Plant grafting is a significant horticultural technique that enables the combination of desirable traits such as enhanced resilience, disease resistance, and productivity. Despite its widespread application, the mechanisms underlying graft compatibility remain poorly understood. Because grafting is largely an anthropogenic process, plants are unlikely to have evolved mechanisms specifically to recognize graft partners. Here, we propose that graft compatibility is not controlled by a dedicated recognition system, but instead emerges from the balance between existing tissue regeneration and immune surveillance pathways that evolved in other plant-plant interactions. We synthesize evidence from inter-plant communication, parasitic interactions, and damage-associated molecular pattern signaling (DAMPs) to show that these systems converge on conserved mechanisms regulating non-self perception, tissue regeneration, and long-distance communication. This evolutionary framework explains diverse observations across graft biology and provides a foundation for developing strategies to expand graft compatibility across economically important crops.

Abstract Graft incompatibility limits the combination of scions and rootstocks, yet the signals that block vascular reconnection remain poorly understood. Using incompatible tomato-pepper ( Solanum lycopersicum-Capsicum annuum ) grafts, we found that salicylic acid (SA) overaccumulates at the graft junction, predominantly in the rootstock, while incompatible scions exhibit enhanced pattern-triggered immunity. SA-deficient nahG- expressing tomato failed to rescue incompatibility and instead showed severely impaired self-graft healing, indicating that successful tissue reunion requires an optimal, rather than minimal, SA response. Defense-associated genes remained activated in failed grafts regardless of SA accumulation, placing SA downstream of incompatibility determination. Exogenous SA application phenocopied incompatibility, blocking xylem reconnection, inducing cell death, and suppressing auxin signaling. Incompatible grafts similarly displayed reduced auxin accumulation and response at the graft junction. Exogenous auxin partially rescued xylem reconnection in incompatible grafts but failed to activate cambial regulator genes or fully restore compatibility. We propose that graft compatibility depends on SA-auxin homeostasis, where moderate SA supports wound-associated defense and regeneration, whereas excessive SA suppresses the auxin-dependent program required for xylem differentiation. These findings identify SA as a dose-dependent regulator of graft healing in tomato and link excessive immune activation to failed vascular regeneration.

Arbuscular mycorrhizal fungi (AMF) and dark septate endophytic fungi (DSE) are pivotal root-associated microbes that promote plant growth and nutrient acquisition. Despite their ecological importance, the interactive mechanism underlying their relationship remains unclear. This study investigated the individual and combined effects of AMF (Rhizophagus irregularis) and Falciphora oryzae (FO, a DSE strain) on pepper (Capsicum annuum) growth, nutrient accumulation, and microbial communities across rhizosphere compartments. The results showed that co-inoculation of AMF and FO significantly increased the AMF root colonization rate while inhibiting FO colonization. All inoculation treatments significantly improved plant height, biomass, and nutrient uptake, with AMF + FO co-inoculation showing the most pronounced effects. While FO alone enriched soil nutrients, including nitrogen, phosphorus, and potassium, it was less efficient than AMF in facilitating plant nutrient uptake. Notably, the AMF + FO combination significantly increased nitrogen uptake in both roots and leaves compared to single inoculations. Microbiome analysis revealed a significant decline in microbial diversity and abundance closer to the internal root tissues. The AMF + FO combination specifically enriched microbial communities with nitrogen-fixing taxa such as Methyloversatilis and Paenibacillus, which correlated positively with soil and root nitrogen levels. In conclusion, the co-inoculation of AMF and FO significantly enhanced nitrogen uptake by improving soil nutrient status and enriching the microbial community, offering a novel strategy for improving crop nitrogen use efficiency.

