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A single-cell multi-omics atlas of rice

Author

Listed:
  • Xiangyu Wang

    (Chinese Academy of Agricultural Sciences)

  • Huanwei Huang

    (Glbizzia Biosciences
    Capital Medical University)

  • Sanjie Jiang

    (BGI Genomics)

  • Jingmin Kang

    (BGI Research)

  • Dongwei Li

    (Chinese Academy of Agricultural Sciences)

  • Kailai Wang

    (Glbizzia Biosciences)

  • Shang Xie

    (Chinese Academy of Agricultural Sciences)

  • Cheng Tong

    (Chinese Academy of Agricultural Sciences)

  • Chaofan Liu

    (Chinese Academy of Agricultural Sciences)

  • Guihua Hu

    (Chinese Academy of Agricultural Sciences)

  • Haoqian Li

    (Chinese Academy of Agricultural Sciences)

  • Cong Li

    (Chinese Academy of Agricultural Sciences)

  • Liwen Yang

    (Chinese Academy of Agricultural Sciences)

  • Yike Ding

    (University of California Riverside)

  • Shang-Tong Li

    (Glbizzia Biosciences)

  • Faming Wang

    (KU Leuven)

  • Jan U. Lohmann

    (Heidelberg University)

  • Zhe Liang

    (Chinese Academy of Agricultural Sciences)

  • Xiaofeng Gu

    (Chinese Academy of Agricultural Sciences)

Abstract

Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure1–3. Here we report a single-cell multi-omics atlas of rice, one of the world’s major crops. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs, we identified cell-type-specific gene regulatory networks and described novel cell states, such as a ‘transitional state’ in floral meristems. On the basis of our network analyses, we uncovered the function of the cell-type-specific regulatory hubs RSR1, F3H and LTPL120 during rice development. Our analysis revealed correlations between cell type and agronomic traits, as well as conserved and divergent cell-type functions during evolution. In summary, this study not only offers a unique single-cell multi-omics resource for a major crop but also advances our understanding of cell-type functions and the underlying molecular programs in rice.

Suggested Citation

  • Xiangyu Wang & Huanwei Huang & Sanjie Jiang & Jingmin Kang & Dongwei Li & Kailai Wang & Shang Xie & Cheng Tong & Chaofan Liu & Guihua Hu & Haoqian Li & Cong Li & Liwen Yang & Yike Ding & Shang-Tong Li, 2025. "A single-cell multi-omics atlas of rice," Nature, Nature, vol. 644(8077), pages 722-730, August.
    • Handle: RePEc:nat:nature:v:644:y:2025:i:8077:d:10.1038_s41586-025-09251-0
    DOI: 10.1038/s41586-025-09251-0
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