Genetic architecture of sugarcane traits in a polyploid genomics framework
13 affiliations
- 1State 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
- 2State 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
- 3State Key Laboratory for Tropical Crop Breeding, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- 4Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
- 5Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China
- 6Key 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
- 7South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
- 8Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- 9Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- 10College of Geography and Oceanography, Minjiang University, Fuzhou, China
- 11Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, China. [email protected]
- 12Center for Genomics and Biotechnology, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China. [email protected]
- 13State 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. [email protected]
Abstract
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. A fully phased genome assembly of the sugarcane foundational cultivar POJ2878 reveals extensive subgenome recombination and non-homologous chromosomal rearrangements.
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BibTeX
@article{wang2026genetic,
title = {{Genetic architecture of sugarcane traits in a polyploid genomics framework}},
author = {Jungang Wang and Xiaofeng Li and Yibin Wang and Jishan Lin and Shuai Chen and Hongbo Liu and X Chen and Kun Chai and Aoqian Dong and Tingting Zhao and Feng Cuilian and Ruijie Wu and Ping Zhao and Yaodong Zheng and Zhongqiang Xia and Shengcheng Zhang and Yi Liu and Shenyang Qu and Ziqi Ye and Yuhan Song and Qingyuan Deng and Xiaofei Zeng and Guangrun Yu and Ran Kong and Baoqing Zhang and Wei Zhang and Peifang Zhao and Jun Mao and Xin Lu and Haifeng Jia and Xue-Ting Zhao and Qianqian Zhang and S Zhang and Wenwei Cai and Dongao Huo and Ling Li and Yuqing Gong and Shiqiang Huang and Yongji Huang and Zehuai Yu and Zuhu Deng and Baoshan Chen and Yuebin Zhang and Muqing Zhang and Ray Ming and Xingtan Zhang},
journal = {Nature},
year = {2026},
month = may,
doi = {10.1038/s41586-026-10576-7},
url = {https://doi.org/10.1038/s41586-026-10576-7},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genetic architecture of sugarcane traits in a polyploid genomics framework
AU - Jungang Wang
AU - Xiaofeng Li
AU - Yibin Wang
AU - Jishan Lin
AU - Shuai Chen
AU - Hongbo Liu
AU - X Chen
AU - Kun Chai
AU - Aoqian Dong
AU - Tingting Zhao
AU - Feng Cuilian
AU - Ruijie Wu
AU - Ping Zhao
AU - Yaodong Zheng
AU - Zhongqiang Xia
AU - Shengcheng Zhang
AU - Yi Liu
AU - Shenyang Qu
AU - Ziqi Ye
AU - Yuhan Song
AU - Qingyuan Deng
AU - Xiaofei Zeng
AU - Guangrun Yu
AU - Ran Kong
AU - Baoqing Zhang
AU - Wei Zhang
AU - Peifang Zhao
AU - Jun Mao
AU - Xin Lu
AU - Haifeng Jia
AU - Xue-Ting Zhao
AU - Qianqian Zhang
AU - S Zhang
AU - Wenwei Cai
AU - Dongao Huo
AU - Ling Li
AU - Yuqing Gong
AU - Shiqiang Huang
AU - Yongji Huang
AU - Zehuai Yu
AU - Zuhu Deng
AU - Baoshan Chen
AU - Yuebin Zhang
AU - Muqing Zhang
AU - Ray Ming
AU - Xingtan Zhang
PY - 2026
DA - 2026/05/27
JO - Nature
DO - 10.1038/s41586-026-10576-7
UR - https://doi.org/10.1038/s41586-026-10576-7
AB - 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. A fully phased genome assembly of the sugarcane foundational cultivar POJ2878 reveals extensive subgenome recombination and non-homologous chromosomal rearrangements.
SN - 0028-0836
SN - 1476-4687
ER -