Transgenic and gene-editing technologies are essential for gene functional analysis and crop improvement. However, the pleiotropic effects and unknown mechanisms of morphogenic genes have hindered their broader application. In this study, we employed the one-step de novo shoot organogenesis (DNSO) method, and demonstrated that overexpression of the morphogenic gene Arabidopsis thanalia GROWTH-REGULATING FACTOR 5 (AtGRF5) significantly enhanced genetic transformation efficiency in cucurbit crops by promoting callus proliferation and increasing dense cells during regeneration. High-resolution time-series transcriptomics and single-cell RNA sequencing revealed that AtGRF5 overexpression induced auxin-related genes and expanded stem cell populations during cucumber DNSO. Using DNA-affinity purification sequencing (DAP-seq) in combination with spatiotemporal differential gene expression analysis, we identified CsIAA19 as a key downstream target of AtGRF5, with its modulation playing a pivotal role in regeneration. Rescuing CsIAA19 in AtGRF5-overexpressing explant reversed the enhanced callus proliferation and regeneration. To address growth defects caused by AtGRF5 overexpression, we developed an abscisic acid-inducible AtGRF5 expression system, significantly improving transformation and gene-editing efficiency across diverse genotypes while minimizing pleiotropic effects. In summary, this research provides mechanistic insights into AtGRF5-mediated transformation and offers a practical solution to overcome challenges in cucurbit crop genetic modification.

The calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) Ca²⁺ sensors play crucial roles in the plant's response to drought stress. However, there have been few reports on the synergistic regulation of drought stress by CBL-CIPK and abscisic acid (ABA) core signaling components. In this study, we discovered that ZmCIPK33 positively regulates drought resistance in maize. ZmCIPK33 physically interacts with and is enhanced by phosphorylation from ZmSnRK2.10. Drought stress can activate ZmCIPK33, which is partially dependent on ZmSnRK2.10. ZmCIPK33 in combination with ZmSnRK2.10 can activate the slow anion channel ZmSLAC1 in Xenopus laevis oocytes independently of CBLs, whereas ZmCIPK33 or ZmSnRK2.10 alone is unable to do so. Furthermore, ZmCIPK33 phosphorylates ZmPP2C11 at Ser60, which leads to a reduction in the interaction between ZmPP2C11 and ZmEAR1 (the ortholog of Arabidopsis Enhancer of ABA co-Receptor 1) and weakens the phosphatase activity of ZmPP2C11, consequently, enhancing the activity of ZmSnRK2.10 in an in vitro assay and in the in-gel assay of the zmcipk33 mutant. Our findings provide novel insights into the molecular mechanisms underlying the reciprocal enhancement of Ca²⁺ and ABA signaling under drought stress in maize.

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

In plants, genetically encoded probes based on redox-sensitive green fluorescent protein (roGFP) have been used to detect hydrogen peroxide (H₂O₂) levels by fusing exogenous thiol peroxidases, such as Orp1 and Tsa2. However, the effectiveness of these thiol peroxidases compared to endogenous ones remains unexplored. Here, we develop a H₂O₂ probe by fusing roGFP2 to an endogenous H₂O₂ sensor, type II peroxiredoxin (PRXIIB), which displayed enhanced responsiveness and conversion kinetics compared to roGFP2-Orp1 in vitro and superior sensitivity to H₂O₂ in vivo. The roGFP2-PRXIIB probe allowed robust visualization of H₂O₂ production in abiotic and biotic stresses, and growing pollen tubes. We further targeted roGFP2-PRXIIB to cytosol, nuclei, mitochondria and chloroplasts to monitor H₂O₂ accumulation in real time in different subcellular compartments during immune activation, and the analyses revealed different temporal patterns of H₂O₂ accumulation during pattern- and effector-triggered immune responses in different compartments. Taken together, the work provides an ultra-sensitive probe for H₂O₂ dynamics in diverse plant biological processes.

