Genetic homogenization due to chronic clonal propagation poses a notable challenge to the sustainable utilization of Coptis chinensis Franch. We developed a novel elite cultivar, ‘Chulian No. 1’, with superior yield (+34%), disease resistance, and pharmacopoeia-standard alkaloid profiles through comprehensive agronomic evaluation. To understand the genetic basis of these traits, we constructed a high-quality chromosome-level genome assembly, revealing long terminal repeat retrotransposon (comprising 41.92% of the genome) shows significant enrichment near expanded stress/alkaloid biosynthesis genes. Whole-genome resequencing of 235 accessions indicated extreme genetic uniformity (π < 0.0018), but our novel geospatial-autoencoder model successfully identified three eco-geographic groups that could not be discriminated using traditional approaches. Genome-wide association analysis identified the leaf glossiness-associated gene CcHAB1 on chromosome 1. Comparative transcriptomics revealed correlations between CcHAB1 expression and cuticular wax biosynthesis gene regulation via ABA and phenylpropanoid pathways, potentially explaining enhanced disease resistance in glossy-leaf accessions. This work enables molecular breeding for medicinal plants with limited genetic diversity and provides insights into trait maintenance despite genetic homogenization.

Understanding domestication in perennial crops is crucial for unraveling the evolutionary trajectories that shaped their genetic diversity and for guiding conservation and breeding. The domestication of Mediterranean fruit trees is less studied than that of annual crops. The common fig (Ficus carica L.) is thought to have been domesticated in the Levant before dispersal across the Mediterranean; however, prehuman fossils in Europe suggest an ancient wild presence, challenging the assumption of a single eastern origin. We genotyped 949 cultivated and spontaneous fig accessions using microsatellite markers from 14 Mediterranean and Near Eastern countries, as well as F. carica subsp. rupestris and Ficus colchica. Principal component analysis showed that F. carica sensu stricto forms a cohesive genetic group distinct from its relatives, which should be considered separate species. Bayesian clustering revealed three major gene pools within F. carica sensu stricto-Moroccan–Algerian, Northern Mediterranean, and Levantine-each containing both cultivated and spontaneous individuals. The Levantine group was the most differentiated, while the other two were more closely related, reflecting a longitudinal Mediterranean structure. Cultivated and spontaneous figs were genetically indistinguishable within regions, supporting a diffuse, regionally independent domestication model rather than a single Levantine origin. These results highlight spontaneous populations and local landraces as critical reservoirs of genetic variation in Morocco, Algeria, and the Levant. Our study provides a foundation for genomic research to identify the basis of key traits and emphasizes that breeding and conservation strategies should rely on regional biodiversity to enhance fig resilience and productivity under global change.

Nervonic acid (NA) is a monounsaturated fatty acid (FA) with multiple therapeutic and hygienic benefits, and accumulates in plant seeds. It is essential for developing innovative plant sources of NA to elucidate the molecular regulation mechanisms underlying NA biosynthesis and accumulation. We present high-quality chromosome-level de novo genome assemblies of two contrasting NA-producing plants: high-NA Macaranga indica and low-NA M. denticulata. Both M. indica and M. denticulata retained considerable repetitive sequences, similar chromosome arrangements, and analogous regulation models in capsule maturation. Correlated to faster accumulation of NA, M. indica concentrated genes and regulators of FA biosynthesis, FA elongation and triacylglycerol biosynthesis in three ways: uniform regulators, fewer analogous duplications and higher expression of genes. In contrast, M. denticulata showed a diverse environment response, and had more analogous redundant duplications. Despite their sympatric distribution, the two species showed staggered flowering. Cold, ABA and phosphate starvation were major elicitors in M. indica, and core genes were identified as KCS, PDAT, and DGAT. Further resequencing analysis of M. indica revealed geography-specific gene polymorphisms and migration pathways. Our results unveil the differences in NA biosynthesis and accumulation mechanisms between M. indica and M. denticulata. This understanding, combined with insights into cultivation strategies and regional genetic diversity, provides a basis for the domestication and breeding of Macaranga species toward efficient NA production.

