yixing Zhang⁵, Tianyou Wang³, Yuhao Wang², Jing Mei⁵, Qing Zhang³, Gang Wang⁶, Haoran Pan⁵, Zhen Li³, Shuangyu Li², Jia Liu⁵, Nameng Qi², Xiaoxi Feng², Mingxing Wu², Shuqi Chen⁵, Cuicui Du², Yihan Li³, Yi Xu³, Yaxue Fang⁵, Panpan Ma⁵, Qingyun Li⁷, Yuanchang Sun⁵, Xiaomin Feng⁸, Wei Yao³, Muqing Zhang³, Baoshan Chen³, Xinlong Liu⁹, Ray Ming⁵, Jianping Wang¹⁰, Zuhu Deng², Haibao Tang⁵

Affiliations

¹ State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China. [email protected].
² College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
³ State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China.
⁴ College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
⁵ Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
⁶ Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, China.
⁷ Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
⁸ Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
⁹ Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China.
¹⁰ Department of Agronomy, University of Florida, Gainesville, FL, USA.

^# Contributed equally.

PMID: 39753769
DOI: 10.1038/s41588-024-02033-w

Abstract

Modern sugarcane, a highly allo-autopolyploid organism, has a very complex genome. In the present study, the karyotype and genome architecture of modern sugarcane were investigated, resulting in a genome assembly of 97 chromosomes (8.84 Gb). The allopolyploid genome was divided into subgenomes from Saccharum officinarum (So_h) and S. spontaneum (Ss_h), with So_h dominance in the Saccharum hybrid (S. hybrid). Genome shock affected transcriptome dynamics during allopolyploidization. Analysis of an inbreeding population with 192 individuals revealed the underlying genetic basis of transgressive segregation. Population genomics of 310 Saccharum accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved S. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from S. spontaneum. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.