2026年10月6日，武汉大学生命科学学院赵鹏等科学家在《细胞》（Cell）发表研究，构建了水稻的3D时空生命周期图谱，解码水稻发育中的空间协调。

基因表达程序如何在空间和时间上协调以构建完整植物，仍知之甚少。在此，研究人员结合高分辨率空间转录组学、单核RNA测序和无缺口参考基因组，构建了水稻的3D时空图谱，涵盖从种子到种子的10个器官和61个阶段。他们的数据集分析了851,725个细胞核和347,640个空间分箱，定义了水稻生命周期中的119种细胞类型和133种亚型。通过多模态整合，研究人员重建了一个推断的发育轨迹图，将原胚到成熟器官的细胞状态联系起来，并识别出与轨迹相关的调控因子。他们进一步将多效性调控因子OsARF1与不同发育背景下的不同空间基因程序联系起来。研究人员还揭示了广泛的轴相关转录不对称性，包括分配淀粉和蛋白质积累的背腹胚乳程序。总之，这一高分辨率图谱为理解水稻发育和指导未来作物改良提供了时空框架。

附：英文原文

Title: A spatiotemporal lifecycle atlas decodes spatial coordination in rice

Author: 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, June 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

Issue&Volume: 2026-10-06

Abstract: 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.

DOI: 10.1016/j.cell.2026.09.023

Source: https://www.cell.com/cell/abstract/S0092-8674(26)01125-6