A multi-omics cell atlas unlocks new frontiers in crop biotechnology.

Defining how plant cell types are specified and regulated has been a central challenge in biology. Previous single-cell studies in plants, relying on either RNA-seq or ATAC-seq, provided valuable insights but could not directly connect chromatin state to transcriptional programs. Writing in Nature, Wang et al. present the first multi-organ single-cell multi-omics atlas of rice. Profiling more than 116,000 nuclei across eight tissues, they delineate 56 distinct cell types with high resolution. Joint analysis of gene expression and chromatin accessibility reveals sharper cell-type boundaries, transient developmental states, and regulatory networks with unprecedented clarity. Importantly, the study links cell-specific regulatory programs to key agronomic traits, identifying candidate regulators of root architecture, photosynthesis, nitrogen metabolism, and yield. This atlas establishes both a foundational resource for comparative plant biology and crop biotechnology, providing a roadmap for precision breeding and resilient agriculture driven by cell-type insights.