Soil cadmium (Cd) pollution threatens global food security. Elucidating plant cellular responses to Cd stress is critical for the breeding of low-Cd-accumulating crops. Here, we investigated Cd-responsive regulatory mechanisms in alfalfa at single-cell resolution and identified key Cd-associated genes. Eight major root cell types were annotated, with significant remodeling under Cd stress. Under Cd stress, root endodermal and phloem cells adopt distinct adaptive strategies: endodermal cells shift toward a Cd sequestration and detoxification state, whereas phloem cells exhibit a response gradient ranging from basic defense to systemic regulation. Integrated multiomics analyses revealed cell-type-specific genome-wide changes in chromatin accessibility, which positively correlated with gene expression-particularly in promoter regions. Key genes including MsGSH1, MsMT2A, MsHMP47, and MsABCC3 were shown to increase Cd tolerance in yeast. Coexpression network analysis revealed 10 cell-type-specific modules, with the calmodulin-like gene MsCML acting as a highly interconnected hub gene, whose overexpression significantly improved Cd tolerance. These findings provide valuable genetic resources and a theoretical basis for the precise breeding of low-Cd-accumulating forage, with implications for understanding Cd-responsive epigenetic and transcriptional regulation in plants.

Abiotic stresses-particularly cold, drought, and salinity-pose significant threats to the productivity and sustainability of horticultural crops. Recent studies have revealed conserved and species-specific regulatory mechanisms that allow plants to adapt dynamically to these environmental constraints. This review synthesizes advances in understanding key transcription factor families-such as CBF/DREB, NAC, MYB, WRKY, and bHLH-that orchestrate stress-responsive gene networks and modulate physiological processes, including osmotic regulation, antioxidant defense, and ionic homeostasis. We also discuss the emerging roles of chromatin remodeling, DNA methylation, histone modifications, and noncoding RNAs in conferring transcriptional plasticity and stress memory. Beyond endogenous pathways, we evaluate transgenic strategies, CRISPR/Cas-based genome editing, and synthetic gene circuits for engineering abiotic stress tolerance. Particular attention is given to trade-offs between growth and defense, challenges in horticultural crop transformation, and gaps in field translation. We further examine the regulatory role of secondary metabolites-such as flavonoids and salicylic acid-as biochemical interfaces between signal transduction and adaptive responses. Finally, we propose a forward-looking roadmap integrating multi-omics, ideotype design, and precision breeding toward climate-resilient horticultural systems.

Tomato yellow leaf curl virus (TYLCV) poses a serious threat to global tomato production. Current management strategies remain limited, highlighting the need for novel antiviral agents. In this study, we evaluated the efficacy of a newly synthesized pyrimidine–guanidine derivative, YYH-6, against TYLCV in tomato (Solanum lycopersicum cv. Micro-Tom) and investigated its underlying mechanisms. Foliar application of YYH-6 significantly reduced viral accumulation and alleviated disease symptoms. Transcriptomic analysis revealed that YYH-6 treatment upregulates defense-related pathways such as plant–pathogen interaction, MAPK signaling, and phenylpropanoid biosynthesis. Results of TRV-based virus-induced gene silencing (VIGS) further indicate that RPP13 and ALS2 function as important resistance genes induced by YYH-6. Activity-based protein profiling, LC–MS/MS, and reverse genetic verification by VIGS indicate that serine hydroxymethyltransferase and STI1 domain-containing proteins are potential target proteins of YYH-6 for TYLCV inhibition. Our findings demonstrate that YYH-6 suppresses TYLCV infection through multitarget modulation of host defense pathways, making it a promising candidate for sustainable management of tomato viral diseases.