Soil salinization has emerged as a major threat affecting crop yields. Global warming leads to a massive loss of terrestrial water and makes soils saltier. Cultivating salt-tolerant crops is the major strategy adopted for utilizing these salinized soils. Sea Rice 86 (SR86) is one such elite salt-tolerant rice variety derived from ancient indica rice. However, SR86 has multiple wild traits, such as tallness and strong photoperiod sensitivity (PS), which have limited its application in agricultural production. In this study, we edited 13 genes responsible for 10 traits in SR86 to develop an improved SR86M line by using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 multiplex-genome-editing technology, high-throughput sequencing, crossing, and progeny selection. Subsequent analysis of SR86M detected nine genes with expected mutations, leading to changes in seven traits, including improvements of plant architecture, plant height and PS decreased, grain number, grain length, fragrance, and nitrogen utilization efficiency increased. The improved agronomic traits in SR86M are similar to modern cultivated rice, along with elite salt tolerance like SR86, indicating suitability for potential cultivation. Our results also reveal the efficiency of multiplex-genome-editing in directional improvement of crop varieties.

Sweetpotato (Ipomoea batatas) starch is in high demand globally as a food and industrial product. However, the regulatory mechanisms governing starch biosynthesis and starch properties in this important crop remain largely unknown. Here we identified a natural allelic variant in the promoter of IbNAC22, encoding a NAC (NAM, ATAF1/2, and CUC2) transcription factor, which is closely linked to starch content in sweetpotato. In high-starch sweetpotato varieties, the T/C haplotype and a 13-bp deletion in the IbNAC22 promoter resulted in higher transcriptional activity. The high-starch IbNAC22 haplotype is more prevalent in regions of China where the sweetpotato starch industry is well developed, indicating that this advantageous allele type has been utilized in breeding starchy sweetpotato varieties in China. IbNAC22 is highly expressed in storage roots and starch-rich sweetpotato accessions. Overexpression of IbNAC22 significantly improved starch and amylose contents, as well as granule size and gelatinization temperature, and decreased starch crystallinity, whereas IbNAC22 knockdown had the opposite effects. IbNAC22 directly activates the expression of IbGBSSI, a key gene for amylose biosynthesis, but suppresses the expression of IbSBEI, a key gene for amylopectin biosynthesis. IbNAC22 directly interacts with IbNF-YA10. Overexpressing of IbNF-YA10 significantly improved starch and amylose contents, and starch gelatinization temperature, but decreased granule size, crystallinity, and amylopectin chain length distribution. IbNF-YA10 directly activates IbAGPL and IbGBSSI, which are key genes involved in starch and amylose biosynthesis. IbNAC22–IbNF-YA10 heterodimers further enhance the IbNF-YA10-induced activation of IbAGPL and IbGBSSI. These findings increase our understanding of starch biosynthesis and starch properties and provide strategies and candidate genes for the improvement of starchy root and tuber crops.

Radish (Raphanus sativus L.) is a globally important root vegetable crop known for its diverse varieties and unique taproot characteristics. The LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene family, specific to plants, plays a pivotal role in the development of lateral plant organs. Nonetheless, the precise biological functions and molecular regulatory mechanisms of LBD genes in radish taproot development remain largely unexplored. In this study, the RsLBD3 gene was identified as a potential candidate affecting taproot size in radish through a genome-wide association study. Further investigation revealed two insertions in the C-terminal region of RsLBD3, with insertion³⁶³ notably enhancing the transcriptional activation capability of RsLBD3. It was observed that radish taproots with RsLBD3^Ins-363 haplotype displayed significantly greater length and weight compared to those with RsLBD3^Del-363 haplotype. RNA in situ hybridization and reverse transcription quantitative polymerase chain reaction analysis revealed that the RsLBD3 gene exhibits high expression level in the vascular cambium and is induced by cytokinin treatment. Silencing the RsLBD3 gene resulted in the inhibition of vascular cambium activity in the taproot, thereby impeding thickening. Exogenous cytokinin treatment could partially rescue the small-taproot phenotypes caused by RsLBD3 silencing. Moreover, RsARF5 (AUXIN RESPONSE FACTOR 5), RsRR7b (RESPONSE REGULATOR 7), and RsCYCD3-1 (CYCLIN D3;1) were identified as target genes of RsLBD3. Notably, RsARF5 was found to directly regulate the expression of RsWOX4 (WUSCHEL-RELATED HOMEOBOX 4). Additionally, biochemical analysis demonstrated that RsTCP14 interacts with RsLBD3, contributing to the binding of RsLBD3 to its target genes. Collectively, these findings contribute to a better understanding of the regulatory mechanisms underlying taproot morphogenesis, and provide novel allelic variations for the genetic enhancement of taproot shape traits in radish.