Abstract Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea , we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

INTRODUCTION:Arbuscular mycorrhizal symbiosis (AMS) is a universal mutualism in natural ecosystems, governed by a complex transcriptional network. Although ethylene response factors (ERFs) are implicated in regulating AMS, their underlying molecular mechanisms remain poorly understood. OBJECTIVE:This study aims to investigate the molecular mechanism by which ethylene response factor 15 (SlERF15) regulates AMS and phosphate uptake in tomato (Solanum lycopersicum). METHODS:We used tomato loss‑of‑function mutants (erf15#1 and erf15#3), liquid chromatography-tandem mass spectrometry (LC-MS/MS), RT-qPCR, electrophoretic mobility shift assay, yeast one-hybrid assay, and dual-luciferase assays to unveil the molecular basis of SlERF15-mediated AMS and phosphate uptake in tomato. RESULTS:SlERF15 expression was significantly up-regulated in tomato roots during the initial stage of AMS. Mutants lacking the SlERF15 gene exhibited a substantial reduction in arbuscular mycorrhizal fungi (AMF) colonization, phosphate uptake, and plant growth. Strigolactones (SLs) and abscisic acid (ABA), which serve as positive regulators of AMS establishment, showed reduced accumulation in the mycorrhizal roots of SlERF15 mutants. Mechanistically, SlERF15 acts as a transcription factor that directly binds and activates the promoters of carotenoid cleavage dioxygenases 7 (SlCCD7), carotenoid cleavage dioxygenases 8 (SlCCD8), and 9-cis-epoxy carotenoid dioxygenase (SlNCED1), key genes for SLs and ABA biosynthesis. Moreover, ABA positively regulated the expression of SlERF15 and SLs biosynthesis genes, forming a feedback loop. CONCLUSION:Our findings demonstrate that SlERF15 functions as a key regulator involved in SLs and ABA signaling to promote AMS in tomato, offering novel insights into the complex phytohormonal regulation network fine-tuning in plant-mycorrhizal fungi interactions.

Brassinosteroids (BRs) regulate cell division and elongation. However, the precise roles of BRs metabolism in root development of horticultural plants remain unclear. Here, we studied the functions of the BRs catabolic gene CYP734A8 and biosynthesis gene DWF in tomato root growth. CYP734A8 and DWF expressed in the root tips. Loss of function of either CYP734A8 or DWF resulted in reduced growth of tomato primary roots. Additionally, mature cell length was decreased in cyp734a8 mutant. BRs biosynthesis inhibitor BRZ exaggerated inhibition of cell elongation in dwf mutant, but mitigated the root growth inhibition in cyp734a8 mutant by reversing the decreases in meristem zone (MZ) size and mature cell length. RNA-seq analysis revealed that the homeostasis of reactive oxygen species (ROS) and auxin were disturbed in cyp734a8 and dwf mutants. Specifically, the expression of auxin response genes were enhanced in cyp734a8 mutant, in association with higher auxin levels in root tips. Furthermore, ROS accumulation pattern was altered in cyp734a8 and dwf mutants. Notably, the inhibitor of peroxidase, SHAM, improved root growth in both mutants through increasing mature cell length in cyp734a8 and MZ size in dwf, respectively. The inhibition of auxin biosynthesis partially rescued the root elongation defects in cyp734a8 mutant. H2O2 treatment restored root elongation in the cyp734a8 mutant in association with suppression of auxin response and transport genes. Collectively, our findings demonstrated that both CYP734A8 and DWF genes are essential for maintaining appropriate spatial-temporal BR signaling, which is critical for ROS and auxin patterning during tomato root growth.

