Chromatin Organization and Nuclear Architecture as Indicators of Plant Cell Developmental Competence

Plant cell totipotency is a fundamental property of the plant kingdom. Although most plant cells contain essentially identical genetic information, only a subset retains the ability to re-enter the cell cycle, and even fewer keep the ability to regenerate whole plants. One possible explanation is that cells differ in their chromatin organization. Here, we investigated whether 3D nuclear architecture reflected cell-cycle probability and cell-cycle re-entry and totipotent reprogramming. Using confocal profiling across root tissue layers (n = 50 nuclei/layer; N ≥ 3 biological replicates) and root protoplast microcultures of Arabidopsis thaliana and Medicago sativa, we show that nuclear geometry serves as a quantifiable physical proxy(marker/indicator) for cell permissiveness. In A. thaliana, non-competent cortical cells face a steep ~78% nuclear volume reduction barrier (>10,000 µm3 to ~2500 µm3), restricting cell-cycle entry (0%). In M. sativa, shallower structural gradients allow cortical cells to divide (>70%), yielding non-regenerative callus. Conversely, pericycle cells maintaining compact nuclear states retain shoot organogenesis (>35%). Uncoupling tissue constraints confirms that cell-cycle re-entry and true totipotency represent two distinct biophysical transitions. Re-establishing whole plants strictly requires transitioning to a low-entropy 3D nuclear state, establishing baseline nuclear geometry as a non-invasive physical indicator of developmental competence. These findings establish baseline nuclear geometry as a non-invasive morphological indicator to distinguish vegetative proliferation from true regenerative competence.