A single-cell multi-omics atlas of rice

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, Faming Wang, Jan U. Lohmann, Zhe Liang () and Xiaofeng Gu ()
Additional contact information
Xiangyu Wang: Chinese Academy of Agricultural Sciences
Huanwei Huang: Glbizzia Biosciences
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

Nature, 2025, vol. 644, issue 8077, 722-730

Abstract: 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41586-025-09251-0 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:644:y:2025:i:8077:d:10.1038_s41586-025-09251-0

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-025-09251-0

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().