How do trees regrow roots after being cut? A new study sheds light on this question using cutting-edge spatial transcriptomics to track how poplar stems regenerate roots. Researchers mapped gene activity during the regeneration process and discovered a sophisticated hormonal interplay between auxin and cytokinin. They identified two genes, SAC56 and LOS1, as spatial markers critical to root primordium formation. This spatial and temporal gene atlas not only deepens our understanding of how trees rebuild their root systems but also offers new molecular tools for improving vegetative propagation in agriculture and forestry.

Spatial transcriptome analysis of adventitious root development

Plants have a remarkable ability to regenerate tissues and organs, a trait widely exploited in agriculture through cutting-based propagation. This process begins when injury signals trigger auxin synthesis at the wound site, initiating a cascade of genetic events that guide root development. Key genes like WOX11, WOX5, and LBD16 orchestrate these early transitions. Yet the spatial and temporal dynamics of hormonal signaling—particularly the role of cytokinin—and the precise cellular origins of adventitious roots remain unclear. Due to these unresolved questions, deeper insights into the spatial regulation and gene networks underlying root

In a study in Horticulture Research, scientists from Peking University Institute of Advanced Agricultural Sciences employed spatial transcriptomics to chart the gene activity driving root regeneration in poplar. Focusing on two pivotal stages of root development, they mapped how cells transition from cambium to root primordia.

To unravel the stages of poplar root regeneration, the research team collected time-series samples and conducted bulk RNA sequencing alongside spatial transcriptomics. They visualized how gene expression changed across four developmental stages and identified six distinct tissue clusters. In stages 2 and 3, the team observed that auxin-related genes concentrated in cambium cells, while cytokinin-responsive genes became highly enriched in root primordia—indicating tightly regulated hormonal zoning.

Strikingly, over 89% of cytokinin-responsive genes featured both AuxREs and WOXCEs in their promoters, suggesting a dual regulation by auxin and WOX11 transcription factors. Trajectory analysis traced how cambium-derived cells differentiated into root structures, revealing a clear path toward root primordia formation. Among the thousands of genes profiled, SAC56 and LOS1 stood out for their robust and localized expression patterns, confirmed through in situ hybridization. These two genes emerged as novel molecular markers for the regenerative root zone and may serve as targets for enhancing rooting ability in other plant species.

“This is the most detailed map of root regeneration we’ve seen in a woody plant,” said Prof. Bosheng Li, corresponding author of the study. “Our integration of spatial data with hormone-responsive gene mapping reveals how poplar orchestrates new root growth from injury. The discovery of SAC56 and LOS1 as root-specific markers opens new avenues for improving propagation, especially in species where rooting remains a bottleneck. It’s a powerful example of how plant cells rewire themselves at the molecular level.”

These insights carry significant implications for forestry, horticulture, and plant biotechnology. By decoding how poplars regenerate roots, the study provides new genetic tools to boost the success of cutting-based propagation. The spatial expression patterns of SAC56 and LOS1 could be harnessed to breed or engineer plants with stronger, faster root systems—key traits in drought resilience and biomass production. The open-access database generated by this research offers a valuable platform for exploring tissue-specific gene activity in other species. Ultimately, this knowledge bridges fundamental plant science with practical applications that could improve global reforestation and crop propagation efforts.

Source – Eurekalert