As sessile organisms, plants have developed intricate strategies to interact with their environment, including a variety of plant-plant interactions that range from mutualistic to antagonistic. Among these interactions, plant grafting stands out as a significant horticultural technique for enhancing productivity, disease resistance, and stress tolerance. Despite its widespread application, the mechanisms underlying graft compatibility remain poorly understood. This review explores the diverse field of plant-plant interactions, focusing on parallel mechanisms from other systems that may explain how “non-self” is determined during graft incompatibility. We first discuss the role of inter-plant signaling and the possibility of exudate-regulated compatibility. Next, we identify similarities between the parasitic plant haustoria and graft junctions, offering valuable insights into overcoming immunologic and physiologic barriers during vascular reconnection. We then delve into the potential roles of wound signaling and damage-associated molecular patterns (DAMPs) in grafting. Lastly, we provide an overview of pollen self-incompatibility as a case study for the detection of non-self throughout the plant kingdom. Overall, this review underscores the need for interdisciplinary approaches to unravel the complexities of graft compatibility, suggesting that future research should integrate knowledge from various fields of plant-plant interactions to improve the utilization of grafting and expand graft compatibility.

Arbuscular mycorrhizal fungi (AMF) have attracted considerable attention for their roles in enhancing plant stress resistance and elucidating the underlying mechanisms. However, the effects and mechanisms of AMF in regulating plant resistance to insect herbivores remain insufficiently understood. Here, we investigated how AMF modulates tomato resistance to Spodoptera litura using a factorial experimental design integrating AMF inoculation and insect herbivory, and further examined the associated physiological and molecular responses to explore the underlying mechanisms. AMF significantly increased the expression of phosphorus transporter genes SlPT4 and SlPT5, enhanced phosphorus content, and promoted tomato growth. AMF inoculation also suppressed larval growth of S. litura, reduced leaf damage, increased antioxidant enzyme activities, and decreased malondialdehyde (MDA) accumulation. At 24 h after herbivory, AMF enhanced the expression of JA biosynthesis-related genes (SlAOC, SlOPR3, and SlLOXD), increased jasmonic acid (JA) and JA-Ile levels, and reduced abscisic acid (ABA) content. At 48 h, AMF increased indole-3-acetic acid (IAA) levels and further upregulated insect resistance-related genes, including SlPI1, SlPI2, and SlTD. These findings suggest that AMF suppresses S. litura feeding and enhances tomato resistance, with temporal changes in hormonal signaling and defense responses.

Shoot branching is a crucial agronomic trait influencing crop yield. Multiple transcription factors orchestrate a sophisticated regulatory network to control shoot branching in response to internal and external cues. However, the role of epigenetic modification in shoot branching is less clear. Here, we found that SIRTUIN1 (SlSRT1), a histone deacetylase, promotes shoot branching by regulating transcription in lateral buds in response to brassinosteroid (BR) signaling in tomato (Solanum lycopersicum). SlSRT1 interacted with BRASSINAZOLE-RESISTANT 1 (SlBZR1), a critical component of BR signaling, to repress the transcription of RELATED TO ABI3/VP1 1 (SlRAV1) and BRANCHED1 (SlBRC1) through decreasing H3K9 acetylation. SlBRC1 and SlRAV1 both inhibited shoot branching in tomato. Intriguingly, the genetic analysis, spatial-temporal expression of SlBRC1 and SlRAV1, and the transcriptomes in the buds of slbrc1 and slrav1 mutants indicated that SlBRC1 and SlRAV1 function through partially independent mechanisms. Our results demonstrate that SlSRT1-dependent histone deacetylation is essential for BR regulation of shoot branching.

Brassinosteroids (BRs) are steroidal phytohormones that play crucial roles in plant growth and resilience. The stability of BRASSINAZOLE RESISTANT 1 (BZR1), the central transcription factor of BR signaling, is controlled by the GSK3-like kinase BRASSINOSTEROID INSENSITIVE 2 (BIN2)-dependent phosphorylation. However, the regulators mediating BZR1 degradation remain elusive. Here, we identify a BZR1-interacting WD40-repeat protein (BIW) that facilitates ubiquitination and degradation of BZR1 in tomato (Solanum lycopersicum). Mutations in BIW lead to growth phenotypes similar to those of plants with elevated BR signaling, accompanied by enhanced chilling tolerance, whereas overexpressing BIW results in the opposite phenotypes and reduced chilling tolerance. Furthermore, phosphorylation of BIW at Ser144 by BIN2 is essential for its stability and activity. Our findings demonstrate that BIW is an integral component of BR signaling and represents a potential target for genetic modification aimed at improving resilience and productivity.

