Rice is one of the world’s most familiar staple foods, but how does a single cell develop into a rice plant with specialized tissues and organs? A new study offers a detailed look at this process through a three-dimensional (3D) spatiotemporal atlas covering 10 organs and 61 developmental stages across the rice lifecycle, from seed to seed.
The study, published in Cell , was conducted by a research team led by Prof. YANG Weicai from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences, in collaboration with several other research teams.
The plant lifecycle alternates between a haploid phase, which produces sperm and egg cells, and a diploid phase, which develops following fertilization. In plants, the diploid zygote develops into a multicellular organism through coordinated cell divisions and cell fate specification. Understanding how these processes are regulated across different tissues and developmental stages is a fundamental goal of developmental biology.
The researchers in this study combined high-resolution spatial transcriptomics, single-nucleus RNA sequencing, and a gap-free reference genome to build datasets spanning the rice lifecycle. These datasets identified 119 cell types and 133 subtypes across different organs and developmental stages.
Through multimodal integration, the researchers reconstructed an inferred developmental trajectory graph linking cell states from the proembryo to mature organs and identified trajectory-associated regulators.
The researchers found that the pleiotropic master regulator OsARF1 —a single gene that regulates many biological processes—achieves multifunctionality through specific regulatory networks in different cells and tissues. They also uncovered widespread asymmetric gene expression across organs, including differences between the upper and lower sides of the endosperm, illustrating how spatial expression patterns guide tissue patterning and resource distribution.
To further characterize intercellular communication dynamics, the researchers used PlantPhoneDB, a database and computational tool for predicting communication between plant cells, to map interactions among different seed cell populations.
The analysis revealed that the seed coat, endosperm, and embryo engage in highly coordinated communication through key signaling peptides and their receptors, with communication patterns changing across different stages of seed development.
According to the researchers, the findings provide a resource of potential ligand–receptor pairs involved in seed development, offering candidates for further experimental investigation into how communication between different cell populations helps coordinate plant development.
A spatiotemporal lifecycle atlas decodes spatial coordination in rice
6-Oct-2026