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.

Rice is a staple food for more than half of the world's population, particularly in Asia. Cadmium (Cd) contamination in rice poses serious risks to human health through the food chain. Understanding the mechanisms governing Cd uptake, translocation, and tissue distribution, as well as its interaction with essential metals such as iron (Fe), zinc (Zn), and manganese (Mn), is critical for improving rice safety. Over the past two decades, key transporters involved in Cd and micronutrient homeostasis have been identified, providing insights into their crosstalk and competition. In this review, we summarize current knowledge on Cd and essential metal transport in rice and discuss the challenges and trade-offs in limiting Cd accumulation while maintaining plant growth and micronutrient balance, highlighting strategies for developing rice varieties with reduced Cd content and enhanced food safety.

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.

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.

Low temperature is a critical abiotic stress constraining rice production by impairing seed germination, seedling establishment, and reproductive development. Rice has developed a multifaceted regulatory system for cold tolerance through physiological adaptation and coordinated gene expression networks. Recent advances in quantitative trait locus (QTL) mapping and functional gene discovery have substantially elucidated the genetic basis of this complex trait. Molecular breeding strategies, including marker-assisted selection (MAS) and genome editing, hold significant promise for the development of novel cold-tolerant rice varieties. This review comprehensively summarizes the current knowledge on physiological responses, molecular mechanisms, and cold adaptation strategies in rice under low-temperature conditions. Specifically, we synthesize the breeding potential of cold-tolerant genes and discuss their application strategies in biological breeding, providing a strategic framework to advance the genetic improvement of cold tolerance in rice.

Drought stress represents a critical challenge to global agriculture, severely compromising plant growth and crop productivity through its disruption of intracellular signaling networks, with particular emphasis on protein kinase-mediated pathways and transcriptional regulation. In this study, we identified and characterized ZmDNL1 as a novel transcriptional regulator that serves as a negative modulator of drought tolerance in maize. Through comprehensive biochemical analyses, we demonstrated that ZmDNL1 physically interacts with ZmYAB15, a known negative regulator of drought tolerance, and potentiates its transcriptional regulatory activity. Most significantly, our investigation revealed that ZmSnRK2.10-mediated phosphorylation of three specific N-terminal residues in ZmDNL1 effectively attenuates ZmYAB15's transcriptional activity while maintaining the structural integrity of the ZmDNL1-ZmYAB15 protein complex, ultimately enhancing drought tolerance. These findings elucidate a previously unrecognized regulatory mechanism in which ZmSnRK2.10 orchestrates drought tolerance through phosphorylation-dependent fine tuning of the ZmDNL1–ZmYAB15 transcriptional regulatory module. Beyond advancing our fundamental understanding of drought response mechanisms in maize, this study provides valuable molecular targets for precision breeding strategies aimed at developing drought-resilient crop varieties.

Herbivorous insects pose a major threat to crop production, with rice suffering significant yield losses due to infestation by the brown planthopper (BPH). To understand the genetic and metabolic basis of BPH resistance in rice, we conducted metabolomic analysis and performed metabolite-based genome-wide association studies (mGWAS) on a rice population composed of 168 varieties, which exhibit a wide range of resistance to BPH. Metabolomic analysis revealed a trend of increasing metabolic divergence with increasing resistance levels compared with the susceptible group, with resistant groups maintaining greater metabolic stability after BPH infestation. Furthermore, using these metabolic biomarkers, we constructed a prediction model for BPH resistance and found that biomarkers in non-infested rice were sufficient to predict BPH resistance. We identified in total 2,738 single-nucleotide polymorphisms (SNPs) associated with key biomarkers in non-infested rice and 1,605 SNPs in BPH-infested rice. Gene Ontology (GO) enrichment analysis revealed that genes associated with biomarkers were enriched in different pathways between non-infested and BPH-infested rice. Notably, the SNP rs6_191562334 was significantly associated with the biomarker β-damascenone, which correlated positively with rice resistance to BPH and has been shown to inhibit BPH feeding on rice. Knockout of LOC_Os06g17970 increased β-damascenone levels and enhanced BPH resistance in rice. Collectively, this integrated approach provided novel insight into the metabolic and genetic mechanisms underlying BPH resistance and facilitated the development of strategies for sustainable control of BPH.