Grain size is an important agronomic trait that largely determines grain yield in rice (Oryza sativa L.). The genes encoding the Growth Regulating Factors (GRFs) and G-proteins are major regulators for grain length regulation, but how these pathways are coordinated in plants remains elusive. Here, we described OsPLATZ1 as a transcriptional activator, a member of the Plant AT-rich sequence- and Zinc-binding family proteins in rice that positively regulates grain length. OsPLATZ1 interacted with multiple GRFs, and the OsPLATZ1-OsGRF4 complex bound to regulatory regions in the promoter of the G-protein gene DENSE AND ERECT PANICLE1 (DEP1) to enhance its expression, thereby regulating grain length. We used gene editing to modify the OsPLATZ1 promoter regulatory region and obtained mutant lines with downregulated or upregulated OsPLATZ1 expression depending on the type of editing event. One of these mutant lines had changes in multiple agronomic traits and improved grain yield and grain appearance quality. Our findings reveal a new regulatory module in which OsPLATZ1 connects the GRFs and G-protein signaling pathways to regulate grain length and suggest that finely modulating OsPLATZ1 activity might be a promising molecular breeding approach.

In higher plants, stomatal movements represent a critical physiological process that matains cellular water homestasis while enabling photosynthetic gas exchange. Open stomata 1 (OST1), a key protein kinase in the abscisic acid (ABA) signaling cascade, has been established as a central regulator of stomatal dynamics. This study reveals that two highly conserved mitogen-activated protein kinase 1 (MAP4K1) and MAP4K2 are positive regulators in ABA promoted stomatal closure, and ABA-activated OST1 potentiates MAP4K1/2 through phosphorylation at conserved serine and threonine residues (S166, T170, and S479/S488). The activated MAP4K1, in turn, phosphorylates two critical downstream targets: plasma membrane H⁺-ATPase 2 (AHA2) at residues T858, T881, and Y946, and slow anion channel-associated 1 (SLAC1) at T114 and S116. Functional analysis demonstrates that the phosphomimetic (3D: S166D/T170D/S479D) MAP4K1, but not non-phosphorylatable (3A: S166A/T170A/S479A) MAP4K1, could fully restore drought tolerance and reduced water loss in detached leaves of map4k1map4k2 double mutant. Our findings delineate a previously unrecognized signaling module comprising OST1–MAP4K1/2–AHA2/SLAC1, which crucially modulates ABA-mediated stomatal regulation. This work advances our mechanistic understanding of phosphorylation cascades governing plant water relations and stress responses.

