A single-cell multiomics atlas of rice

Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the world’s major crop plants. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs we were able to identify cell-type specific gene regulatory networks and describe novel cell states, such as the “transition status” in floral meristems during panicle development. Based on our network analyses we uncovered the function of cell type-specific regulatory hubs RSR1, F3H and LTPL120 for rice development. Importantly, our analysis revealed a correlation between cell type and agronomic traits, and conserved and divergent cell type functions during evolution. In summary, this study not only offers a valuable single-cell multiomics resource for a major crop, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice. The experimental design involves single-cell RNA sequencing of root cells from Nip and osltpl120 mutant using the 10x Genomics Chromium Single Cell 3' Gene Expression technology. Cells were isolated and processed according to 10x Genomics protocols. Sequencing was performed on an Illumina NovaSeq 6000 platform. The dataset includes single-cell gene expression profiles with quality control steps to exclude low-quality cells and doublets, followed by normalization and batch effect correction.