Drought stress and abscisic acid (ABA) have been known to play a critical role in modulating sugar accumulation in fruit, and yet, the underlying molecular mechanisms remain elusive. In this study, we have demonstrated that drought-mimicking film mulching increased sucrose levels in Satsuma mandarin (Citrus unshiu) fruit, coinciding with upregulation of CuSPS4, which encodes the sucrose phosphate synthase (SPS), in the transcriptome profiling. CuSPS4 was further shown to be drought- and ABA-inducible and functionally essential for sucrose synthesis. Mechanistically, two transcription factors, CuWRKY41 and CuWRKY23, directly bound to and activated the CuSPS4 promoter via the W-box element, with CuWRKY41 additionally regulating CuWRKY23 expression. Consistently, both CuWRKY41 and CuWRKY23 positively regulated sucrose synthesis by upregulating CuSPS4. Meanwhile, the substrate-interacting subunit (CuSnRK1β1) and catalytic subunit (CuSnRK1α) of SUCROSE NON-FERMENTING RELATED KINASE 1 (SnRK1) interacted with CuWRKY41, triggering CuSnRK1α-mediated phosphorylation and subsequent degradation of CuWRKY41, thereby suppressing its activation. However, ABA promoted cytoplasmic translocation of CuSnRK1α and CuSnRK1β1 and reduced nuclear interaction with CuWRKY41, leading to its phosphorylation alleviation and protein stabilization, concurrent with enhanced transcription activation of CuWRKY23 and CuSPS4. Taken together, these findings reveal a sophisticated regulatory mechanism whereby drought promotes sucrose accumulation by suppressing CuSnRK1α-mediated phosphorylation and degradation of CuWRKY41, enabling its transcriptional activation of CuSPS4 directly or via CuWRKY23. Our study provides significant insights into the molecular basis of drought-induced sucrose accumulation and presents valuable regulatory components that could be targeted for fruit quality improvement.

Malic acid is a crucial determinant of apple (Malus domestica) fruit quality, influencing acidity and flavor. While transcriptional regulation of malic acid metabolism is well-studied, post-transcriptional control and the role of jasmonate (JA) remain largely unexplored. We identify a novel regulatory pathway involving JA signaling, a microRNA (miRNA), and vacuolar transport regulators that control malic acid accumulation in apple fruit. We show that mdm-miR858, which increases during fruit maturation, directly targets and cleaves MdMYB73 transcripts. MdMYB73 is a known positive regulator of vacuolar H+-pumping and malate transport, activating genes like MdVHA-A, MdVHP, and MdALMT9. Overexpression of mdm-miR858 suppressed MdMYB73, thereby reducing MdVHA-A, MdVHP, and MdALMT9 expression and malic acid content in apple calli, fruits, and GL-3 plantlets, while silencing mdm-miR858 had opposite effects. Crucially, the JA-responsive transcription factor MdMYC2, the expression of which increases during fruit maturation, directly binds the mdm-miR858 promoter and activates its expression. Furthermore, the Mediator complex subunit MdMED25 interacts with MdMYC2, enhancing this activation. Manipulating MdMYC2 or MdMED25 expression altered mdm-miR858 levels, MdMYB73 expression, and malic acid accumulation, mirroring exogenous methyl jasmonate (MeJA) treatment effects. A miR858-resistant MdMYB73 variant confirmed the miRNA-target interaction's specificity and functional significance. Our findings reveal a novel JA–MdMYC2/MdMED25–miR858–MdMYB73 regulatory cascade controlling malic acid accumulation in apple, providing a mechanistic link between hormonal signaling and post-transcriptional regulation of fruit acidity. This discovery offers new targets for manipulating fruit quality.