Low temperature severely limits grapevine growth and productivity. In this study, VpCDPK13, a calcium-dependent protein kinase, was identified as a cold-inducible positive regulator in Vitis pseudoreticulata. Protein–protein interaction assays demonstrate that VpCDPK13 physically interacts with the transcription factor VpCAMTA3. Functional analyses reveal that both VpCAMTA3 and VpCDPK13 positively regulate grapevine cold tolerance. Moreover, in vitro kinase assays show that VpCDPK13 phosphorylates VpCAMTA3 at Thr588, Ser834, and Ser1049, and this phosphorylation further enhances the biological function of VpCAMTA3 under cold. Collectively, these findings establish the VpCDPK13–VpCAMTA3 signaling module as a key regulatory pathway that promotes grapevine adaption to cold stress.

Base editing enables precise substitution of single nucleotides and is a promising technology for improvement of agronomic traits, including those of potato (Solanum tuberosum), the third most important food crop globally. Here, we developed efficient cytosine base editors (CBEs) for potato via multidimensional optimization. By evaluating several highly active cytidine deaminases, we identified two deaminases with high efficiency and distinct characteristics, which were used to construct CBEs for divergent editing applications. Furthermore, the editing efficiency of CBEs was significantly enhanced through several strategies: employing the Arabidopsis thaliana RPS5A promoter and the tobacco mosaic virus Ω enhancer to boost the expression of the editing reagents, fusing chromatin-modulating peptides, and co-expressing the human RNA m⁶A demethylase gene hFTO to enhance chromatin accessibility. In a hairy root assay, an efficient optimized base editor, RF-Sdd7-HNHN, elevated the average editing efficiency nearly 3-fold, from 26.8% (pre-optimization) to 76.7%. Using RF-Sdd7-HNHN, we achieved an 85.7% efficiency for simultaneous editing of target nucleotides in ACETOLACTATE SYNTHASE 1 (StALS1) and StALS2 and obtained homozygous mutant potato germplasm exhibiting herbicide resistance. In conclusion, this research established new and efficient CBEs for potato and offers insights and strategies for optimizing other CRISPR-based editing tools.

The circadian clock synchronizes a multitude of biological events with environmental changes, thereby optimizing plant growth and development. In legumes, nodule formation, a pivotal process that sustains symbiotic nitrogen fixation, is one such event regulated by the circadian clock. Nevertheless, the mechanisms underlying the circadian clock’s regulation of nodule formation and nitrogen fixation are still poorly elucidated. Herein, we unveil that the core clock gene LUX ARRHYTHMO (LUX) exerts a crucial role in modulating nodule formation and root development via auxin biosynthesis pathways in the model legume Medicago truncatula. Our findings indicate that MtLUX directly associates with the promoter of MtRVE1, a clock output gene involved in auxin biosynthesis, both in vivo and in vitro, thereby repressing its expression. Biochemical and genetic data further corroborate that the MtLUX-MtRVE1 regulatory module adjusts root architecture and nodule formation through the fine-tuning of auxin biosynthesis. These discoveries reveal a mechanism whereby the circadian clock integrates hormonal pathways to regulate nodule formation, thereby linking circadian regulation, auxin biosynthesis, and nitrogen fixation in legumes. This research lays the groundwork for enhancing legume growth and nitrogen acquisition under fluctuating environmental conditions.

The apical bud-break is an important stage in the regulation of lotus (Nelumbo nucifera Gaertn.) flowering. Phytohormones play a key role in the development of plant buds, but the molecular mechanisms underlying the crosstalk between different phytohormone signals, especially abscisic acid (ABA) and jasmonic acid (JA), in lotus bud-break remain unclear. In this study, we found that the exogenous application of ABA inhibited the lotus apical bud-break. In addition, the expression of the gene encoding ABSCISIC ACID INSENSITIVE 5 (NnABI5), a crucial regulator of ABA signaling, was gradually downregulated during lotus apical bud-break. The transient overexpression of NnABI5 in lotus and heterologous expression in Arabidopsis thaliana (L.) Heynh. demonstrated that NnABI5 negatively regulates apical bud-break and seed germination. NnABI5 interacted with the JA pathway inhibitors NnTIF[F/Y]XG10A/B (NnTIFY10A/B), reducing the binding ability of NnABI5 to response genes EARLY METHIONINE-LABELED 1 (NnEM1) and NnEM6. In contrast, NnTIFY10A/B positively regulates apical bud break and seed germination. Notably, exogenous application of the JA biosynthesis inhibitor DIECA alleviated the inhibitory effect of ABA. In vitro protein degradation assays revealed that ABA could accelerate the degradation of NnTIFY10A/B. In summary, our data reveal the crosstalk of the JA and ABA signaling pathways in lotus apical bud-break, laying a theoretical foundation for understanding the regulation of flowering in this species.

