Yi Jing#, Qiong Chen#, Yifan Chen#, Wei Yan#, Yuejing Gui#, Yicheng Zhong#, Mumu Qin#, Han Zhang#, James Whelan, Chuanxiu Li, Shiyu Chen, Chunyan Xu, Weiming He, Zhiyao Lv, Feng Yang, Rouxi Chen, Jing Zhang, Zongan Wang, Zhenyu Xiong, Xun Liao, Keke Xia, Tong Wei, Longjiang Fan, Tao Yang, Yinqi Bai, Jiwei Xu, Ying Dai, Fang Zhang, Shenhui Yang, Yanting Qiao, Shengwu Xiong, Yi Rong, Cunman He, Huixia Shou, Lei Wang, Qian Wang, Xueqing Xia, Xiongbo Peng, Kaiting Sun, Yongzhong Xing, Lin Du, Rui Han, Chao Qin, Likun Jiang, Xinsen Yang, Jun'e Jiang, Xinle Yu, Jiantao Wu, Rui Li, Yinru Yan, Yizhou Wang, Ying Gu, Jian Wang, Pengfei Jia*, Xiaodong Fang*, Peng Zhao*, Zhen Yue*, Hongwei Guo*, Yidan Ouyang*, Xun Xu*, Fan Chen*
Cell, Online now, October 06, 2026
Highlights
• Integrated 3D spatiotemporal atlas captures rice seed-to-seed developmental dynamics
• Transcriptomic trajectories link OsARF1 to context-specific regulatory modules
• Endosperm dorsoventral asymmetry guides distinct starch-protein partitioning
• Open-access portal and RICE scGPT model enable plant single-cell data exploration
Summary
How gene expression programs are coordinated across space and time to build a complete plant remains poorly understood. Here, we combine high-resolution spatial transcriptomics, single-nucleus RNA sequencing, and a gap-free reference genome to build a 3D spatiotemporal atlas of rice, spanning 10 organs and 61 stages from seed to seed. Our datasets profile 851,725 nuclei and 347,640 spatial bins, defining 119 cell types and 133 subtypes across the rice lifecycle. Through multimodal integration, we reconstruct an inferred developmental trajectory graph that links cell states from the proembryo to mature organs and identifies trajectory-associated regulators. We further implicate the pleiotropic regulator OsARF1 in distinct spatial gene programs across developmental contexts. We also uncover widespread axis-associated transcriptional asymmetry, including dorsoventral endosperm programs that partition starch and protein accumulation. Collectively, this high-resolution atlas provides a spatiotemporal framework for understanding rice development and guiding future crop improvement.
Graphical abstract
Keywords
rice, seed-to-seed lifecycle, spatiotemporal cell atlas, Stereo-seq, snRNA-seq, developmental trajectory, OsARF1, transcriptional asymmetry, ligand-receptor crosstalk, RICE scGPT
论文链接：https://www.cell.com/cell/fulltext/S0092-8674(26)01125-6