Greenhouse cultivation ensures year-round tomato production. However, optimizing key fruit quality attributes is still challenging. Current practices often fail to achieve the desired sensory and nutritional profiles, necessitating a systematic review of innovative regulation techniques. This review aimed to bridge this gap by offering a comprehensive summary of recent advances in techniques for regulating the quality of greenhouse tomatoes. These include cultivar selection (cultivars with varying sensory, flavor, and nutritional qualities) and advancements in breeding technologies (molecular marker-assisted selection and gene editing), regulation of environmental factors (light, temperature, humidity, and CO2 concentration), and agronomic practices (irrigation, fertilization, and other management measures). Moreover, the multifactor synergistic regulation of tomato quality has been discussed. Finally, the prospects for optimizing quality control strategies in greenhouse tomato production, as well as the strengths and limitations of emerging technologies, have been discussed to guide future technological innovations.

Auxin plays a central role in lateral root (LR) development, with other hormones modulating this process by interacting with auxin. However, the interplay between brassinosteroids (BRs) and auxin in LR development remains poorly understood. Here, we demonstrate that PIN5 and PIN10 are involved in BR-mediated LR development in tomato. LR formation is impaired in the tomato BR biosynthesis mutant dwf and the signaling mutant bzr1, which is defective in the key transcription factor BZR1. Treatment with 28-homobrassinolide (HBR) increases the density of LRs (including emerged and unemerged), as does BZR1 overexpression. Further analysis revealed that BZR1 regulates the auxin response and directly enhances the transcription of PIN5 and PIN10, which are expressed in LR primordia and the root apical meristem. PIN5 and PIN10 regulate the balance of free and conjugated auxin levels, presumably by controlling auxin transport from the endoplasmic reticulum to the nucleus. Mutation in PIN5 or PIN10 reduces nuclear auxin import and impairs auxin signaling, impeding BR-induced LR formation. Molecular docking and isotopic yeast assays confirmed that PIN5 and PIN10 function as bona fide auxin transporters. Collectively, these results show that BR signaling promotes LR development by transcriptionally activating the expression of PIN5 and PIN10, which are essential for maintaining auxin homeostasis. These findings advance our understanding of the regulatory networks that control root development, providing insights for improving agricultural productivity.

Plants orchestrate stress responses through the integration of light and temperature signals, yet the molecular mechanisms involved in this crosstalk are incompletely elucidated. Here, we identify the transcription factor SlWRKY2 as a critical hub linking phytochrome-mediated light perception with cold stress adaptation in tomato (Solanum lycopersicum). Under cold stress, low red/far-red light ratios significantly induce SlWRKY2 expression and protein accumulation, with phytochrome B (SlphyB) repressing and SlphyA promoting this process. Genetic analyses confirm that SlWRKY2 functions downstream of SlphyB and SlphyA, physically interacts with both SlphyB1 and SlphyA, and acts in a regulatory module where SlphyB negatively regulates cold tolerance while SlphyA exerts a positive effect. Moreover, both cold stress and light signals promote the formation of SlWRKY2 condensates consistent with liquid-liquid phase separation. Functionally, SlWRKY2 directly interacts with and stabilizes the light-signaling regulator PHYTOCHROME-INTERACTING TRANSCRIPTION 4 (SlPIF4). Furthermore, SlWRKY2 directly activates SlPIF4 transcription, and the 2 factors function synergistically to enhance the expression of SlCBFs, as evidenced by genetic data indicating that SlPIF4 is required for SlWRKY2-dependent cold tolerance. Mechanistically, SlWRKY2 competes with SlphyB1 for interaction with SlPIF4. Our findings reveal the SlphyB1/A-SlWRKY2-SlPIF4 signaling module as a pivotal mechanism underlying light quality-dependent cold adaptation, advancing our understanding of how plants integrate environmental cues to fine-tune cold adaptation.