Agrobacterium-mediated transient transformation is a fundamental tool for plant research and molecular pharming, but its application is often limited by host immune responses, post-transcriptional gene silencing, and the lack of a robust, quantitative reporter for species beyond Nicotiana benthamiana. To address these challenges, we developed a sensitive reporter system based on the fungal bioluminescence pathway (FBP). As an autonomous, substrate-free metabolic pathway, the FBP enables high-throughput, quantitative screening without external manipulations. Using this system, we systematically evaluated factors affecting transformation efficiency across more than 20 plant families. This cross-lineage analysis identified that co-expressing NahG and P19, termed the NaP19 module, not only mitigates P19-induced cytotoxicity but also synergistically enhances transient expression in diverse species, including agroinfiltration-recalcitrant crops and horticultural plants. We demonstrate the platform’s in vivo utility in its native genetic background for applications, such as protein localization, interaction assays, and transcriptional regulation studies. By integrating a quantitative, substrate-free reporter with a broadly effective NaP19 enhancer, this work establishes a robust and versatile platform for advancing functional genomics and biotechnology throughout the land plant lineages.

Radish (Raphanus sativus L.) represents a major root vegetable crop exhibiting remarkable variation in taproot morphology, yet the underlying genetic and molecular mechanisms remain poorly understood. Through a structural variant (SV)-based genome-wide association study (GWAS), we identified RsOFP2.3 , encoding an OVATE Family Protein (OFP), as a major determinant of fleshy taproot shape. Comprehensive expression profiling and RNA in situ hybridization revealed that RsOFP2.3 is broadly expressed, with the highest transcript accumulation in cambial tissues. Notably, RsOFP2.3 expression was markedly higher in the round-rooted accession than in the long-rooted one. Population-wide analysis showed that RsOFP2.3 expression was negatively correlated with taproot length and shape index, but positively correlated with taproot width. A 312-bp transposable element (TE) insertion in the RsOFP2.3 promoter repressed its expression and was strongly associated with taproot shape variation, revealing a TE-mediated cis-regulatory mechanism underlying morphological divergence. Functional analyses showed that RsOFP2.3 overexpression (OE) promotes radial expansion by enhancing cambial cell division and xylem differentiation, resulting in thicker and shorter taproots, whereas silencing RsOFP2.3 produced opposite phenotypic effects. Mechanistically, RsOFP2.3 physically interacts with the TONNEAU1-recruiting motif (TRM) protein RsTRM4, recruiting it from microtubules to the cytoplasm. Downregulation of RsTRM4 reduced taproot length, while RsTRM4 OE partially alleviated the shortened organ phenotypes caused by RsOFP2.3 OE, indicating an antagonistic relationship that fine-tunes organ morphology. These findings uncover two coordinated regulatory mechanisms involving TE-mediated cis-regulatory variation and a conserved OFP-TRM interaction module that jointly shape the balance between radial and longitudinal growth during radish taproot development, providing valuable molecular targets for precision breeding of storage root crops.