Soybean is one of the most economically important crops worldwide and a valuable source of protein for human consumption and animal feed. The use of wild soybean accessions as a source of new alleles for improvement of soybean quality remains challenging owing to linkage drag. Here, using segregating populations derived from a set of wild soybean chromosome segment substitution lines, we fine-mapped quantitative trait loci (QTLs) (qPC-06-1) for seed protein content to a 48.8-Kb interval on chromosome 6. A gene encoding an S-adenosyl- L-methionine-dependent methyltransferase (GmMET) was determined to be the causal gene underlying the qPC-06-1 locus. Three single-nucleotide polymorphism/insertion-deletion markers (SNPs/InDels) in the coding region were found to modulate the methyltransferase activity of different GmMET alleles, thereby influencing seed protein content. Transgenic and multi-omics analyses provided preliminary evidence for the pathways through which GmMET influences seed protein content and exerts pleiotropic effects on seed oil content, oil composition, and related traits. Additional analyses showed that an elite GmMET allele was under selection during soybean domestication and improvement and is now widespread in modern cultivars, particularly in southern China. Our findings thus reveal that a methyltransferase gene affects the protein content of soybean seeds, providing a foundation for the continued development of high-protein soybean cultivars.

The anthracnose caused by Colletotrichum gloeosporioides poses a significant threat to the global mango (Mangifera indica L.) fruit industry. Although histone deacetylases (HDACs) are well recognized to be involved in plant immunity, the role of HDAC-mediated nonhistone deacetylation in the fruit immune response remains elusive. In the present study, MiHDA3, an HDAC from the RPD3/HDA1 subfamily, was identified as a candidate for regulating mango resistance based on the greatest induction of MiHDA3 in response to infection of C. gloeosporioides among the 19 tested HDAC genes. Transient overexpression of MiHDA3 in mango fruit strengthened the disease resistance by enhancing the activities of defense-related enzymes (phenylalanine ammonia-lyase (PAL) and β-1,3-glucanase (GLU)) and upregulating the expression levels of MiPAL and MiGLU. These increases occurred concomitantly with increased accumulation of local H₂O₂, a critical signaling molecule. The opposite effects on resistance and H₂O₂ production were observed in MiHDA3-silenced mango fruit. Physiological assays revealed that exogenous H₂O₂ treatment suppressed anthracnose development in mango fruit after inoculation with C. gloeosporioides, whereas treatment with diphenylene iodonium, an inhibitor of endogenous H₂O₂ generation, exacerbated disease symptoms. Furthermore, the mango catalase 1 (MiCAT1), a redox homeostasis-related protein, was confirmed to negatively regulate the resistance of mango fruit to C. gloeosporioides by catalyzing the decomposition of H₂O₂. Mechanistic investigations revealed that MiHDA3-mediated deacetylation of MiCAT1 at lysine residues K227 and K233 reduced the enzymatic activity and protein stability of MiCAT1, contributing to enhanced resistance in mango fruit. Collectively, these findings highlight that the functional interplay between HDACs and catalases can modulate the immune response in post-harvest fruits, and reveal a novel mechanism by which HDACs enhance mango disease resistance through the deacetylation of nonhistone proteins and the regulation of their biochemical functions.

Hyperosmolality-triggered physiological drought hinders plant growth and development, leading to a drop in crop yields. Hyperosmolality triggers calcium signaling, and yet how osmotic-induced calcium signaling participates in cellular osmotic response remains enigmatic. To date, several Ca²⁺ channels and transporters have been identified to regulate osmotic-induced calcium signal generation (CaSG) or Ca²⁺ homeostasis. However, there has been no report on their function in calcium signal clearance (CaSC) in plants, especially in crops. Here, we investigated the role of a rice cation/calcium exchanger OsCCX2 in modulating calcium signaling dynamics using two distinct calcium reporters aequorin and GCaMP6s. The results showed that, under osmotic stress conditions, CaSC was significantly delayed in both root and guard cells of ccx2 mutants compared with the wild-type. Further studies revealed that hyperosmotic stress-triggered influxes of sodium (Na⁺), potassium (K⁺), and chloride (Cl⁻) ions were significantly reduced in ccx2 mutants, resulting in a significantly smaller range of osmotic pressure and water potentials (Ψ_w) adjustment. In addition, the stomatal response was impaired, with a faster water loss in ccx2 in response to hyperosmotic stress. Furthermore, the absence of OsCCX2 altered the expression patterns of key osmotic-responsive genes, but their transcriptional activation was unaffected. Collectively, these changes ultimately led to reduced hyperosmotic stress tolerance in the mutants. Additionally, OsCCX2 is likely to be located in the endoplasmic reticulum and plasma membrane, and possess Na⁺/Ca²⁺ exchange activity. To sum up, our findings provide evidence that OsCCX2, as a CaSC regulator, is involved in cell osmotic adjustment, water homeostasis and osmotic stress tolerance in rice, which offers new insight into potential applications in drought-resistant crop improvement.