Chloroplasts are key organelles for capturing solar energy and establishing plant immunity. During photosynthesis and pathogen defense, highly redox-active reactions take place in chloroplasts and generate large amounts of reactive oxygen species (ROS). However, our knowledge of chloroplast-produced ROS biosynthesis in plant immunity under varying light conditions is limited. Here, we report that the chloroplast-localized protein HYPERSENSITIVE TO HIGH LIGHT 1 (HHL1) functions as a dual regulator of AvrRpt2-triggered immunity in Arabidopsis (Arabidopsis thaliana), by modulating levels of chloroplast-produced ROS to activate appropriate responses to pathogen infection under various light intensities. Under normal light conditions, HHL1 positively regulates AvrRpt2-triggered immunity by promoting AvrRpt2-induced chloroplast-produced ROS accumulation, initiating salicylic acid signaling, and inducing the expression of genes encoding ROS-scavenging enzymes. By contrast, under high light (HL) conditions, HHL1 has an opposite role, functioning as a repressor of these immune responses while HL stress attenuates AvrRpt2-triggered immunity. These findings reveal that HHL1 modulates AvrRpt2-triggered immunity by regulating ROS homeostasis in a light intensity-dependent manner. Collectively, our results offer insight into the role of chloroplasts in the crosstalk between plant immunity and light intensity.

Salt stress, especially the increasing secondary salt stress, severely compromises apple production worldwide. Mitigation of oxidative damage caused by salt stress is critical for salt tolerance in apple plants. However, it remains unclear how the salt signal triggers the excessive reactive oxygen species (ROS) mitigation system in apple. In this study, we identified a salt-induced gene MdGRF10 (encoding a 14-3-3 protein), whose overexpression conferred transgenic apple plants reduced oxidative damage and enhanced salt tolerance. Furthermore, a salt-activated receptor-like cytoplasmic kinase MdPBL34 was found to interact with and phosphorylate the C-terminal of MdGRF10. This phosphorylation promoted the interaction between MdGRF10 and a melatonin rate-limiting synthetase MdASMT1 (N-acetylserotonin methyltransferase). Its overexpression or knockdown by CRISPR/Cas9 in transgenic apple plants demonstrated that MdASMT1 is critical in melatonin-mediated ROS scavenging for salt tolerance. Their interaction stabilizes MdASMT1 by decreasing its ubiquitin-mediated degradation for increased melatonin level, decreased oxidative damage and therefore promoted salt tolerance. Our findings revealed that 14-3-3 protein could integrate the salt signal in a phosphorylation-dependent manner. Moreover, MdPBL34 was also identified for the first time to be involved in salt signaling. Our research uncovered a novel MdPBL34–MdGRF10–MdASMT1 regulatory module in response to salt stress in apple, which will contribute to the molecular breeding of melatonin-enriched salt-tolerant apple trees.

Late blight, caused by the oomycete plant pathogen Phytophthora infestans, is a destructive disease that leads to significant yield loss in potatoes and tomatoes. The introgression of disease resistance (R) genes, which encode nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs), into cultivated potatoes, is highly effective in controlling late blight. Here, we generated transgenic 2R and 3R potato lines by stacking R genes Rpi-blb2/Rpi-vnt1.1 and Rpi-vnt1.1/RB/R8, respectively, in the susceptible cv. Desiree background. The resulting 2R and 3R transgenic potato plants showed resistance to highly virulent P. infestans field isolates. We hypothesized that stacking R genes either resulted in up-regulation of a broader range of immune-related genes, or, more importantly, increase in the fold change of gene expression. To test our hypotheses, we performed transcriptome analysis and identified a subset of core immune-related genes that are induced in response to P. infestans in transgenic lines carrying single R genes versus lines carrying stacks of multiple R genes. In our analysis, stacking R genes resulted not only in the induction of a broader range of defense-associated genes but also a global increase in gene expression fold change, caused by the pathogen. We further demonstrated that the calcium-dependent protein kinase 16 (StCDPK16) gene significantly contributed to resistance to a virulent P. infestans strain, in the R gene background, in a kinase activity-dependent manner. Thus, our data suggest that stacking the R genes enhances late blight resistance through modulating the expression of a broader range of defense-related genes and highlights CDPK16 as a novel player in potato R gene-mediated resistance.

