Nature Plants

Coumarins are phenylpropanoid-derived specialized metabolites that contribute to plant defence, shape plant-microbe interactions in the rhizosphere, and promote iron acquisition. In Arabidopsis thaliana, a model plant for iron-responsive coumarin metabolism, the enzymatic origin of the catecholic coumarin esculetin has long remained unresolved. Here we identify the first O-demethylation reaction in Arabidopsis specialized metabolism and show that 2-oxoglutarate- and Fe(II)-dependent dioxygenases catalyze scopoletin 6-O-demethylation to form esculetin. We designate these enzymes scopoletin 6-O-demethylases (S6ODs) and validate their activity through biochemical characterization, together with metabolomic profiling and independent loss-of-function mutant lines providing genetic evidence in planta. Disruption of S6OD activity remodels coumarin profiles and alters plant performance under limited iron availability, indicating that esculetin biosynthesis contributes to plant responses under these conditions. Our findings resolve the long-sought missing step in esculetin biosynthesis. It establishes O-demethylation as a previously unrecognized reaction in Arabidopsis specialized metabolism and suggest that 2OGD-mediated O-demethylation is recurrently recruited during evolution of plant metabolism, with implications for metabolic engineering and improvement of iron acquisition traits in crops.

Gibberellins (GAs) influence cell division and elongation, profoundly shaping plant architecture and yield. GA perception occurs when bioactive GAs bind the receptor GID1, promoting DELLA degradation and activating transcriptional programs. While GA signaling in the root endodermis is essential for promoting root elongation, functions of other layers in spatial control of GA responses have not been explored. Here, we developed a synthetic GA (sGA) that does not bind endogenous GID1, together with a modified GID1 (mGID1) engineered to selectively recognize sGA, enabling cell-specific activation of GA signaling in vivo. Using this system in Arabidopsis, we demonstrate that coordinated action of GA signaling in the endodermis, epidermis, and other layers is required for full root elongation. Moreover, cell type-specific expression of GA biosynthetic enzymes indicates the existence of intercellular GA transport. The sGA-mGID1 system provides a versatile platform for spatially precise reprogramming of hormone signaling, enabling synthetic control of developmental processes such as root-shoot growth balance, thereby advancing applications in plant synthetic biology and sustainable crop improvement.

Plant biology now publishes thousands of experimental research articles each year, but their core research logic, namely what questions are being asked, with what methods, and what is being found, remains locked inside free text and invisible to systematic analysis. Here we present a structured, 20-year atlas of The Plant Cell in which every paper is converted into a typed, directed Research Process Graph (RPG) of Question (Q), Method (M) and Finding (F) nodes connected by Q[->]M and M[->]F edges. A benchmarked large language model pipeline applied to 2,633 Plant Cell research articles published 2005-2026 recovered >110,000 Q/M/F nodes and >126,000 directed Q[->]M[->]F chains with>98% precision. A second LLM pass generalises each node into a paper-independent canonical form and assigns it to one of 10 top-level (L1) and [~]90 sub-level (L2) categories for each node type, producing the first comprehensive map of plant-biology research logic at the resolution of individual research questions. The atlas reveals that Plant Cell papers fall into seven canonical paper recipes with characteristic Q[->]M[->]F sub-structures, that peripheral experimental techniques have largely turned over while a stable methodological core persisted, and that the strongest correlate of per-PI citation impact is methodological breadth, not productivity or topical breadth. We release the atlas as a public, browsable database with five complementary interfaces: paper views, an LLM-powered research assistant, expert profiles, a taxonomy browser, and a method explorer. The database, available at https://rpg.connectome.tools/, turns the literature into a queryable community resource.

Agrobacterium-mediated transformation is the dominant method for plant transgenesis, yet it frequently produces multi-copy, structurally complex T-DNA insertions associated with transgene silencing, unpredictable expression, and genome instability. Here, leveraging a high-throughput phenotypic reporter, we systematically dissect how T-DNA vector architecture, plasmid biology, and regulatory element choice shape transformation outcomes in Arabidopsis thaliana. We discover a pronounced trade-off between transformation efficiency and T-DNA copy number, uncovering the virulence enhancing overdrive sequence as a major determinant of this relationship. Guided by these insights, we engineered a new T-DNA vector that balances efficient transformation with predominantly single-copy integration. Additionally, we replaced viral elements, such as the widely used CaMV 35S promoter, with Arabidopsis-derived regulatory elements to minimise undesired enhancer effects, and developed a streamlined workflow for efficient T-DNA insertion mapping in the genome. Together, these advances form the T1 vector series, an Arabidopsis-optimised T-DNA vector system that enables clean, single-copy, and readily mappable transgene integration with predictable expression in the first generation after transformation.