Hydrogen sulfide (H₂S), a well-established gaseous signaling molecule, can effectively enhance plant tolerance to various environmental stresses. However, there is still a lack of suitable methods to release H₂S in agricultural production, and the mechanism by which H₂S improves stress resistance remains poorly understood. Here, we show the novel role of sodium butyrate (NaB) in producing H₂S consistently in rice rhizosphere soil and the epigenetic mechanism of H₂S to enhance rice drought tolerance. We found that NaB increased sulfate-reducing bacteria (SRB) abundance in the rhizosphere soil, resulting in higher expression of sulfite reductase (SiR), and consequently increased H₂S production. Mechanistic investigation showed that H₂S enhanced the level of H4K5ac in promoter regions of drought-tolerant genes, facilitating their expression by repressing the histone deacetylase (HDAC) gene OsHDA710. Loss-of-function mutants of OsHDA710 exhibited enhanced drought tolerance compared to wild-type (WT) plants, while OsHDA710 overexpression plants showed drought hypersensitivity. Moreover, we demonstrated that OsHDA710 could bind directly to promoters of drought-tolerance genes by recognizing the TGACC motif. Our findings illustrate an efficient way to produce H₂S and a novel mechanism for H₂S in improving the drought resistance of plants.

Drought stress orchestrates a phosphorylation-dependent signaling cascade that reprograms transcriptional networks to enhance crop resilience. Through a large-scale transgenic screening, we identified ZmCRK5A, a Ca²⁺-independent calcium-dependent protein kinase (CDPK)-related kinase, as a master regulator of drought tolerance in maize. Mechanistically, ZmCRK5A directly phosphorylates the MYB transcriptional repressor ZmSMH4 (Single MYB Histone 4) at three conserved serine residues (Ser42/43/59) within its SANT domain, as demonstrated by in vitro kinase assays and site-directed mutagenesis. This post-translational modification abolishes ZmSMH4's DNA-binding capacity to ACC cis-elements, thereby de-repressing the potassium influx channel gene ZmKCH1 (K⁺ Channel 1). Functional validation revealed that ZmKCH1 overexpression confers drought resilience through optimized stomatal dynamics and water retention, whereas clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9(Cas9)-generated zmkch1 mutants display hypersensitivity to water deficit. Crucially, field evaluations demonstrated preserved grain yield alongside enhanced drought tolerance in plants with activated ZmCRK5A–ZmSMH4–ZmKCH1 signaling. Our findings delineate a kinase-transcription factor-ion channel axis that dynamically fine-tunes drought responses while maintaining productivity, providing a strategic framework for engineering stress-adapted crops without yield penalties.

Cryptochromes (CRYs) are photolyase-like blue-light receptors originally identified in Arabidopsis thaliana (Arabidopsis) and have since been identified across diverse evolutionary lineages. Cryptochromes not only transduce blue-light cues to the circadian clock but also maintain the temperature compensation of circadian clock. However, the precise mechanism by which CRYs integrate blue light signals into the circadian clock in Arabidopsis is still under investigation. This study revealed that, when blue light was filtered out from white light, the circadian period length in Col-0 was extended, but not in the cry1 cry2 double mutant. This indicates that both blue light and CRYs are crucial for regulating the circadian rhythm. Furthermore, we discovered that CRY2 interacted with PSEUDORESPONSE REGULATOR 5 (PRR5), a key component of the circadian clock under blue light, which suppressed PRR5's transcriptional inhibition ability on CCA1 and LHY. These findings illuminate the pathway through which blue light influences the circadian clock via the CRY2–PRR5 module.

