[en] Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10-12 sets of chromosomes). This complexity resulted from nobilization-a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts to elucidate the genetic basis of its considerable sucrose-storing capacity. Here we present a fully phased genome assembly of the foundational cultivar POJ2878, achieved using a Pore-C-based assembly algorithm. This assembly resolved 118 chromosomes, revealing extensive subgenome recombination and non-homologous chromosomal rearrangements. Using identity-by-descent and allele-specific expression profiling, we identified breeder-favoured haplotypes, including a SUS2 haplotype with enhanced sucrose content. Resequencing of 981 Saccharum accessions traced POJ2878's pervasive contribution to modern cultivars and identified key domestication and improvement sweeps. Genes under selection include CBL1 for cold tolerance, TIP1 for cell size regulation and TB1 for tillering control. A genome-wide association study tailored for polyploid genomes resolved loci associated with parenchyma cell size and sucrose storage capacity, including the functionally validated sucrose transporter Saccharum hybrid SUT2. These findings clarify the genetic architecture underlying sugarcane's biomass productivity and sugar yield, offering a genomic foundation for accelerating improvement in sugarcane and other polyploid crops critical for global food and bioenergy security.
Disciplines :
Genetics & genetic processes
Author, co-author :
Wang, Jungang ✱; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Li, Xiaofeng ✱; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Wang, Yibin ✱; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Lin, Jishan ✱; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Chen, Shuai ✱; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Liu, Hongbo ✱; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Chen, Xiao ✱; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Chai, Kun; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China ; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China ; Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
Dong, Aoqian; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
Zhao, Tingting; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Feng, Cuilian; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Wu, Ruijie; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Zhao, Ping; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Zheng, Yaodong; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
Xia, Zhongqiang; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Zhang, Shengcheng ; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Liu, Yi ; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Qu, Shenyang; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Ye, Ziqi; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Song, Yuhan ; Université de Liège - ULiège > TERRA Research Centre > Plant Sciences ; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Deng, Qingyuan; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Zeng, Xiaofei; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Yu, Guangrun; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Kong, Ran; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
Zhang, Baoqing; Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
Zhang, Wei; Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
Zhao, Peifang; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Mao, Jun; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Lu, Xin; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Jia, Haifeng; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China
Zhao, Xueting; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Zhang, Qianqian; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Zhang, Shuzhen; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Cai, Wenwei; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Huo, Dongao; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Li, Ling; State Key Laboratory of Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops Ministry of Agriculture and Rural Affairs, Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ; Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions of Hainan Province, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
Gong, Yuqing; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
Huang, Shiqiang; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
Huang, Yongji; College of Geography and Oceanography, Minjiang University, Fuzhou, China
Yu, Zehuai; Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
Deng, Zuhu; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
Chen, Baoshan; Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
Zhang, Yuebin; State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
Ming, Ray ; Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China. rayming@illinois.edu
Zhang, Xingtan ; State Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzheng, China. zhangxingtan@caas.cn
We thank S. Huang and H. Wang for discussions on this work. This work was supported by National Natural Science Foundation of China grant (32222019, 32370714 and 32572476), Basic Research Center for Agricultural Frontiers and Interdisciplinary Sciences (BRC-AFIS), Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-BRC-AFIS-2025-02), the Project of State Key Laboratory for Tropical Crop Breeding (NKLTCBCXTD23, NKLTCB-ZX03, NKLTCB202313), the Key R&D Program of Hainan Province (ZDYF2025XDNY104, ZDYF2025GXJS139), the Central Public-interest Scientific Institution Basal Research Fund (1630052023015), Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center (CATASCXTD202307).
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