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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	258
Pages (from-to)	242–253
Number of pages	12
Journal	Nature Genetics
Volume	57
Issue number	1
DOIs	https://doi.org/10.1038/s41588-024-02033-w
State	Published - Jan 2025
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1038/s41588-024-02033-w

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Zhang, J., Qi, Y., Hua, X., Wang, Y., Wang, B., Qi, Y., Huang, Y., Yu, Z., Gao, R., Zhang, Y., Wang, T., Wang, Y., Mei, J., Zhang, Q., Wang, G., Pan, H., Li, Z., Li, S., Liu, J., ... Tang, H. (2025). The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum. Nature Genetics, 57(1), 242–253. Article 258. https://doi.org/10.1038/s41588-024-02033-w

Zhang, J, Qi, Y, Hua, X, Wang, Y, Wang, B, Qi, Y, Huang, Y, Yu, Z, Gao, R, Zhang, Y, Wang, T, Wang, Y, Mei, J, Zhang, Q, Wang, G, Pan, H, Li, Z, Li, S, Liu, J, Qi, N, Feng, X, Wu, M, Chen, S, Du, C, Li, Y, Xu, Y, Fang, Y, Ma, P, Li, Q, Sun, Y, Feng, X, Yao, W, Zhang, M, Chen, B, Liu, X, Ming, R, Wang, J, Deng, Z & Tang, H 2025, 'The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum', Nature Genetics, vol. 57, no. 1, 258, pp. 242–253. https://doi.org/10.1038/s41588-024-02033-w

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title = "The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum",

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 (Soh) and S. spontaneum (Ssh), with Soh 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.",

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

note = "This work was supported by the National Key Research and Development Program (grant nos. 2021YFF1000101 to J.Z. and 2021YFF1000104 to H.T.), the Guangxi Science and Technology Major Program (grant nos. AA24206023 to J.Z. and AA24206006 to Q.Z.) and the National Natural Science Foundation of China (grant nos. 32272196 and U24A20387 to J.Z.).",

year = "2025",

month = jan,

doi = "10.1038/s41588-024-02033-w",

language = "English (US)",

volume = "57",

pages = "242–253",

journal = "Nature Genetics",

issn = "1061-4036",

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T1 - The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

AU - Zhang, Jisen

AU - Qi, Yiying

AU - Hua, Xiuting

AU - Wang, Yongjun

AU - Wang, Baiyu

AU - Qi, Yongwen

AU - Huang, Yumin

AU - Yu, Zehuai

AU - Gao, Ruiting

AU - Zhang, Yixing

AU - Wang, Tianyou

AU - Wang, Yuhao

AU - Mei, Jing

AU - Zhang, Qing

AU - Wang, Gang

AU - Pan, Haoran

AU - Li, Zhen

AU - Li, Shuangyu

AU - Liu, Jia

AU - Qi, Nameng

AU - Feng, Xiaoxi

AU - Wu, Mingxing

AU - Chen, Shuqi

AU - Du, Cuicui

AU - Li, Yihan

AU - Xu, Yi

AU - Fang, Yaxue

AU - Ma, Panpan

AU - Li, Qingyun

AU - Sun, Yuanchang

AU - Feng, Xiaomin

AU - Yao, Wei

AU - Zhang, Muqing

AU - Chen, Baoshan

AU - Liu, Xinlong

AU - Ming, Ray

AU - Wang, Jianping

AU - Deng, Zuhu

AU - Tang, Haibao

N1 - This work was supported by the National Key Research and Development Program (grant nos. 2021YFF1000101 to J.Z. and 2021YFF1000104 to H.T.), the Guangxi Science and Technology Major Program (grant nos. AA24206023 to J.Z. and AA24206006 to Q.Z.) and the National Natural Science Foundation of China (grant nos. 32272196 and U24A20387 to J.Z.).

PY - 2025/1

Y1 - 2025/1

N2 - 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 (Soh) and S. spontaneum (Ssh), with Soh 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.

AB - 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 (Soh) and S. spontaneum (Ssh), with Soh 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.

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DO - 10.1038/s41588-024-02033-w

M3 - Article

C2 - 39753769

AN - SCOPUS:85213890218

SN - 1061-4036

VL - 57

SP - 242

EP - 253

JO - Nature Genetics

JF - Nature Genetics

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M1 - 258

ER -

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

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