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<p>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 <i>Saccharum officinarum</i> (So<sub>h</sub>) and <i>S. spontaneum</i> (Ss<sub>h</sub>), with So<sub>h</sub> dominance in the <i>Saccharum</i> hybrid (<i>S</i>. 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 <i>Saccharum</i> accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved <i>S</i>. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from <i>S. spontaneum</i>. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.</p>

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

  • 期刊论文

  • 发表日期：

    2025年1月3日

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  • 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

摘要

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.