Plants comprise both cell types shared across organs and those restricted to specific tissues. How the transcriptional programs defining cell identity are maintained or remodeled across organ contexts remains poorly understood, particularly in long-lived perennials, for which cell type-resolved transcriptomic data remain scarce. We generated a multi-organ single-nucleus transcriptomic atlas of the dwarf grapevine cultivar Pixie, comprising over 220,000 nuclei from nine organs, including roots, green stems, pre-anthesis flowers, dormant buds, young and old leaves, and berries at three developmental stages, each sampled in duplicates. We annotated 46 distinct cell types, reconstructed developmental trajectories within selected cell types, and inferred gene regulatory networks at cell type resolution. Broadly distributed cell types, including epidermis, xylem parenchyma, and phloem parenchyma, exhibited pronounced organ-dependent transcriptional divergence, with organ identity accounting for 65% of regulon activity variance across the atlas. In contrast, companion cells maintained organ-independent regulatory programs, representing the stable end of a continuum of transcriptional plasticity that spans shared cell types. We identified cell-type-specific transcription factor expression and inferred gene regulatory networks using motif-based regulon analysis, revealing candidate regulators of cell identity and tissue specialization. Together, this atlas provides a reference framework for cell type-resolved functional genomics in a perennial woody crop.

Polyamines (PAs) are ubiquitous metabolites that, despite their simple structure, profoundly influence plant growth, development, and stress adaptation. Their cellular levels are largely determined by arginine decarboxylase (ADC), a key rate-limiting enzyme in their biosynthesis. We previously identified a [~]50 bp GC-rich sequence in the 5' untranslated region (UTR) of plant ADC genes, termed the ADC-box, that is conserved across land plants. Transient reporter assays in tomato, in which ADC upstream regions were decoupled from their native coding sequences and fused to reporter genes, suggested that this element represses translation. However, its function in the native genomic context and its impact on PA homeostasis remain unclear. Here, we combined CRISPR-Cas9 genome editing, metabolite profiling, enzymatic assays, and RNA structure probing to define ADC-box function in tomato and in the seedless land plant Marchantia polymorpha, which retains a conserved [~]20 bp core region. Mutation of the M. polymorpha ADC-box increased ADC activity and altered PA levels, indicating that the ADC-box functions as a conserved translational repressor. In tomato, disruption of the ADC-boxes in SlADC1 and SlADC2 increased ADC activity, demonstrating that the ADC-box acts as a translational repressor in its native context. These ehects were most pronounced under cold stress, when ADC transcript levels increase, suggesting that the ADC-box buhers stress-induced translation. Metabolically, ADC-box disruption led to agmatine accumulation and alterations in upstream intermediates, while downstream PA pools remained largely unchanged. SHAPE analysis revealed that the tomato ADC-box folds into a three-stem RNA structure, with a central stem representing the major inhibitory module. ADC-box mutants displayed altered plant-microbe interactions, with enhanced resistance to Pseudomonas syringae and Tobacco rattle virus, but increased susceptibility to Ralstonia solanacearum and Tomato yellow leaf curl virus. Together, these findings establish the ADC-box as an evolutionarily conserved cis-regulatory element that stabilizes PA homeostasis and modulates plant-microbe interactions.

Quantitative pollen viability analysis is a critical but labor-intensive step in plant reproductive biology. Existing deep-learning Segment Anything Models (SAM) fail to reliably segment viable pollen in Alexander-stained anthers. To address this, we fine-tuned an existing Cellpose-SAM model for pollen segmentation. We integrated it into PAT (Pollen Analysis Tool), a cross-platform desktop application. PAT features instance segmentation with interactive quality control, an in-app model retraining module, and publication-ready statistical outputs. We deployed PAT in an EMS suppressor screen of semi-sterile Arabidopsis smg7-6 mutants, enabling efficient candidate prioritization for whole genome sequencing and mapping candidate mutation. This screen led to the identification of a point mutation in CAP-D2 (capd2-2), a Condensin I subunit, that rescues the smg7-6 meiotic phenotype. Notably, mutation in a Condensin II subunits (CAP-D3 and CAP-H2) does not confer rescue. Further characterization suggests the capd2-2 allele is hypomorphic, showing no defects in vegetative growth, chromocenter compaction, or transposable element silencing. Collectively, we demonstrate that accessible AI tools have the potential to bridge gaps in plant phenotyping and accelerate the pace of biological discovery. HighlightWe combined AI-powered image analysis with an easy-to-use desktop app to automate plant pollen counting, then used it to identify a new genetic suppressor of meiotic defects.

