Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, Xiuting Hua, Xiaokai Ma, Fan Zhu, Tyler Jones, Xinguang Zhu, John Bowers, Ching Man Wai, Chunfang Zheng, Yan Shi, Shuai Chen, Xiuming Xu, Jingjing Yue, David R. Nelson, Lixian Huang, Zhen Li, Huimin XuDong Zhou, Yongjun Wang, Weichang Hu, Jishan Lin, Youjin Deng, Neha Pandey, Melina Mancini, Dessireé Zerpa, Julie K. Nguyen, Liming Wang, Liang Yu, Yinghui Xin, Liangfa Ge, Jie Arro, Jennifer O. Han, Setu Chakrabarty, Marija Pushko, Wenping Zhang, Yanhong Ma, Panpan Ma, Mingju Lv, Faming Chen, Guangyong Zheng, Jingsheng Xu, Zhenhui Yang, Fang Deng, Xuequn Chen, Zhenyang Liao, Xunxiao Zhang, Zhicong Lin, Hai Lin, Hansong Yan, Zheng Kuang, Weimin Zhong, Pingping Liang, Guofeng Wang, Yuan Yuan, Jiaxian Shi, Jinxiang Hou, Jingxian Lin, Jingjing Jin, Peijian Cao, Qiaochu Shen, Qing Jiang, Ping Zhou, Yaying Ma, Xiaodan Zhang, Rongrong Xu, Juan Liu, Yongmei Zhou, Haifeng Jia, Qing Ma, Rui Qi, Zhiliang Zhang, Jingping Fang, Hongkun Fang, Jinjin Song, Mengjuan Wang, Guangrui Dong, Gang Wang, Zheng Chen, Teng Ma, Hong Liu, Singha R. Dhungana, Sarah E. Huss, Xiping Yang, Anupma Sharma, Jhon H. Trujillo, Maria C. Martinez, Matthew Hudson, John J. Riascos, Mary Schuler, Li Qing Chen, David M. Braun, Lei Li, Qingyi Yu, Jianping Wang, Kai Wang, Michael C. Schatz, David Heckerman, Marie Anne Van Sluys, Glaucia Mendes Souza, Paul H. Moore, David Sankoff, Robert VanBuren, Andrew H. Paterson, Chifumi Nagai, Ray Ming

Research output: Contribution to journalArticle

Abstract

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

Original languageEnglish (US)
Pages (from-to)1565-1573
Number of pages9
JournalNature Genetics
Volume50
Issue number11
DOIs
StatePublished - Nov 1 2018

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ASJC Scopus subject areas

  • Genetics

Cite this

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., Zhu, F., Jones, T., Zhu, X., Bowers, J., Wai, C. M., Zheng, C., Shi, Y., Chen, S., Xu, X., Yue, J., Nelson, D. R., Huang, L., Li, Z., ... Ming, R. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, 50(11), 1565-1573. https://doi.org/10.1038/s41588-018-0237-2