Deciphering seed development and germination in the single-cell era

Abstract Seeds are complex structures that serve as dispersal units in angiosperms. Seeds consist of three specialized tissues with distinct roles and molecular compositions. Hence, the characterization of the genetic regulators that act within individual seed tissues, and how their activity changes during seed development and germination, has been a primary focus of seed research. However, our knowledge of the spatiotemporal modulation of genetic regulators within seeds, across different seed cell types, has been limited by the resolution of available techniques. In the last few years, the development and application of single-cell technologies in plants have enabled the elucidation of gene networks involved in various developmental processes at the cellular level. Some studies have applied these technologies to seeds, enabling further characterization of seed development and germination at the cellular level. Here, we review the current status of the application of single-cell technologies to seeds and present a workflow for conducting single-cell transcriptomics. Additionally, we discuss the integration of single-cell multi-omics, aiming to demonstrate the potential of single-cell technologies in enhancing our comprehension of the spatiotemporal regulations governing seed development and germination.