C4 photosynthesis improves light, water and nitrogen-use efficiencies and can raise yield by 50% compared with the ancestral C3 pathway. Engineering C4 traits into C3 crops could substantially boost food production but requires coordinated modifications to leaf anatomy and cell-specific photosynthetic function. For example, C4 leaves contain more numerous, shorter bundle sheath cells that are photosynthetically active. In searching for transcriptional regulators of bundle sheath development in C3 rice, we unexpectedly found OSA3, a plasma membrane H+-ATPase that is expressed in bundle sheath cells as they elongate, and when knocked out reduces their length due to reduced apoplastic acidification. Bundle sheath cell number and chloroplast occupancy are increased. Thus, switching between C3 and C4 bundle sheath identity is controlled by acid growth, and OSA3 represents a simple tool for C4 engineering.

Ribosome stalling caused by polyproline (PPs) motifs is common. Their translation is enhanced by accessory proteins such as YebC in bacteria, whose homolog, TRANSLATIONAL ACTIVATOR OF CYTOCHROME C OXIDASE 1 (TACO1), aids the translation of mitochondria-encoded proteins. The prevalence of PP motifs across plastid-encoded genes and their impact on the translation of photosynthesis-relevant proteins remains unexplored. Equally, a translation-enhancer of PP motifs equivalent to TACO1 for plastid ribosomes has not been reported. Here, we show that plastid genomes encode 24 proteins with a minimum of one PP motif on average, half of which are conserved in their cyanobacterial homologs, and that the vast majority of eukaryotes, including plants, encode a single TACO1 that we demonstrate to be dually targeted to mitochondria and plastids of Marchantia polymorpha. We resolved the MpTACO1 structure at 2.34 [A] by X-ray crystallography and the flexibility by small-angle X-ray scattering. Through modelling, we demonstrate that MpTACO1 can fit into the peptidyl transfer centre of plant chlororibosomes in a similar manner as human TACO1 in the mitoribosome. The identification and structure determination of the first plastid-targeted YebC/TACO1 allows us to sketch a unified model for the function and evolution of this ancient family of ribosomal accessory proteins, underscoring their indispensable role in the translation of bioenergetic membrane proteins reaching back almost 4 billion years. HighlightsO_LIDozens of GC-rich polyproline (PP) encoding regions are retained by AT-rich genomes C_LIO_LIPP motif conservation hints at regulatory mechanisms and required translation pauses C_LIO_LIChloroplast targeting of a (mitochondrial) translation enhancer of PP motifs C_LIO_LIMpTACO1 structure at 2.34 [A] resolution demonstrates its high level of conservation C_LI

Polyacetylene glycosides exhibit notable pharmacological activities, yet the glycosyltransferases acting on their polyacetylene scaffolds remain unknown. Here we report a telomere-to-telomere genome assembly of Codonopsis pilosula and, guided by spatial metabolomics, characterize three UDP-glycosyltransferases: CpUGT76BG1 and CpUGT76BG2 catalyze the direct glycosylation of lobetyol to lobetyolin, while CpUGT94BY2 performs subsequent sugar-sugar coupling to produce lobetyolinin, with each activity confirmed by in planta overexpression. Structural modeling reveals that CpUGT76BG1 and CpUGT76BG2 employ a deep hydrophobic tunnel to fully encase the linear polyacetylene chain, a binding architecture distinct from the shallow pockets used by canonical plant UGTs for planar aromatic substrates. Ancestral sequence reconstruction across eleven nodes partitions the UGT76 lineage into three functionally distinct evolutionary stages, tracing the trajectory from an ancestral shallow pocket to this specialized deep architecture. These findings establish the key glycosylation steps of polyacetylene glycoside biosynthesis, define a tunnel-based paradigm for non-planar substrate recognition, and reveal how tandem duplication-driven active site remodeling generates metabolic novelty.

