Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination
Jie Yao, Qinjie Chu, Xing Guo, Wenwen Shao, Nianmin Shang, Kang Luo, Xiaohan Li, Hongyu Chen, Qing Cheng, Fangyu Mo, Dihuai Zheng, Fan Xu, Fu Guo, Qian-Hao Zhu, Shuiguang Deng, Chengcai Chu, Xun Xu, Huan Liu, Longjiang Fan
Dev Cell; 2024 Sep 9; 59(17):2320-2332.e5. doi: 10.1016/j.devcel.2024.05.016.
Abstract
Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.
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