Polymethoxyflavones (PMFs) are a distinct class of plant flavonoids with significant therapeutic potential, particularly as anticancer agents. This potent bioactivity is largely attributable to O-methylation. However, a major bottleneck for the industrial-scale production of PMFs is the lack of suitable precursors and available O-methyltransferases (OMTs), which are essential for constructing a viable biosynthetic pathway. Here, we discovered a caffeic acid O-methyltransferase (CsOMT5) whose transcriptional dynamics closely mirrored the PMF levels in the flavedo of sweet orange (Citrus sinensis). In vivo validation further verified that CsOMT5 indeed promoted PMF accumulation in citrus. And its recombinant protein possessed broad substrate promiscuity for various PMF intermediates. Notably, CsOMT5 exhibited specialized C5-regioselectivity for naringenin, a readily available precursor for de novo synthesis of PMFs. Furthermore, critical residues involved in this methylation activity (N14, T18, I120, I256, and G305) were revealed through mutational analysis. This study not only provides deeper insights into the PMF biosynthetic pathway but also opens new avenues for the industrial biosynthesis of PMFs.

Domestication reshapes plant genomes and traits, yet the genomic basis of floral scent loss remains unclear. Here, we present an 876 Mb pseudo-chromosome genome assembly of the wild carnation Dianthus broteri (2 n = 2 x = 30) and compare it with the cultivated D. caryophyllus, which exhibits reduced floral scent. Transposable elements occupy 82.4% of the D. broteri genome, dominated by Gypsy LTRs, whereas D. caryophyllus exhibits more recent insertions near genes, consistent with domestication associated effects. Volatilome profiling of D. broteri revealed 59 floral volatiles, dominated by sesquiterpenoids, with lineage-specific differences in composition. Terpenoid-biosynthesis genes are upregulated in flowers of the scented western lineage, while the weakly scented eastern lineage shows reduced expression of upstream pathway components despite constitutive transcription of some terpene synthases. Variant discovery within terpenoid pathway genes showed that the most highly and constitutively expressed gene, DbrTPS18, accounted for almost 50% of all lineage-specific variants. Several nonsynonymous substitutions in DbrTPS18 were identified within the catalytic domains and the predicted chloroplast transit peptide, and these variants were significantly associated with variation in scent production. These results uncover the basis of terpenoid biosynthesis in the genus Dianthus and, together with the presented reference genome, provides a foundation to explore the genomic consequences of domestication and enhance fragrance in cultivated carnations.

Ichang papeda (Citrus ichangensis), a wild primitive citrus species, exhibits remarkable cold tolerance, yet the transcriptional regulation of cold-responsive genes in C. ichangensis remains poorly explored. In this study, we identified the small heat shock protein (sHSP) CiHSP26.5 as a crucial member that was substantially induced under cold stress and played a positive role in cold tolerance. Furthermore, two APETALA2/Ethylene Responsive Factor (AP2/ERF) family transcription factors, CiERF023 and CiERF041, were found to directly bind to the dehydration-responsive element (DRE) motifs in the promoter of CiHSP26.5 and function as its negative and positive regulators, respectively. In addition, CiERF023 was proven to repress CiERF041 through interacting with the DRE element in the promoter. These two TFs were differentially induced during cold stress, with CiERF023 peaking at early stages and CiERF041 at later stages. Consistently, CiERF023 acts as a negative regulator, whereas CiERF041 serves as a positive regulator, of cold tolerance by regulating CiHSP26.5. Taken together, our findings reveal that CiERF023 and CiERF041 form a hierarchical transcriptional cascade that antagonistically regulates CiHSP26.5 expression under cold stress in C. ichangensis. This study provides fresh insights into the regulatory network governing HSP-mediated cold adaptation and identifies potential targets for enhancing cold tolerance in plants.