A central question in plant biology is whether natural transcriptome variation primarily reflects environmental adaptation or intrinsic genetic programs. Using transcriptomes from 665 natural Arabidopsis thaliana accessions, we show that inherited population structure, not environmental gradients, is the primary organizer of global transcriptome architecture. Genomic population structure uniquely explains 30.0% of transcriptome-wide variation, while environmental variables account for only 2.5%. This architecture is dominated by a single co-expression program (proliferation Module Eigengene: prolifME), enriched for cell cycle regulation and ribosome biogenesis, regulated by a bipartite transcription factor architecture, and genetically encoded at discrete loci with broad trans-regulatory effects. This proliferation program is associated with reduced plant size, biomass, growth rate and water-use efficiency, and these relationships persist under common-garden conditions. Gene contributions to this proliferation program are non-randomly conserved in rice and maize across 150-200 million years of divergence. These findings identify an intrinsic transcriptional proliferation program as a primary state of plant population transcriptomes, conserved across plant species.

The medicinal herb Panax notoginseng produces a structurally diverse array of triterpene saponins (ginsenosides), yet the genetic basis of this chemical complexity remains unclear. Here we present a high-quality chromosome-level genome of diploid P. notoginseng and integrate comparative genomics with multi-tissue, multi-year metabolomics and transcriptomics. Surprisingly, unlike tetraploid Panax species, P. notoginseng shows no general expansion of core saponin biosynthetic gene families. Instead, lineage-specific diversification of UDP-glycosyltransferase (UGT) families, a recent burst of LTR retrotransposons, and enrichment of species-specific genes in metabolic modification pathways point to an alternative evolutionary route. Saponin accumulation follows strict spatiotemporal compartmentalisation, and co-expression network analysis reveals that the biosynthetic machinery is not static but continuously rewired during development-from a basic synthesis module in the first year to a modular pattern supporting both broad accumulation and branch-specific modification by the third year. Seventeen differentially expressed UGTs show clear tissue preferences and saponin-branch correlations. As a representative example, PnUGT33 is tightly linked to the PPD-type saponin branch; structural modelling, molecular docking and 100 ns molecular dynamics simulations demonstrate its differential recognition of diverse triterpene skeletons. Collectively, our findings establish that ginsenoside diversity in diploid P. notoginseng arises primarily from UGT lineage diversification, developmentally rewired regulatory networks and UGT mediated branch selective post-modification, rather than from expansion of core pathway genes. This work provides a new paradigm for understanding how plants achieve metabolic complexity without whole genome duplication or massive gene amplification.

The nitrogen-fixing root-nodule symbiosis provides a sustainable source of nitrogen for plants within the Nitrogen (N)-fixing clade (NFC). A debate has raged over whether nodulation evolved once, with many losses or multiple times following a predisposition event. Here we demonstrate that nodule-organogenesis is fully conserved between an actinorhizal nodulator Datisca glomerata and the legume Medicago truncatula, showing entirely conserved programmes for Nodule INception (NIN)-controlled development leading to nodule emergence. Convergent losses of N-fixation within the NFC is associated with loss of NIN and we show the engineering of nodule-like development into strawberry, a non-nodulating member of the NFC, through the repair of NIN-functionality. Similar NIN-engineering resulted in altered-root developmental responses in barley. Our work is consistent with the single-gain hypothesis, where repair of NIN can recapitulate nodules in species within the NFC, demonstrating that understanding the ancestral state of nodulation facilitates its engineering.

Reported CRISPR/SpCas9 editing efficiencies in crops span 0-100%, but no quantitative synthesis has separated taxonomic family from delivery method, ploidy, clustering or publication bias. This meta-analysis estimated pooled per-T0-line editing efficiency across Cucurbitaceae, Brassicaceae, Solanaceae and Poaceae, and tested whether family is an independent moderator after adjustment for delivery and ploidy. A PRISMA 2020 systematic review identified peer-reviewed studies using SpCas9 with extractable per-line T0 edit counts; data were extracted independently by two reviewers, with inter-rater agreement reported. Logit proportions were synthesised with a binomial-normal generalised linear mixed model, and the family-as-moderator hypothesis was tested by a small-sample CR2 cluster-robust F-test on a three-level model with study-level clustering. Publication bias was assessed by Eggers regression and trim-and-fill. Twenty-two studies contributed 172 per-line effect sizes (Cucurbitaceae k=14, Brassicaceae k=20, Solanaceae k=68, Poaceae k=70). Pooled editing efficiency was 61.8% (95% CI 54.5-68.6%) with I{superscript 2}=93.4% ({tau}{superscript 2}=3.21) and a 95% prediction interval of approximately 5-98%. Per-family estimates ranged from 47.8% (Poaceae) to 73.8% (Brassicaceae); the univariate Q test was significant (p=0.0016), but family did not survive cluster-robust adjustment (F=0.73, p=0.63). Intraclass correlation placed 64.4% of variance at the study level, and Solanaceae remained dominated by a single study (58/68 rows). Funnel asymmetry was severe (Egger p<0.0001), and trim-and-fill reduced the bias-adjusted estimate to 45.2% (95% CI 39.0-51.5%). Apparent crop-family differences dissolve once within-study clustering and methodological covariates are accounted for; the bias-adjusted pooled estimate is closer to 45% than to 62%, and reported editing efficiencies reflect study-level factors more than taxonomic family. Key MessageApparent between-family differences in CRISPR/SpCas9 editing efficiency across four crop families reflect within-study clustering and publication bias, not intrinsic biology; family is not an independent moderator after cluster-robust adjustment.

