Yanfu Wang , Danyan Ding

Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
Rice Genomics and Genetics, 2025, Vol. 16, No. 4   
Received: 20 May, 2025    Accepted: 02 Jul., 2025    Published: 20 Jul., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Rice grain filling is a critical determinant of yield and quality, relying on tightly coordinated gene regulation across diverse cell types. In this study, we applied single-cell RNA sequencing (scRNA-seq) to dissect the transcriptomic landscape of individual cell populations within developing rice grains, enabling the construction of cell-type specific gene regulatory networks (GRNs). We identified and classified distinct cell types involved in grain filling, characterized their unique gene expression patterns, and traced dynamic transcriptional changes across developmental stages. Through GRN inference, we uncovered key transcription factors and regulatory hubs governing starch biosynthesis, nutrient transport, protein accumulation, and stress responses, as well as their integration with hormonal and metabolic pathways. A focused case study on endosperm-specific starch biosynthesis revealed candidate regulators validated by transgenic and CRISPR-based approaches. Integration with spatial transcriptomics, proteomics, and metabolomics further reinforced the functional significance of these networks. These findings provide a high-resolution view of cell-type specific transcriptional regulation during rice grain filling, offering novel targets and strategies for genetic improvement of grain yield and quality.

Rice grain filling; Single-cell RNA sequencing; Gene regulatory networks; Cell-type specificity; Transcriptional regulation