Anthocyanins are the primary determinants of floral pigmentation in Chrysanthemum × morifolium , and ethylene acts as a key regulator of their biosynthesis. Although the ethylene-mediated regulatory circuitry is functionally important, its underlying mechanism in chrysanthemum has remained unclear. In this study, we identified CmMYB4 as a transcriptional repressor that directly suppresses the expression of key anthocyanin biosynthetic genes, including CmDFR (dihydroflavonol 4-reductase), CmUFGT (flavonoid 3- O -glucosyltransferase), and Cm3MaT (anthocyanin 3- O -glucoside -6′′- O -malonyltransferase). Time-ordered gene co-expression network analysis comparing the transcriptomes of CmMYB4 -overexpressing and control plants, together with molecular biology experimental results, further revealed CmERF3 (ethylene response factor 3) as a hierarchical upstream regulator of anthocyanin biosynthesis. Exogenous ethylene treatment induced CmERF3 expression while reducing anthocyanin accumulation. Subsequent functional characterization showed that the overexpression of CmERF3 suppresses anthocyanin biosynthesis in both tobacco and chrysanthemum by directly activating CmMYB4 and repressing CmDFR , CmUFGT , and Cm3MaT CmMYB4 − LBGs (late biosynthetic genes) regulatory module. This study not only elucidates the molecular mechanism governing ethylene-mediated anthocyanin inhibition but also provides new perspectives for the molecular engineering of ornamental traits in chrysanthemum

Although ERF transcription factors (TFs) play critical roles in abiotic stress tolerance, the molecular mechanisms underlying this role remain incompletely understood. This study identified BpERF1A in birch (Betula platyphylla) as a drought-responsive TF through co-expression regulatory network analysis. Expression of BpERF1A was stalwartly induced by drought stress, and drought treatment markedly boosted its promoter activity. Functional analyses demonstrated that overexpression of BpERF1A markedly improved drought tolerance compared with wild-type (WT) birch, whereas its repression increased drought sensitivity. Overexpression lines also exhibited higher antioxidant enzyme activities and proline content relative to WT. Chromatin immunoprecipitation-polymerase chain reaction, yeast one-hybrid and dual-luciferase (dual-LUC) assays confirmed that BpERF1A directly binds to G-box elements in the promoters of BpDHN (dehydrin) and BpAOS (allene oxide synthase), activating their transcription. Furthermore, overexpression of BpDHN/BpAOS enhanced drought tolerance and promoted reactive oxygen species (ROS) scavenging in transgenic plants. Protein–protein interaction analysis using bimolecular fluorescence complementation revealed that BpERF1A interacts with BpRAV1 to form a heterodimer, which further enhances BpERF1A binding to the BpDHN promoter and its transcriptional activation. Collectively, these findings establish a central role for the BpERF1A regulatory module in drought acclimation and highlight its synergistic interaction with BpRAV1, providing an effective strategy to enhance drought tolerance through improved ROS scavenging capacity.

Agrobacterium-mediated transformation remains challenging for economically important citrus crops because of low transformation and regeneration efficiencies. REGENERATION FACTOR1 (REF1), a plant elicitor peptide, is a local wound signal perceived by PROPEP RECEPTOR-LIKE KINASE 1 (PORK1) and transduced via WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1). Exogenous REF1 peptide application has recently been reported to improve transformation and regeneration of herbaceous plants including tomato, which was explored on Agrobacterium-mediated citrus transformation in this study. We identified REF1, PORK1, and WIND1 orthologs in sweet orange (Citrus sinensis), which encodes two REF1 isoforms, CsREF1–1 and CsREF1–2. REF1 of tomato (SlREF1) and the two CsREF1 isoforms of different concentrations were tested for their effect on Agrobacterium-mediated transformation of citrus via exogenous application. CsREF1–1 at 10 or 100 nM and CsREF1–2 at 100 nM significantly increased GFP-positive transgenic callus formation, whereas SlREF1 had no significant effect. In addition, CsREF1–1, CsREF1–2, and SlREF1 reduced shoot regeneration. To overcome this trade-off, we exposed epicotyl explants to 100 nM CsREF1–2 only during the first month and then transferred them to REF1-free regeneration medium, yielding 4.1-fold more GFP-positive shoots than the untreated control. Such a staged application of CsREF1–2 also improved GFP-positive shoot recovery in Carrizo citrange by 3.3-fold. Reverse transcription-quantitative PCR (RT-qPCR) showed that CsREF1–2 induced CsWIND1 and CsESR1, which are critical for callus formation and shoot regeneration, but continuous CsREF1–2 exposure also suppressed shoot/meristem regulators, which was mitigated by removal of CsREF1–2 in the later stage. AlphaFold3 and PRODIGY predictions indicated the highest binding affinity for CsREF1–2 with CsPORK1, consistent with its superior activity. Overall, both CsREF1 peptides enhance citrus transformation but suppress regeneration, and staged exogenous application of CsREF1 peptides improves genetic improvement of recalcitrant perennial crops such as citrus, which decouples early dedifferentiation from later organogenesis, substantially expanding the toolbox for high-throughput functional genomics in citrus.