The inflorescence stem of Arabidopsis thaliana is a powerful model to study vascular development and carbon allocation, yet the translational landscape underlying xylem differentiation remains poorly defined. Here, we address this gap using tissue-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) to resolve the translatomes of xylem vessels, xylem parenchyma, and interfascicular fibers. We show that the very early stage of metaxylem differentiation involves coordinated activation of primary metabolism, plastid functions, and cell wall biosynthesis, supporting the metabolic demands of secondary wall formation. Xylem parenchyma displays enrichment in hormone signaling, stress, and immune pathways, consistent with a role in integrating environmental and metabolic cues. Interfascicular fibers exhibit increased translation of ribosomal proteins and spliceosome components, pointing to high translational activity and a role for alternative splicing during late development and programmed cell death. We further identify the tonoplast sugar transporter SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 2 (SWEET2) as a key regulator of stem radial growth. Preferentially translated in early stage of metaxylem differentiation, SWEET2 acts as a rate-limiting component of vacuolar sugar exchange, controlling cytosolic hexose availability for secondary wall biosynthesis. By contrast, SWEET16 and SWEET17 exert more specialized, tissue-specific functions. Together, our findings establish subcellular sugar partitioning as a central determinant of vascular development and highlight the power of translatome profiling.

The transition from combined to separate sexes in plants drives genomic change, from recombination suppression at sex-determining loci to shifts in selection across autosomes and cytoplasmic genomes. In Amaranthus, a genus that includes ancient grain crops and noxious weeds, separate sexes arose twice through non-homologous sex-determining architectures, with at least one reversion to monoecy, yet plastid and mitochondrial phylogenies group the two dioecious lineages together despite independent origins. The source of this discordance and whether independent origins of dioecy produced parallel or lineage-specific genomic responses remain unknown. We sampled nuclear, plastid, and mitochondrial genomes across 19 species, resolving the backbone phylogeny of the genus and dating the crown to 2-5 Ma. Coalescent simulations rejected incomplete lineage sorting in favor of multiple organelle capture events, implying historical exchange across reproductive barriers separating the two dioecious clades. Nuclear allele sharing was concentrated within each dioecious clade rather than between them, consistent with recombination eroding nuclear donor ancestry while captured cytoplasmic genomes persist. Dioecy was associated with genome-wide shifts in selection intensity, with positive selection concentrated on the stems of each dioecious clade but targeting largely non-overlapping genes and leaving little signature within sex-determining regions. Plastid coding sequences evolved under relaxed purifying selection, and nuclear-encoded plastid-targeted genes were enriched for episodic positive selection, consistent with compensatory cytonuclear evolution. The probable reversion to monoecy in A. pumilus, within a lineage shaped by repeated organelle capture, raises the possibility that hybridization and the lability of separate sexes are connected in this group.

Cytokinin ribosides are major mobile and precursor forms of cytokinins, but the mechanisms that control their intracellular availability remain poorly understood. Here, we identify Arabidopsis thaliana EQUILIBRATIVE NUCLEOSIDE TRANSPORTER1 (ENT1) as a tonoplast-localized cytokinin riboside transporter that gates intracellular cytokinin riboside homeostasis. ENT1 transported trans-zeatin riboside and isopentenyladenosine, but not the corresponding free bases, and mutational analysis combined with molecular docking identified residues required for riboside recognition and discrimination from nucleobases. A functional internally tagged reporter resolved previous ambiguity in ENT1 localization, showing predominant tonoplast association under native-like conditions and enrichment in epidermal and other outer root tissues. Increasing ENT1 abundance enhanced plant sensitivity specifically to cytokinin ribosides and elevated cytokinin signalling output, while radiotracer assays supported a role for ENT1 in cytokinin riboside accumulation in roots. Conversely, loss of ENT1 did not cause a pronounced developmental phenotype under standard conditions, but reconfigured tissue-specific profiles of adenosine and cytokinin riboside-related metabolites, with the strongest effects on cis-zeatin-type and riboside O-glucosylated cytokinin pools. ENT1 function became physiologically apparent during plant-microbe interactions, where ent1 mutants showed reduced beneficial microbe-associated protection against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000. These findings reveal a vacuolar gatekeeping mechanism that controls intracellular cytokinin riboside availability and links cytokinin riboside homeostasis to beneficial microbe-associated defence outputs.