Rosids, comprising 90,000–120,000 species, form a large clade of angiosperms, including extensively studied families with many economically and scientifically important plants. They are also ecologically important, dominating many temperate and tropical ecosystems. Great progress in understanding rosid phylogenetic relationships has facilitated evolutionary studies, but phylogenetic uncertainties remain. To construct a more comprehensive nuclear phylogeny with expanded taxon coverage at the familial levels, we generated 203 new transcriptomes and two shotgun genomes. Along with other available data sets, our sample includes 419 eudicots, including 316 rosids, representing 83 families and all 16 rosid orders. Compared to the 1KP study, our highly resolved rosid phylogeny provides strongly supported internal relationships for one additional order and 16 families. We uncovered cytoplasmic-nuclear discordance for several deep rosid relationships with possible evidence of hybridization/gene flow and incomplete lineage sorting. By tracing ancestral states of morphological characters, we revealed putative floral evolutionary trends in some major clades. We detected strong evidence for 27 putative whole-genome duplication (WGD) events distributed across 20 rosid families, including five novel WGDs. Additionally, our expanded taxon sampling allowed for revised phylogenetic positions of several previously reported WGD events. Most of the supported WGDs correspond to origins of families or large subclades and occurred near times of geological and global climate upheavals, including those at the Cretaceous–Paleogene boundary. Our findings support the idea that large-scale genomic changes and key morphological innovations might have contributed to adaptive evolution and increased biodiversity in rosids.

Rapeseed (Brassica napus) is one of the most important oilseed crops worldwide, with its seed oil content (SOC) and quality directly determining its economic value. To resolve the challenges of growing demand for vegetable oil and advancements in rapeseed production, substantial progress has been achieved in the genetic improvement of SOC. This review systemizes genetic optimization strategies across three hierarchical processes: source expansion via enhanced photosynthesis, optimized carbon allocation, and metabolic redirection of photoassimilates; sink enhancement through targeted elevation of fatty acid (FA) synthesis, triacylglycerol (TAG) assembly, and seed coat development coupled with suppression of lipolytic pathways; flow optimization by modifying carbon partitioning, sucrose phloem loading and channeling to developing seeds. We synthesize reported genetic determinants of these processes and underscore their potential for enhancing SOC. Furthermore, we postulate that synergistic integration of source–flow–sink coordination with push–pull–package–protect frameworks could maximize oil accumulation, thereby establishing a multi-tiered roadmap for transcending SOC ceilings in rapeseed.

Soil salinity significantly affects plant survival and limits crop productivity. Under salt stress, plants can transport sodium ions (Na⁺) out of cells and sequester them into vacuoles for detoxification. The salt excretion process is governed by the SALT OVERLY SENSITIVE (SOS) pathway, which involves the calcium sensors SOS3 and SOS3-LIKE CALCIUM BINDING PROTEIN 8, the protein kinase SOS2, and the plasma membrane Na⁺/H⁺ antiporter SOS1. While previous studies have provided insights into Na⁺ transport through the SOS system, the role of this pathway in Na⁺ compartmentalization within vacuoles remains poorly understood. In this study, we demonstrate that SOS1 partially internalizes to the tonoplast under salt stress, which is crucial for Na⁺ compartmentalization in vacuoles in Arabidopsis (Arabidopsis thaliana). We show that SOS2 phosphorylates the endosomal sorting complex required for transport-I (ESCRT-I) component FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), which disrupts its interaction with VPS23A, an ESCRT-I component. This phosphorylation event inhibits the formation of intraluminal vesicles (ILVs) in prevacuolar compartments and multivesicular bodies (PVCs/MVBs), thereby remodeling endosomal sorting during salt stress. Additionally, our previous research indicated that SOS2-mediated phosphorylation of FREE1 leads to vacuole fragmentation by altering endomembrane fusion, thereby regulating intracellular Na⁺ homeostasis. Taken together, our findings reveal how the SOS2-FREE1 module orchestrates both endomembrane fusion and endosome sorting processes to enhance plant salt tolerance, providing novel insights into the cellular mechanisms underlying salt stress adaptation.

