Single-Nucleus Transcriptome Profiling Unveils Cell-Type Specific Ethylene and TOR Signaling in Tomato

Abstract Plant etiolation, a critical process for seedling emergence, is regulated by ethylene and Target of Rapamycin (TOR) signaling pathways. However, the cell-type-specific regulation of these pathways remains poorly understood. To address this, we generated a comprehensive single-nucleus RNA (snRNA) transcriptome atlas of etiolated apical hooks and hypocotyls in tomato seedlings treated with either the ethylene precursor ACC, the TOR inhibitor Torin2, or a mock treatment. In total, we obtained high-quality gene expression profiles for 117,929 nuclei across these tissues and treatments. Our analysis identified seven major cell types within each tissue, revealing distinct cellular compositions and transcriptional programs. ACC treatment increased the proportion of epidermal cells in apical hooks, while Torin2 had limited impact on cellular composition. Differential gene expression analysis demonstrated tissue-specific sensitivity to these treatments: apical hooks exhibited extensive ACC-responsive differentially expressed genes (DEGs), whereas hypocotyls were highly responsive to Torin2. Cellular responsiveness analysis uncovered divergent ethylene/auxin pathway activities, such as ACC-repressed auxin transport in hook endodermis. Dynamic trajectory analysis indicated both treatments altered cell differentiation, authenticating epidermis as the key cell type for ethylene-mediated etiolated growth. Crucially, we identified JA1 (HD-ZIP I TF) as a negative ethylene regulator enriched in epidermis, and CRISPR knockout ja1 mutants exhibited hypersensitive to ACC. This study deciphers cell-type-specific ethylene-TOR crosstalk, providing a robust single-cell RNA sequencing framework to dissect signaling networks in crops.