Plasmodesmata are intercellular channels that mediate symplastic communication between plant cells. Molecular transport through these channels is critically regulated by dynamic callose deposition and degradation, yet the secretory mechanisms that deliver regulatory components to plasmodesmata remain poorly understood. Here, we identify and characterize a non-canonical plasmodesmata-associated module of the exocyst, an evolutionarily conserved protein complex involved in secretory vesicle tethering and exocytosis. Exocyst subunits EXO70G1, SEC15A, EXO84C, and SEC10A specifically accumulate at plasmodesmata, whereas the canonical exocyst subunits EXO70A1 and SEC8 do not. Genetic and interaction analyses show that EXO70G1 acts as a landmark for recruiting SEC15A and EXO84C to plasmodesmata, revealing a distinct mode of exocyst targeting at these membrane domains. EXO70G1-dependent exocyst targeting to plasmodesmata depends on phosphoinositides and sphingolipids, consistent with the specialized lipid environment of plasmodesmal membranes. Loss of EXO70G1 results in increased callose accumulation and reduced symplastic transport, and strongly enhances developmental defects of a callose-overproducing mutant. In addition, exo70G1 mutants display enhanced resistance to bacterial pathogen Pseudomonas syringae, linking reduced plasmodesmal permeability to anti-bacterial defense. Cross-species analysis further indicates that plasmodesmata association is a derived feature of the EXO70G clade, present in angiosperms but absent from non-angiosperm EXO70 homologs. Together, our findings show that exocyst diversification in plants has generated a specialized trafficking module - plasmodesmata-associated exocyst - that links vesicle delivery to callose homeostasis at plasmodesmata, thereby regulating intercellular communication, development, and immunity. TeaserA specialized secretion module of the exocyst complex regulates plant cell-to-cell connectivity by controlling callose turnover at plasmodesmata

Nitrate induces widespread transcriptional reprogramming in plants, but how transcription factors coordinate these responses across cell types and evolve across species with divergent root patterning remains unclear. Using single-cell transcriptomics in Arabidopsis thaliana and Solanum lycopersicum (tomato) under varying nitrate conditions, we demonstrate that many transcriptional responses are cell type and developmental stage-specific. Arabidopsis NIN-LIKE PROTEIN 7 (NLP7) directly modulates both broadly expressed and cell-type-specific targets, but is not required to establish the cell type specific nature of these patterns. Comparative analysis reveals evolutionary shifts; key nitrogen programs are localized to different cell types in tomato, with the exodermis as a major regulatory hub. Identification of tomato NLP7a and NLP7b direct targets at cellular resolution supports their role in direct modulation of cell type N-transcriptional programs. This is evidenced by NLP7-controlled exodermal cell wall remodeling in low nitrate, highlighting functional conservation despite divergent cellular topographies.

Integrating spatial morphogens with temporal developmental clocks is fundamental to optimizing plant architecture and crop yield, yet their molecular interface remains elusive. Here, we characterize Branched shoot 1 (Bsh1), a semi-dominant wheat mutant exhibiting non-canonical upper-aerial branching and aberrant spike development, caused by a T265I substitution in the DNA-binding domain of the auxin response factor TaARF4-A2. Unlike flanking mutations governing protein stability in basal land plants, this central substitution uniquely converts TaARF4-A2 into an auxin-insensitive hypermorphic repressor. The mutant protein disrupts auxin-cytokinin homeostasis and markedly enhances the native repression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, the core timers of developmental phase transitions. This spatial and temporal uncoupling unleashes upper axillary buds from dormancy, promoting aerial branching and diverting resources from reproductive development. Our findings demonstrate how a conserved spatial morphogen effector was evolutionarily rewired in polyploid wheat to dictate the temporal SPL clock, orchestrating species-specific shoot architectural innovation.