TY - JOUR
T1 - A single-cell multi-omics atlas of rice
AU - Wang, Xiangyu
AU - Huang, Huanwei
AU - Jiang, Sanjie
AU - Kang, Jingmin
AU - Li, Dongwei
AU - Wang, Kailai
AU - Xie, Shang
AU - Tong, Cheng
AU - Liu, Chaofan
AU - Hu, Guihua
AU - Li, Haoqian
AU - Li, Cong
AU - Yang, Liwen
AU - Ding, Yike
AU - Li, Shang Tong
AU - Wang, Faming
AU - Lohmann, Jan U.
AU - Liang, Zhe
AU - Gu, Xiaofeng
N1 - Funding information:
We thank H. Xue for providing rice rsr1 seeds. This work was supported by the Biological Breeding-National Science and Technology Major Project (2023ZD04076), the National Natural Science Foundation of China (32130080 to X.G.), the Central Public-interest Scientific Institution Basal Research Fund (to Z.L.), ERC synergy grant 810296 ‘DECODE’ (to J.U.L.) and the Central Laboratory of Biotechnology Research Institute, Chinese Academy of Agricultural Sciences.
Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature Limited 2025.
PY - 2025/8/21
Y1 - 2025/8/21
N2 - Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure. 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.
AB - Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure. 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.
UR - https://www.scopus.com/pages/publications/105010284611
U2 - 10.1038/s41586-025-09251-0
DO - 10.1038/s41586-025-09251-0
M3 - Journal article
C2 - 40634611
AN - SCOPUS:105010284611
SN - 0028-0836
VL - 644
SP - 722
EP - 730
JO - Nature
JF - Nature
ER -