High-temperature stress caused by global warming can induce leaf senescence, which adversely affects plant growth and agricultural productivity worldwide. However, the molecular mechanism of high temperature–induced leaf senescence remains largely unexplored. In this study, a Stay-green-like protein (PlSGRL) that regulates chlorophyll degradation was identified in herbaceous peony (Paeonia lactiflora Pall.). PlSGRL was localized to the chloroplasts, and its expression was upregulated under high-temperature stress. Virus-induced PlSGRL silencing markedly delayed high temperature–induced leaf senescence in P. lactiflora, as evidenced by higher chlorophyll content, sustained photosystem II efficiency, and alleviated oxidative damage-reflected in reduced malondialdehyde content, relative electrical conductivity, and reactive oxygen species accumulation. Conversely, PlSGRL overexpression accelerated high temperature–induced leaf senescence. Subsequently, we identified an atypical MYB transcription factor, PlMYB3RL, that directly promoted PlSGRL expression. PlMYB3RL was localized to the nucleus, and its expression was also upregulated under high-temperature stress. Similarly, PlMYB3RL silencing significantly delayed high temperature–induced leaf senescence. Additionally, PlMYB3RL formed a homodimer through self-interaction, and this homodimer enhanced the transcriptional activation of PlSGRL in a dose-dependent manner. Collectively, these data demonstrate that the PlMYB3RL homodimer activates PlSGRL expression to promote chlorophyll degradation and leaf senescence under high-temperature stress in P. lactiflora. These findings reveal a novel regulator y module underlying high temperature–induced leaf senescence in P. lactiflora, providing key gene resources and theoretical support for breeding high-temperature-resistant cultivars.

Insect pollination is critical for fruit production, particularly for pears, most of which have high self-incompatibility and are less preferred by pollinators than other fruit trees. Research has focused on fruit traits, and less is known about how floral traits may influence pollination and fruit production. Hypothesising that pollination-related traits differ between Asian and European pears, which exhibit large variation in pollination and distinct domestication processes, we conducted a systematic review of pear pollination studies published globally from 1922 to 2025. Research on pollination has increased rapidly over the last 25 years. Compared to European pears, we found that Asian pears are more pollinator-dependent and exhibit different floral traits: lower nectar sugar concentration and lower relative content of attractive floral scents, but higher pollen production and a higher relative content of N-containing floral scents. Although Asian pear flowers attract a similar number of insect pollinator taxa as European pears, current Asian pear production still relies mainly on artificial pollination. Moreover, various artificial pollination techniques and pollination management practices, including introducing indigenous Asian honey bees, which outperformed in collecting pear pollen, had uncertain effects on pollination and fruit production, as less attention was paid to understanding the nature of plant–pollinator interactions. Further studies are needed to investigate how the domestication process and the co-adaptations of Asian honey bees influence the pollination-related floral traits of pears. This may provide valuable insights into enhancing floral attractiveness, improving pollination efficiency, and increasing fruit production in monoculture Asian pears.