Leaf curvature significantly contributes to important economic traits in vegetable crops. The upward-curling leaf phenotype has been consistently observed upon overexpression of a miR156/157-resistant version of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 (SPL10) transcription factor (rSPL10). However, the role of SPL10 in regulating leaf curvature has not been well characterized. In this study, using DNA affinity purification sequencing followed by transient transactivation assays, we found that SPL10 can bind to the promoter and gene body of REVOLUTA (REV), augmenting its expression. The rSPL10 rev-6 double mutant plant displayed a downward-curling leaf phenotype similar to the rev-6 plant, supporting the notion that REV functions downstream of SPL10. Importantly, the SPL10 protein physically interacts with the REV protein, which attenuates the expression of REV promoted by SPL10, leading to the downregulation of REV-regulated genes involved in leaf curvature, such as HB2 and HB4. These findings suggest that the SPL10–REV module acts as a molecular rheostat to prevent excessive amplification of REV transcripts in Arabidopsis. Furthermore, overexpression of the BrpREV1 gene in Chinese cabbage caused the transformation of rosette leaves from flat to upward-curving and accelerated heading. Taken together, our findings reveal the role of SPL10–REV module in orchestrating leaf curvature, which could potentially be utilized for molecular breeding of economical traits in vegetable crops.

Alternative splicing (AS) is a crucial post-transcriptional mechanism in plants, significantly contributing to the diversification of biological processes and adaptive responses. Distinct splice isoforms are generated by exon skipping (ES), intron retention (IR) and other mechanisms, enabling plants to adapt to a range of biotic stresses, including those posed by bacteria, fungi and viruses. Advances in bioinformatics have greatly improved the detection and characterization of AS events, revealing their critical roles in plant immunity. This review highlights the involvement of AS in regulating RNA interference (RNAi), hormone signaling pathways, and immune responses such as pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). In addition, pathogens exploit AS to produce effectors that subvert plant immunity. Beyond its role in natural immunity, AS also holds promise for pesticide development, offering opportunities to enhance plant disease resistance by targeting pest-associated or immunity-related genes. Future research on AS under biotic stress is expected to uncover novel regulatory mechanisms and provide new strategies for crop improvement and sustainable agriculture.

Vertical farming offers significant potential to tackle global challenges like urbanization, food security, and climate change. However, its widespread adoption is hindered by high costs, substantial energy demands, and thus low production efficiency. The limited range of economically viable crops further compounds these challenges. Beyond advancing infrastructure, rapidly developing crop cultivars tailored for vertical farming (VF) are essential to enhancing production efficiency. The gibberellin biosynthesis genes GA20-oxidase fueled the Green Revolution in cereals, while the anti-florigen genes SELF-PRUNING (SP) and SELF-PRUNING 5G (SP5G) revolutionized tomato production. Here, we engineer tomato germplasm optimized for VF by leveraging genome editing to integrate Green Revolution gene homologs and anti-florigen genes. Knocking out the tomato SlGA20ox1 gene, but not SlGA20ox2, results in a promising VF-suitable plant architecture featuring short stems and a compact canopy. When cultivated in a commercial vertical farm with multi-layered, LED-equipped automated hydroponic growth systems, slga20ox1 mutants saved space occupation by 75%, achieving a 38%–69% fruit yield increase with higher planting density, less space occupation, and lower lighting power consumption. Stacking SlGA20ox1 with SP and SP5G genes created a more compact plant architecture with accelerated flowering and synchronized fruit ripening. In commercial vertical farms, the sp sp5g slga20ox1 triple mutant reduced space occupation by 85%, shortened the harvest cycle by 16% and increased effective yield by 180%, significantly enhancing production efficiency. Our study demonstrates the potential of integrating agriculture practice-validated genes to rapidly develop tomato cultivars tailored for VF, providing a proof-of-concept for leveraging genome editing to boost production efficiency in VF.