Arbuscular mycorrhizal (AM) fungi are common root-associated endophytic fungi that enhance host plant growth and induce resistance against various stresses. However, their role in mediating insect resistance in vegetable crops remains poorly understood. In this study, the effects of AM fungi inoculation on growth and insect resistance against Spodoptera litura in four representative vegetable species (tomato, pepper, cucumber, and lettuce) were investigated. Lettuce (Lactuca sativa), which exhibited the strongest mycorrhiza-induced resistance, was subsequently selected for detailed mechanistic investigation through physiological and biochemical measurements, phytohormone profiling, gene expression analysis, and targeted metabolomics. AM fungi-inoculated lettuce exhibits both elevated growth and pronounced insect resistance. During the early stages of herbivory, AM fungi rapidly activates the jasmonic acid (JA) signaling pathway, leading to increased levels of 12-oxo-phytodienoic acid (OPDA), JA, and bioactive jasmonyl-isoleucine (JA-Ile), as well as the upregulation of key JA biosynthetic gene LsOPR3 and the defense-related gene LsPI. Mycorrhizal inoculation also mitigates lipid peroxidation induced by insect feeding and enhances the activities of antioxidant enzymes (superoxide dismutase and catalase) in leaves. Targeted metabolomic analysis reveales that AM fungi significantly altered secondary metabolism in lettuce, particularly promoting the accumulation of L-tryptophan (L-Trp) and its derivatives (such as methyl indole-3-acetate and indole-3-carboxaldehyde) under insect stress, alongside notable increases in phenylpropanoid and flavonoid pathway metabolites. Exogenous application assays further confirmed that JA treatment strongly induced the expression of insect defense-related polyphenol oxidase genes (LsPPO3, LsPPO4) and enhanced resistance but suppressed plant growth. In contrast, L-Trp treatment elevated LsPPO3 and LsPPO4 expression while maintaining biomass accumulation. These results show that AM fungi inoculation promotes lettuce growth and insect resistance through elevating JA signaling and L-tryptophan accumulation. Moreover, this study emphasizes the potential role of L-Trp in improving vegetable crops biomass and insect defense.

Photorespiration is vital for C3 plant carbon (C) and nitrogen (N) metabolism, yet most engineering ignores N-related constraints. Here, we engineered a chloroplast-targeted bypass in tomato (GCMG), comprising glycolate oxidase 1 (SlGLO1), catalase 2 (SlCAT2), malate synthase A (SlMSA), and glutamine synthetase 2 (SlGS2). This bypass integrates carbon concentration with enhanced ammonium reassimilation via the GS2/ferredoxin-dependent glutamate synthase (Fd-GOGAT) cycle. GCMG plants showed synergistic improvements in photosynthesis, biomass, and fruit quality; while total yield significantly increased over wild-type (WT), GCMG maintained a favorable trend beyond C-focused GCM lines. Mechanistically, GCMG partitions glycolate flux into parallel routes, maintaining N assimilation while enhancing chloroplastic CO2 enrichment. 15N-labeling confirmed this metabolic synergy, revealing a 146% higher N turnover rate (fnew). GCMG also sustained robust N assimilation under elevated CO2 and conferred resilience to N-deficiency, high oxygen, and heat stress. Coordinating C/N metabolism boosts productivity and resilience, offering a blueprint for crop improvement.

