Toughbranching: Discovering how root branching is affected in compacted soil

Soil compaction is a major constraint on root growth, reducing lateral root branching and limiting plant access to water and nutrients. While the physical effects of compaction are well documented, the hormonal and genetic mechanisms underlying root responses—particularly lateral root branching—remain largely unexplored. Auxin is a central regulator of lateral root development, but how auxin signaling interacts with mechanical stress to influence branching is not well understood. To address this, I will use state-of-the-art high-resolution X-ray computed tomography (X-ray CT) to examine how lateral root branching is altered as roots grow across compacted soil zones. This approach mimics natural field conditions, where roots encounter heterogeneous soil with randomly present compacted and non-compacted regions.The host lab has made groundbreaking discoveries showing that ethylene accumulation in compacted soil triggers a cascade of signaling events that modulate ABA and auxin signaling to reshape root growth. Recently, the lab published a single-cell transcriptomic analysis of rice roots grown in compacted and non-compacted soils in Nature journal, identifying key auxin signaling genes induced by soil compaction in the pericyle cells from where lateral root development initiates. Building on these findings, I will investigate whether these genes are also involved in regulating lateral root branching under soil compaction. To uncover cell-specific gene expression changes associated with this process, I will apply spatial transcriptomics, enabling the identification of novel genes and pathways that control lateral root development under mechanical stress. This integrated approach will advance our understanding of root branching plasticity in response to soil compaction and contribute to strategies for breeding crops with improved resilience to challenging soil conditions.