Single-cell transcriptional decoding of iron deficiency responses in maize root tips

Abstract

Maize roots respond to iron stress through cell type specificity and enhanced radial transport of Fe-DMA in root cells. Iron (Fe) deficiency, resulting from low Fe solubility in aerated soils, represents a major constraint for crop productivity. Maize (Zea mays), a Strategy II plant, acquires Fe through phytosiderophore (PS)-mediated chelation of rhizospheric Fe (III) and subsequent uptake of Fe (III)-PS complexes. However, cell-type-specific responses governing this process under Fe deficiency remain uncharacterized. Leveraging single-cell RNA sequencing (scRNA-seq), we constructed a root tip atlas using 15,306 high-quality cells from V3 stage primary roots under Fe-sufficient and Fe-deficient conditions, resolving seven distinct cell types. Under iron deficiency stress, significant changes were observed in the cell populations of cortex, epidermis, stele, and xylem. The cortex undergoes functional reprogramming following iron deficiency, with heme-binding and glutathione metabolism-related genes playing crucial roles in the iron deficiency response. Expression analysis of iron homeostasis genes revealed that iron-deficient root tips are associated with the biosynthesis of nicotianamine (NA) and 2'-deoxymugineic acid (DMA) and facilitated radial Fe-chelator transport. Notably, both scRNA-seq and bulk RNA-seq data revealed the downregulation of a FER-like iron deficiency-induced transcription factor (FIT) gene homologous to Arabidopsis AtFIT. This contrasts with the well-established role of AtFIT in Arabidopsis, where it acts as a positive regulator under iron-deficient conditions. Phylogenetic analysis suggests that AtFIT, OsFIT, and ZmFIT may share conserved functions, while their divergent expression patterns could be associated with differences between monocots and dicots. Through weighted gene co-expression network analysis (WGCNA), we identified cell-type-specific co-expression modules for the cortex, stele, epidermis, and xylem. The stele-specific module was significantly enriched with transcription factors, suggesting its role as a transcriptional regulatory hub for the iron deficiency response. Protein-protein interaction (PPI) network analysis revealed that core regulatory transcription factors (ZmWRKY76, ZmbHLH49, ZmMKK9) were distributed across various cell types including epidermis, xylem, phloem, and lateral root cap, indicating that the iron deficiency response is coordinated by a distributed regulatory network where the stele integrates signals and different cell types execute specific functions. In this study, we constructed a transcription map of iron-deficient maize root tips at single-cell resolution, uncovering fundamental adaptation strategies and potential targets for enhancing crop Fe efficiency.

Keywords: Cellular heterogeneity; Fe efficiency; Single-cell RNA sequencing; Transcriptional regulation.