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Cell functions across all eucaryotes are driven by specific gene expression programs, which are dependent on chromatin structure. Here, we report a single-cell multiomics atlas from rice, one of the major crop plants. We have simultaneously profiled chromatin accessibility and RNA expression in 116,564 cells from eight tissues. By computational and experimental approaches, we annotated the majority of cell types and identified cell type expression programs that are shared across tissues. Overall, we find a high correlation between RNA and chromatin accessibility across cells. We constructed single-cell gene regulatory networks and gene co-expression networks, which allowed us to identify the cell type-specific regulators RSR1, F3H and LTPL120 in rice development. Furthermore, our analysis revealed the correlation between cell type and agronomic traits of rice and the conserved and divergent functions of cell type during evolution. In summary, this study not only offers a valuable single-cell multiomics resource but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.