Ubiquitination, a critical post-translational modification, plays a pivotal role in fine tuning the immune responses of plants. The tomato (Solanum lycopersicum) suffers significant yield and quality losses caused by the devastating pathogen Botrytis cinerea. We have discovered the role of SlRAE1, a gene encoding an E3 ubiquitin ligase, as a pivotal negative regulator of resistance to B. cinerea. SlRAE1 interacts with SlSKP1, a component of the SKP1–Cullin1–F-box (SCF) complex, to modulate the protein stability of the transcription factor SlWRKY1 through the 26S proteasome pathway. SlWRKY1 targets and inhibits the transcription of SlJAZ7, a suppressor of jasmonic acid (JA) signaling, thereby activating the JA-induced defense system and affecting tomato susceptibility to B. cinerea. The resistance enhancement observed with knock-out SlRAE1 was reduced when SlWRKY1 was also knocked out, highlighting SlWRKY1's role in SlRAE1's regulation of tomato defense against B. cinerea. Our findings elucidate the defense mechanism in tomato and suggest that targeting SlRAE1, by modulating SlWRKY1 stability, could help to develop resistant tomato varieties. These insights have broader implications for using gene-editing technologies to enhance crop defense against fungi.

Shoot branching is an important crop agronomic trait that directly affects plant architecture and crop productivity. Although phytochrome B (phyB), BRANCHED1 (BRC1), and abscisic acid (ABA) mediate axillary bud outgrowth, it is unknown if there is any integrating factor among them in the Plantae. We report that mutation of CsphyB or inactivation of CsphyB by shade inhibits lateral bud outgrowth in cucumber. Cucumber PHYTOCHROME INTERACTING FACTOR 4 (CsPIF4) interacts with CsphyB and directly binds to the promoter of CsBRC1 to activate CsBRC1 expression. CsBRC1 also directly promotes the expression of ABA biosynthesis gene 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (CsNCED3). Functional disruption of CsPIF4 decreased expression of CsBRC1 and CsNCED3, reduced ABA accumulation, and increased bud outgrowth in cucumber. Csnced3 mutants had reduced ABA levels and increased lateral bud outgrowth. These results suggest that a regulatory network involving CsphyB-CsPIF4-CsBRC1 exists that integrates light signaling and ABA biosynthesis to modulate bud outgrowth. This provides a strategy to manipulate branch numbers in crop breeding to realize ideal branching characteristics to maximize yield.

Drought severely impedes plant growth and production as a primary abiotic stress. GIGANTEA (GI) regulates flowering and responds to various stresses in model plants; however, its function remains poorly understood in non-model plants. In this study, a Citrus limon GI homologous (CiGI) was identified and two alternative splicing transcripts (CiGIα and CiGIβ) were found. CiGIα overexpressing tobacco exhibited early flowering and drought sensitivity, whereas the phenotype of CiGIβ-overexpressing plants was similar to that of wild-type (WT) plants. Overexpression of CiGIα in citrus increased drought sensitivity and upregulated citrus FLOWERING LOCUS T (CiFT) expression, and downregulation of CiGI enhanced drought tolerance. Further studies revealed that CiGIα, CiGIβ, and LATE ELONGATED HYPOCOTYL (CiLHY) form a complex that binds to the Nuclear Factor YA1 (CiNF-YA1) promoter and activates its expression. Subsequently, CiNF-YA1 activates the expression of NADP-DEPENDENT MALIC ENZYME 2 (CiNADP-ME2) by binding its promoter, leading to increased reactive oxygen species (ROS) accumulation, which enhances plant drought sensitivity. Exogenous ROS treatment induced citrus flowering and reduced drought tolerance. Furthermore, the CiGI–CiLHY complex also activates CiFT and may participate in the regulation of citrus flowering. These results reveal a novel mechanism by which CiGI regulates citrus flowering and drought tolerance.

