Comparative transcriptome analysis of maize root tips and whole roots in response to iron deficiency

Transcriptomic studies investigating root responses to iron (Fe) deficiency have typically used entire underground root systems or mixed whole-root samples, which can dilute the strong transcriptional signals originating from root tips. To uncover the spatially resolved transcriptomic features of Fe deficiency responses in maize primary roots and elucidate the spatial division of labor in Fe uptake and homeostasis, we employed the maize inbred line B73. Seedlings at the three-leaf stage were grown under control (25 μmol L-1 Fe-EDTA) or Fe-deficient (0 μmol L-1 Fe-EDTA) conditions. RNA sequencing (RNA-seq) was performed on root tips (0-2 cm) and whole primary roots. An integrated analysis—including differentially expressed genes (DEGs), multi-level gene function enrichment, weighted gene co-expression network analysis (WGCNA), and qRT-PCR validation—was used to systematically compare the molecular mechanisms of Fe deficiency responses between root tips and whole roots. A total of 4206 DEGs (2450 upregulated) were identified in root tips, substantially more than the 325 DEGs (84 upregulated) found in whole roots, highlighting root tips as the key region for Fe sensing and response. Functional enrichment analysis revealed that root tips primarily activated metabolic pathways such as ribosome assembly and the TCA cycle, while whole roots were significantly enriched in processes including lignin biosynthesis and antioxidant defense. Several secondary metabolite biosynthesis pathways—including phenylpropanoid biosynthesis, various plant secondary metabolite biosynthesis, and flavonoid biosynthesis—were enriched in distinct root regions, suggesting diverse roles of secondary metabolites in Fe homeostasis. Genes involved in siderophore biosynthesis were specifically induced in root tips, supporting the synthesis of mugineic acids (MAs), the main phytosiderophores (PS) in grasses, and subsequent Fe chelation. Key transporter genes, such as natural resistance-associated macrophage protein 2 (NRAMP2) and yellow stripe-like protein 12 (YSL12), were predominantly expressed and upregulated in whole roots, facilitating Fe translocation within the plant. Additionally, several bHLH family transcription factors, known regulators of Fe homeostasis, were highly expressed in whole roots, indicating their potential role in coordinating Fe uptake and redistribution. This study delineates the spatially partitioned transcriptional landscape of Fe deficiency responses in primary roots, revealing a strategy in which root tips dominate PS biosynthesis, while whole roots coordinate Fe transport and systemic defense. The identification of spatially specific genes and pathways provides new insights into the molecular mechanisms underlying maize root adaptation to Fe deficiency stress.