How do plants regenerate roots from scratch after being wounded? In this study, scientists used spatial transcriptomics and time-series gene expression analysis to trace poplar root regeneration from its earliest stages. They identified key hormonal signals, gene clusters, and two promising biomarkers—SAC56 and LOS1—that orchestrate the transformation of cambium cells into root structures. The findings spotlight a sophisticated interplay between auxin and cytokinin, revealing how these hormones coordinate to drive regeneration. This detailed molecular roadmap not only deepens our understanding of plant developmental plasticity but also offers new tools to enhance propagation in agriculture and forestry.
Plants possess a remarkable capacity to regenerate organs after injury, a process widely utilized in horticulture and forestry through techniques like cuttings. When wounded, plant tissues activate a cascade of hormonal responses—primarily the synthesis of auxin—that initiates cellular reprogramming and root formation. While auxin’s role in this process is well documented, the spatial and temporal coordination between hormones and gene expression remains poorly understood. The precise cellular transitions, especially those involving cytokinin activity and cambium-derived cells, have not been fully mapped. Due to these knowledge gaps, there is an urgent need to decode the cellular choreography that underlies de novo root regeneration.
On August 20, 2024, researchers from the Peking University Institute of Advanced Agricultural Sciences published (DOI: 10.1093/hr/uhae237) a study in Horticulture Research that sheds light on how poplar trees regenerate roots after stem detachment. Using high-resolution spatial transcriptomics, the team captured the gene expression landscape across different stages of root development. Their work uncovered the precise roles of hormone-responsive genes and introduced two new molecular markers, offering valuable insights into the spatial dynamics and genetic regulation of root regeneration in woody plants.
The team conducted a comprehensive study combining bulk RNA sequencing and spatial transcriptomics to map gene activity during four stages of root regeneration in poplar cuttings. Through clustering and trajectory analysis, they tracked how cambium cells differentiate into root primordium cells. Six distinct cell clusters emerged, each associated with unique gene signatures and tissue identities. Notably, the team identified SAC56 and LOS1 as highly expressed in the developing root primordium—both genes were validated by in situ hybridization. Hormone analysis revealed that 94% of cytokinin-responsive genes also contained regulatory elements linked to auxin and WOX11, indicating a complex cross-talk between these hormonal pathways. Cytokinin activity was concentrated in the root meristem, while auxin-responsive genes were enriched in cambium cells, suggesting a tightly regulated spatial distribution. Pseudo-temporal mapping further illustrated how these signals guide cellular transitions from cambium to epidermis and xylem to fully formed roots. This work presents a rare cell-by-cell reconstruction of regeneration, linking hormonal signals to developmental outcomes with high spatial fidelity.
“Our findings offer a vivid snapshot of how plant tissues respond to wounding by reprogramming themselves into new roots,” said Prof. Bosheng Li, the study’s senior author. “By using spatial transcriptomics, we could see when and where key genes are activated, revealing a precise hormonal dialogue between auxin and cytokinin. Identifying marker genes like SAC56 and LOS1 provides new molecular handles to enhance rooting in hard-to-propagate species. This research brings us closer to harnessing the regenerative power of plants more effectively.”
This research offers practical value for agriculture, forestry, and conservation. By pinpointing gene markers and hormone interactions critical for root formation, the study opens new avenues to breed or engineer plants with improved rooting ability. This could be especially beneficial for difficult-to-propagate trees or endangered species requiring clonal reproduction. The authors have also launched an open-access online platform for researchers to explore root regeneration gene maps in poplar, fostering collaborative discoveries. Ultimately, understanding the spatial genetics of root regeneration could transform vegetative propagation practices, making them more efficient and predictable in a changing climate.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae237
Funding information
This work was supported by the Key R&D Program of Shandong Province, China (grant no. ZR202211070163), the Shandong Provincial Natural Science Foundation (grant no. ZR2023QC106), the National Natural Science Foundation of China (grant no. 32170574), the Young Taishan Scholars Program and Yuandu Scholars.
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.
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