Leaf angle (LA) and tassel branch angle (TBA) are two important agronomic traits influencing maize plant architecture, thereby affecting its adaptability to high-density planting. Liguleless1 (LG1) acts as a key regulator of LA and TBA, yet its precise regulatory mechanism remains largely obscure. In this study, we have identified ZmTCP23, a teosinte branched1/CYCLOIDEA/proliferating cell factors (TCP) transcription factor that is highly expressed in tassel and leaf primordia, serving as a pivotal upstream transcriptional regulator of LG1. The functional loss of ZmTCP23 results in a significant reduction in both TBA and LA ranges. Moreover, in vitro and in vivo studies revealed that LG1 directly represses the expression of ZmXERICO1, a gene encoding an inhibitor of abscisic acid (ABA) degradation that can also influence LA and TBA upon overexpression. Additionally, ZmTCP23 physically interacts with the previously identified TBA regulator BAD1, forming a complex that co-activates the expression of LG1 via direct binding to its promoter. This dynamic duo established a positive feedback loop, mutually enhancing each other's expression within the tassels, and consequently influencing TBA. Our findings establish a ZmTCP23-LG1-ZmXERICO1 transcriptional regulatory cascade that orchestrates LA and TBA through influencing ABA content, and provide new targets for the genetic manipulation of LA and TBA for molecular breeding of high-density tolerant maize cultivars.

Germinating seeds undergo elaborate de-etiolation developmental transitions upon initial soil emergence. As central transcription factors promoting cotyledon greening, the abundance of ETHYLENE-INSENSITIVE 3 (EIN3) and PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) are strictly controlled by physically associating themselves with the EIN3-BINDING F BOX PROTEINS 1 and 2 (EBF1/2) for ubiquitination. Here, we report that the B-box zinc-finger protein BBX32, as a positive regulator during seedling de-etiolation. BBX32 is robustly elevated during the dark-to-light transitions. Constitutively expressing BBX32 ultimately protects against severe photobleaching damage by synchronizing the accumulation of protochlorophyllide (Pchlide) and the differentiation of etioplast–chloroplast apparatus in buried seedlings. Specifically, BBX32 directly interacts with EIN3, PIF3 and EBF1/2. These associations disrupt the assembly of the SCF^EBF1/2-EIN3/PIF3 E3 ligation protein complexes, thus dampening E3 ligase activity and robustly controlling EIN3/PIF3 stability. Under soil conditions, BBX32-ox largely rescues the greening deficiency of EBF1ox, and all EIN3ox/bbx32 seedlings override the bbx32 mutant defect and successfully turn green. Both biochemical findings and genetic evidence reveal a novel regulatory paradigm by which the B-box protein dampens the E3 ligase binding activity to achieve green seedlings upon changes in light or soil environmental conditions.

Potassium (K⁺), an essential macronutrient, strongly influences myriad fundamental processes, while its deficiency inhibits plant growth. Jasmonic acid (JA) regulates plant growth; however, its role in plant growth inhibition under K⁺ deficiency remains nebulous. Herein, we determined that JA significantly inhibits low K⁺ tolerance and K⁺ uptake in tomato. Methyl jasmonate treatment induced the expression of SlMYC3-like under low K⁺ stress, which bound the promoters of the genes that encode KT/KUP/HAK-type transporter (SlHAK5) and voltage-gated K⁺ channel (SlLKT1) and inhibited their expression. Knockdown of SlMYC3-like enhanced low K⁺ stress tolerance and decreased JA responses, while its overexpression led to low K⁺ stress sensitivity and promoted jasmonate responses in tomato. In addition, jasmonate ZIM-domain transcriptional repressor 2/3 (SlJAZ2/3) interacted with SlMYC3-like; this interaction decreased DNA-binding activity of SlMYC3-like. SlMYC3-like promoted SlJAZ2/3 expression, forming a negative feedback circuit in JA signaling. Silencing SlJAZ2/3 increased plant susceptibility to low K⁺ stress. Our findings demonstrate the involvement of the JA–SlJAZ2/3–SlMYC3-like module in K⁺ uptake and plant growth in tomato under low K⁺ stress, providing novel insights into the regulation of plant growth and K⁺ uptake.