Zinc deficiency induces spatially distinct responses in roots and impacts ZIP12-dependent zinc homeostasis in Arabidopsis

How zinc (Zn) deficiency shapes root development remains unclear, with conflicting reports on its effect on primary root growth in Arabidopsis thaliana (Arabidopsis). The impact of Zn shortage on the root apical meristem (RAM) in particular has not been systematically explored. Using an integrative approach combining cell biology, transcriptomics, and ionomics, we dissected how Zn deficiency alters root zonation and function. We showed that Zn deficiency triggers a striking reorganization of the root tip (RT): the RAM size is reduced, yet meristematic activity and local Zn levels are preserved. This is accompanied by promoted cell elongation and differentiation. Transcriptome profiling revealed a distinct Zn deficiency response in the RAM-enriched RT compared to mature root tissues, with ZIP12 emerging as the most strongly induced gene in the RT. Functional analysis of zip12 mutants uncovered major defects in root growth, RAM structure, expression of Zn-responsive genes, and metal partitioning. Our work unveiled a new layer of root developmental plasticity under Zn deficiency and identified ZIP12 as a central player in maintaining Zn homeostasis and root meristem function in Arabidopsis. These findings provide a framework to better understand how plants adapt root growth to fluctuating micronutrient availability.