Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum

Qing Zhang, Yiying Qi, Haoran Pan, Haibao Tang, Gang Wang, Xiuting Hua, Yongjun Wang, Lianyu Lin, Zhen Li, Yihan Li, Fan Yu, Zehuai Yu, Yongji Huang, Tianyou Wang, Panpan Ma, Meijie Dou, Zongyi Sun, Yibin Wang, Hengbo Wang, Xingtan ZhangWei Yao, Yuntong Wang, Xinlong Liu, Maojun Wang, Jianping Wang, Zuhu Deng, Jingsheng Xu, Qinghui Yang, Zhong Jian Liu, Baoshan Chen, Muqing Zhang, Ray Ming, Jisen Zhang

Research output: Contribution to journalArticlepeer-review


Saccharum spontaneum is a founding Saccharum species and exhibits wide variation in ploidy levels. We have assembled a high-quality autopolyploid genome of S. spontaneum Np-X (2n = 4x = 40) into 40 pseudochromosomes across 10 homologous groups, that better elucidates recent chromosome reduction and polyploidization that occurred circa 1.5 million years ago (Mya). One paleo-duplicated chromosomal pair in Saccharum, NpChr5 and NpChr8, underwent fission followed by fusion accompanied by centromeric split around 0.80 Mya. We inferred that Np-X, with x = 10, most likely represents the ancestral karyotype, from which x = 9 and x = 8 evolved. Resequencing of 102 S. spontaneum accessions revealed that S. spontaneum originated in northern India from an x = 10 ancestor, which then radiated into four major groups across the Indian subcontinent, China, and Southeast Asia. Our study suggests new directions for accelerating sugarcane improvement and expands our knowledge of the evolution of autopolyploids.

Original languageEnglish (US)
Pages (from-to)885-896
Number of pages12
JournalNature Genetics
Issue number6
StatePublished - Jun 2022

ASJC Scopus subject areas

  • Genetics


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