Seedling emergence is one of the most vulnerable stages in plant life. In darkness, seedlings undergo skotomorphogenesis, forming elongated hypocotyls and curved apical hooks that protect the shoot tip as it pushes through soil. Ethylene, auxin, and target of rapamycin (TOR) signaling are known to regulate this process, but most previous studies used whole-tissue analyses, which can mask how individual cell types behave. Tomato is an important horticultural crop and a useful model for understanding how early growth is coordinated under limited light. Due to these challenges, in-depth research is needed to determine how specific cell types coordinate ethylene, TOR, and auxin signaling during etiolated seedling development.
A research team led by Cong Tan at the State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, together with collaborators from BGI Bioverse, the University of Chinese Academy of Sciences, Tarim University, Yunnan University, Western Sydney University, Wuhan University, and Adelaide University, published (DOI: 10.1093/hr/uhag044) the study on 28 February 2026 in Horticulture Research. The article reports a high-resolution snRNA-seq atlas of tomato (Solanum lycopersicum) apical hooks and hypocotyls, revealing how hormone and growth-related signals guide seedling development before light exposure.
The researchers grew tomato seedlings in darkness and treated them with 1-aminocyclopropane-1-carboxylic acid (ACC), an ethylene precursor, Torin2, a TOR kinase inhibitor, or a mock control. They then isolated nuclei from apical hooks and hypocotyls and generated high-quality expression profiles for 117,929 nuclei. The atlas resolved seven major cell types in each tissue: epidermis, exodermis-like cells, endodermis-like cells, cortex, phloem, procambium, and xylem.
The two tissues showed sharply different responses. ACC increased the proportion of epidermal and exodermis-like cells in apical hooks and triggered extensive ACC-responsive differentially expressed genes (DEGs), while hypocotyls showed stronger transcriptional sensitivity to Torin2. The study also uncovered ethylene–auxin crosstalk: ACC and Torin2 repressed auxin transport genes such as SlPIN3 and SlPIN4 in apical hook epidermis and endodermis-like cells. Pseudo-time analysis showed that ACC and Torin2 altered cell differentiation trajectories, with epidermis emerging as a central cell layer for ethylene-mediated etiolated growth. Finally, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein 9 (CRISPR-Cas9) knockout of JA1 produced ja1 mutants that were hypersensitive to ACC, with exaggerated hook curvature and shortened hypocotyls and roots.
The authors said the study moves seedling biology from a tissue-level picture to a cell-by-cell view of growth control. Rather than asking only whether ethylene or TOR signaling affects young tomato seedlings, they said, the atlas shows where these signals act and which cell populations carry the strongest responses. The epidermis stood out not simply as a surface layer, but as a dynamic regulator of cell wall remodeling, hormone response, and seedling shape. They said the identification of JA1 provides a useful genetic entry point for testing how plants fine-tune ethylene sensitivity during early growth.
This snRNA-seq atlas provides a framework for dissecting complex signaling networks in tomato and other crops. Because seedling emergence affects stand establishment, early vigor, and stress resilience, understanding cell-type-specific regulation could support future breeding or biotechnological strategies aimed at improving crop performance under challenging soil and light conditions. The discovery that JA1 negatively regulates ethylene-mediated etiolated growth suggests that modulating ethylene sensitivity may help balance protective hook formation with hypocotyl and root growth. More broadly, the study shows how single-nucleus profiling can reveal hidden regulatory layers in horticultural crops, linking hormone signaling, energy sensing, cell differentiation, and developmental architecture.
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References
DOI
10.1093/hr/uhag044
Original Source URL
https://doi.org/10.1093/hr/uhag044
Funding information
This work was supported by the National Natural Science Foundation of China (32200263 to W.H.), the Shenzhen Science and Technology Program (KQTD20230301092839007 to C.T.), and the Science and Technology Major Special Project of Shenzhen (KCXFZ20240903093900001 to W.H.).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.