It is demonstrated that inorganic fertilization induced stress associated and management pathways and soil metagenomic analysis showed that host soil microbial functions overlap with differentially expressed genes (DEGs) in shared functional categories, linking host regulome dynamics to rhizosphere processes.
Abstract
Improving nitrogen use efficiency in maize (Zea mays) requires understanding how distinct root cell types and regulatory networks process fertilizer inputs. Given the current limited understanding of fertilizer-induced, cell-type-resolved maize roots and regulatory networks, computational biology frameworks are needed to model and predict how nutrient inputs are translated into transcriptional responses. Here, we integrated fertilizer-induced maize root bulk RNA-seq with reference atlases of single-cell RNA-seq and scATAC-seq to construct and predict a cell-specific regulome of the maize root under inorganic and mixed amendments. We demonstrate that inorganic fertilization induced stress associated and management pathways. Regulome analysis identified transcription factors (TF) from the AP2/ERF, NAC, HSF, and WRKY superfamilies that were preferentially active across root tissues. Deconvolution of the regulome onto single-cell atlases predicted core TF activity to the vascular cylinder and pith across both regimes, while mature cortex regulatory programs diverged. Construction of a gene regulatory network revealed that shared TF–target edges maintained the same regulatory orientation across fertilizer regimes. However, a small number of stress related TFs, including WRKY24, DREB1A, and NAC61, underwent a directional change between fertilization treatments. In silico knockout analysis predicted the activation targets for six of the seven regulators in their resident vascular/pith tissues, indicating the network behaves as a coherent, perturbable system. Additionally, soil metagenomic analysis showed that host soil microbial functions overlap with differentially expressed genes (DEGs) in shared functional categories, linking host regulome dynamics to rhizosphere processes. These findings and predictions suggest that the maize root regulome is spatially organized and dynamically reprogrammed by master regulators, predicting high-priority candidate nodes for engineering improved nutrient use efficiency.
ABSTRACT The legume crop soybean forms a symbiosis with rhizobia to fix atmospheric nitrogen (N) in specialized organs called root nodules. However, the mechanisms regulating early infection of the root epidermis and nodule‐primordium formation in the cortex for proper nodule formation remain unclear in soybean. Here, we report a single‐cell transcriptome analysis of mock‐ and rhizobia‐inoculated soybean roots at 4 days after inoculation, an important control point for autoregulation of nodulation and nodule‐primordium formation. We profiled 21,500 cells and detected 12 major cell clusters, and identified 193 infected‐cell‐specific, 205 epidermis‐specific and 180 cortex‐specific DEGs. Gene‐ontology enrichment and gene‐regulatory network analyses uncovered key pathways such as reactive oxygen species‐mediated hormone signaling involved in coordinating defense signaling and symbiotic pathways. We also identified and functionally validated an ethylene‐activated circuit comprising GmWRKY6.3/6.4 transcription factors and select downstream GmNod19 targets, in which genes act as positive regulators by promoting infection‐thread formation during early nodulation, thereby shaping nodule formation. This study showcases how single‐cell transcriptomics and gene‐regulatory networks provide hypotheses for identification and characterization of previously unappreciated regulatory circuits, broadens our understanding of precise genetic control underlying symbiosis establishment, and underscores how functional diversification of nodulation genes has occurred across legumes.
Yongbin Zhuang, Yu Geng, Xinyue Guo et al.· Advancement of science· 0 citations
It is demonstrated that heterologous expression of TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively, which enhances the tolerance of Arabidopsis to salt and osmotic stress.
Jinxian Chen, Wenhao Wu, Ming-Hua Luo et al.· Phytochemistry· 0 citations
Cereal crops collectively account for more than half of global human caloric intake, yet the molecular mechanisms governing their root systems under water and nitrogen limitation remain poorly understood relative to their agronomic importance. The C-terminally encoded peptide (CEP) family has emerged, primarily from work in Arabidopsis thaliana and Medicago truncatula, as a class of post-translationally modified peptide hormones that coordinate nitrogen demand signalling through a root-to-shoot-to-root relay involving CEPR1 leucine-rich repeat receptor-like kinases and phloem-mobile CEPD glutaredoxins, regulate lateral root gravitropic set-point angle through integrated auxin and cytokinin pathway interactions, and contribute to abiotic stress responses through stabilisation of AUX/IAA transcriptional repressors under osmotic stress. This review synthesises CEP biology with the specific architectural and agronomic characteristics of cereal root systems, explicitly distinguishing between findings established in model dicots, evidence for receptor-ligand conservation in cereals, and mechanisms that remain untested in crops. CEPR1 orthologues in barley, maize, and rice restore wild-type phenotypes in Arabidopsis complementation assays, and CRISPR-Cas9 knockout of CEPR1 in barley confirms effects on seminal root angle, though an associated fecundity defect highlights translational complexity. Proposed connections between CEP signalling and ABA pathways remain hypothetical. In wheat, TaCEP15 modulates primary root length and drought tolerance through a receptor pathway mechanistically distinct from the canonical CEP-CEPR1-CEPD nitrogen relay, indicating functional diversification within the CEP family. Five tractable research priorities are identified, and CRISPR-based approaches, synthetic peptide application, and marker-assisted selection are discussed as near-term strategies for cereal crop improvement under drought and nitrogen-limited conditions.
Baber Ali, Zeeshan Khan, N. Imin· Plant, Cell and Environment· 2 citations
Gleditsia sinensis
Lam. is a widely distributed tree species in China characterized by its remarkable tolerance to barrenness and salinity, making it a valuable candidate for the ecological restoration of saline-alkali lands. Understanding its ion regulatory mechanisms is a prerequisite for salt tolerance evaluation and molecular breeding. However, the molecular mechanisms coordinating root ion fluxes and overall defense strategies in
G. sinensis
under salt stress remain largely unclear. In this study, we investigated the root ion flux characteristics and underlying molecular mechanisms of hydroponic
G. sinensis
seedlings under 100 mmol·L⁻¹ NaCl stress using non-invasive micro-test technology (NMT) and transcriptomic sequencing. The results demonstrated that while salt stress induced substantial Na⁺ accumulation, roots actively responded by promoting Na⁺ efflux and H⁺ influx in the elongation zone. Transcriptomic analysis revealed that seedlings adopted a “growth-defense trade-off” strategy. By down-regulating energy-intensive metabolic pathways, the seedlings reallocated limited energy to significantly up-regulate key ion transporters, including
AHA11
,
AKT1
, and
SKOR
. This transcriptional reprogramming established a transmembrane proton gradient that drove effective Na⁺ efflux and maintained intracellular K⁺ homeostasis. These findings provide a theoretical basis and genetic resources for targeted molecular breeding of
G. sinensis
in saline environments.