Acylsugars are defensive glycolipids in Solanaceae glandular trichomes, and their biosynthesis offers an exemplary system for understanding the evolutionary mechanisms of plant chemical defense, yet their transcriptional regulation is poorly understood. Here, we identified and characterized WRINKLED3 (WRI3), which is critical for acylsugar biosynthesis in tomato. SlWRI3 is specifically expressed in trichome tip cells, and its knockout reduces acylsugar accumulation. Using transcriptomics, DNA-protein interaction assays, and metabolomics, we demonstrate that SlWRI3 acts via a dual regulatory mechanism: directly activating the acyltransferase gene SlASAT1 for the initial acylation of sucrose core and upregulating multiple acetyl-CoA carboxylase (ACCase) subunits to provide acyl chain precursors. Silencing these ACCase genes similarly decreased acylsugar levels. Phylogenetic analysis indicates that the function of WRI3 in acylsugar biosynthesis is evolutionarily conserved in Solanaceae. These findings elucidate how a primary metabolism-associated regulator was repurposed to coordinate precursor supply and specialized metabolite production, deepening our understanding of plant metabolic evolution, providing a target for engineering pest-resistance in Solanaceae crops.

As the primary energy source for photosynthesis, light also serves as a critical environmental cue regulating developmental plasticity through photomorphogenesis. While extensive research has characterized light-mediated shoot development, including hypocotyl de-etiolation, cotyledon expansion and chloroplast biogenesis, emerging evidence demonstrates that light signals also profoundly influence the root. Phenotypic analyses of photoreceptor mutants have revealed that roots, like above-ground tissues, perceive and respond to light signals through sophisticated signalling networks. This review synthesizes current understanding of core light signalling cascades and the systemic mechanisms facilitating shoot-to-root signal transmission. We highlight recent advances in understanding how light quality and intensity modulate root development through hormonal crosstalk and transcriptional reprogramming. By integrating molecular mechanisms with agronomic applications, we further provide a detailed summary of the application of plant photobiology. It suggests practical strategies for optimizing root development through light-mediated control.

Light and temperature can regulate auxin production which has been recently shown to be key during graft healing, suggesting that abiotic factors may be vital variables for future graft studies. Grafting is an important horticultural tool used to combine advantageous plant traits. Despite its broad usage, the mechanisms that underlie graft healing remain poorly understood. Recent work has highlighted the influence of high temperature-mediated auxin flow on graft success. Light and temperature sensing utilize partially overlapping mechanisms to regulate auxin biosynthesis, signaling, and transport. In this review, we explore the sensors and transcriptional regulators that modulate auxin response, specifically emphasizing how these components regulate graft success and vascular reconnection. We also discuss areas of graft biology regulated by auxin and underexplored areas of photobiology that may be key to a better understanding of graft mechanisms. This review underscores the importance of translating genetic findings from model systems into horticultural crops to expand our knowledge of economically valuable techniques like grafting.

Arbuscular mycorrhizal symbiosis (AMS) is a ubiquitous mutualistic interaction between many terrestrial plants and fungi, with lipids playing a pivotal role in nutrient exchange. However, few genetic regulators of AMS have been functionally validated in tomato. To investigate candidate genes, we employed CRISPR‐Cas9 and VIGS to generate knockout and knockdown lines. A comprehensive suite of molecular biology techniques, including yeast‐1/2‐hybridization, BiFC, ChIP‐qPCR, and RNA‐sequencing, was used to elucidate the regulatory roles of SlWRI5a, SlHY5, and SlFatM in fatty acid (FA) biosynthesis and AMS in tomato. FA composition was analyzed using gas chromatography. In this study, we validated SlWRI5a and SlFatM as key regulators of 16‐carbon FA biosynthesis during AMS in tomato and demonstrated physical interactions between SlWRI5a and SlHY5. SlHY5 expression was induced by AMS and promoted root FA biosynthesis. Finally, we demonstrated that SlWRI5a and SlHY5 can co‐regulate SlFatM‐mediated FA accumulation, thereby influencing AMF colonization efficiency in tomato. Our findings reveal the SlWRI5a/SlHY5–SlFatM regulatory module, offering new insights into lipid‐mediated AMS in tomato. This work also highlights a novel role for HY5 during fungal symbiosis, underscoring its broader significance in plant–microbe interactions.