A single-cell multi-omics atlas of rice

• 成果类型: Article
• 署名作者: Wang, Xiangyu; Huang, Huanwei; Jiang, Sanjie; Kang, Jingmin; Li, Dongwei; Wang, Kailai; Xie, Shang; Tong, Cheng; Liu, Chaofan; Hu, Guihua; Li, Haoqian; Li, Cong; Yang, Liwen; Ding, Yike; Li, Shang-Tong; Wang, Faming; Lohmann, Jan U.; Liang, Zhe; Gu, Xiaofeng
• 署名单位: Chinese Academy of Agricultural Sciences; Biotechnology Research Institute, CAAS; Capital Medical University; Beijing Genomics Institute (BGI); University of California System; University of California Riverside; KU Leuven; Ruprecht Karls University Heidelberg
• 刊物名称: Nature
• ISSN/ISSBN: 0028-1139
• DOI: 10.1038/s41586-025-09251-0
• 发表日期: 2025-08-21
• 关键词: chromatin; regulators; landscape; QUALITY

摘要

Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure1, 2-3. 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.