Both biotic and abiotic factors are expected to drive species diversification, yet demonstrating their synergistic effects within a single framework is challenging and has rarely been studied. The recent and rapid radiation of the genus Aspidistra (cast-iron plant) provides an ideal system for examining these processes. Here, we generated restriction site-associated DNA sequencing data for 123 Aspidistra taxa and reconstructed well-resolved phylogenies using both concatenation- and coalescent-based approaches. Using a comprehensive suite of diversification models, we quantified the contributions of multiple biotic and abiotic factors and applied phylogenetic path analysis to detect their synergistic effects. Our phylogenetic analyses recovered two main clades that differ in stem habits. We found that the diversification of Aspidistra has been driven by both abiotic factors (paleotemperature and the East Asian monsoon) and biotic factors (interspecific competition and pollination mutualism). Notably, these drivers operated both independently and synergistically to facilitate the rapid radiation of Aspidistra. Beyond providing a robust phylogeny useful for classifying Aspidistra, we present a statistical framework for better understanding the macroevolutionary processes underlying rapid plant radiations. Our findings underscore the critical importance of integrating multiple biotic and abiotic drivers into a unified analytical framework to comprehensively understand diversification history.

Leaf morphology varies substantially across plant species. In soybeans, the regulation of compound leaf development remains poorly characterized, despite its critical role in plant architecture. Some soybean cultivars have compound leaves with up to five leaflets, while most are trifoliolate. Using genetic mapping, we identified a gene behind the leaflet number variation as LF1, an AP2/ERF transcription factor. High expression levels of LF1 were further observed in leaf primordium initiation sites, leaf primordia, and leaflet initiation domains. Transgenic overexpression of LF1 increased leaflet number. Further investigation revealed that LF1 regulates leaflet development through negative autoregulation via GCC-box cis-element binding. In addition to the role of LF1, the CRISPR-edited mutant of TEOSINTE-BRANCHED1/CYCLOIDEA/PCF3 (GmTCP3) displayed serrated blade margins in juvenile leaves and increased compound leaflet numbers. Protein interaction assays confirmed LF1 binding affinity for GmTCP3. Furthermore, we demonstrate that LF1 induces the expression of GmLFY, a key regulator of leaflet development. Altogether, our findings establish LF1 as a central regulator of soybean leaflet morphogenesis and reveal its mechanistic interactions with GmTCP3 and LEAFY (GmLFY), offering novel mechanistic insights into the genetic control of compound leaf development.

Rice is one of the most important food crops in the world and it is prone to attack by many diseases, such as the rice blast, sheath blight, bacterial leaf blight, and so on. These diseases represent the main constraints in rice production, threatening food security and safety. Here, new control strategies against these major rice diseases have been developed either by heterologous expression of a pathogen effector UvScd1 from false smut fungus Ustilaginoidea virens or by spraying the engineered biocontrol agent Bacillus subtilis secreting the effector UvScd1. Compared to the wild-type rice Zhonghua11 (ZH11), the rice line heterologously expressing UvScd1 showed lesion mimics and upregulated the expression of defense-related genes in leaves, including genes related to the JA and SA signaling pathways. As expected, the transgenic rice line showed broad-spectrum resistance to hemibiotrophic fungus Magnaporthe oryzae, necrotrophic fungus Rhizoctonia solani, and bacterium Xanthomonas oryzae pv. oryzae (Xoo), while there was no effect on yield-related agronomic traits compared with ZH11, suggesting that the effector UvScd1 confers both plant resistance via induction of ROS and defense-related genes, and maintains the balance between plant resistance and yield. In field experiments, comparable control efficiencies against these major rice diseases were achieved by spraying B. subtilis engineered to secrete UvScd1 and corresponding chemical pesticides, underscoring that use of biocontrol agents to secrete certain pathogen effector proteins is an effective strategy for the management of plant diseases. It is noteworthy that the application of B. subtilis engineered to secrete UvScd1 also achieved effective control for a variety of crop diseases, suggesting its excellent potential for use in practice.