Chlorophyll, the pigment in plant leaves, is crucial for capturing light during photosynthesis. Mutations that disrupt chlorophyll production or chloroplast development frequently lead to changes in leaf color. Here, we report the identification and characterization of a chlorotic mutant in cucumber (Cucumis sativus L.), named tnyl3, which exhibits chlorotic cotyledons and seedling lethality. Map-based cloning revealed that the tnyl3 mutation results from a Tnt1 retrotransposon insertion in a gene encoding nuclear factor Y subunit B3 (NF-YB3), a transcription factor subunit. Compared with the wild type, the mutant exhibited dramatic decreases in chlorophyll a and b levels and a significantly lower net photosynthetic rate. Ultrastructural analysis revealed that the chloroplasts in the tnyl3 mutants are structurally abnormal and characterized by underdeveloped thylakoid membranes. Gene expression analyses revealed that CsNF-YB3 is highly expressed in young seedling tissues and is upregulated by light. CRISPR/Cas9 analyses subsequently confirmed that the tnyl3 phenotype is caused by the loss of CsNF-YB3. Yeast two-hybrid and split-LUC assays demonstrated that CsNF-YB3 interacts directly with the cucumber NF-YC2 protein and promotes CsTIC21 transcription, suggesting that it functions as part of an NF-Y transcriptional complex. Transcriptome profiling of the mutant revealed extensive downregulation of photosynthesis-related genes, which is consistent with its impaired chloroplast function. Our findings establish CsNF-YB3 as a crucial genetic factor for chloroplast development and pigment synthesis in cucumber. This work provides new insight into the NF-Y–mediated regulatory network controlling chloroplast biogenesis and offers a potential genetic target for improving plant photosynthetic performance and vigor.

Partitioning of genetic variance into additive and non-additive components using the pedigree-based best linear unbiased prediction (P-BLUP) model is possible because of the family structure and replicated clones in clonally propagated crops, but this model may overestimate these components. However, the genomic best linear unbiased prediction (G-BLUP) method, which integrates the genetic relationship through molecular marker information reduces the overestimation. Alternatively, a combination of the P-BLUP and G-BLUP, sourcing to create a hybrid matrix that estimates hybrid best linear unbiased prediction (H-BLUP), is proposed. We investigated if integrating molecular information into the clonal model could improve the partitioning of the variance components leading to more accurate estimates of genetic parameters and prediction accuracy of breeding values of 14 key traits in diploid banana. In this study, we used clones of 14 full-sib families from a factorial mating design of four female and five diploid male banana (Musa acuminata) parents, generated at the International Institute of Tropical Agriculture in Arusha. The genomic-based relationship matrices were constructed using a set of 2792 filtered single-nucleotide polymorphism markers. Additive variance and heritability derived from G-BLUP and H-BLUP models reduced bias compared to the P-BLUP model. The H-BLUP estimated the highest prediction accuracies for yield-related and cycling traits, while the P-BLUP model had the highest prediction accuracy estimates for agronomic traits. The use of marker-based models enhances the accuracy of predicting breeding values, contributing to accurate estimates of genetic gain while paving a way for further genomic exploration in diploid banana breeding programs.

Apple replant disease (ARD) is a soil-borne disease that arises from replanting apple trees on land previously used for apple cultivation. There is interest in biomarkers that can reliably assess the severity of ARD by quantifying how strongly apple plants react to the disease in soils of different agro-environments. Thus far, transcriptomic studies of ARD-affected plants have examined only a few soils at a time, revealing that expression patterns vary among different soils. Here, we analyzed the expression of 90 candidate genes in the roots of apple plants (rootstock genotype ‘M.26’) grown in ARD-affected soils from 151 sites across Germany to test whether a consistent pattern of gene expression under ARD-conditions exists. Additionally, the expression of the candidate genes was analyzed in the leaves of apple plants grown in 18 different ARD-affected soils. Most of the genes (72) showed significantly upregulated expression in roots under ARD conditions, while only 11 showed significantly upregulated expression in leaves, suggesting that these genes play a significant role in the ARD reaction in roots but only a limited or no role in leaves. The candidate genes were evaluated for their potential as ARD biomarkers, defined by their consistently increased expression under ARD conditions across different soils and correlation with ARD severity. The accordingly selected ARD biomarker genes in roots include genes involved in phytoalexin biosynthesis, lignin metabolism, ethylene metabolism, cyanogenesis, detoxification, programmed-cell-death, and plant defense. These biomarkers have the potential to assess the severity of ARD and open up new possibilities for disease diagnosis.

Cucurbita moschata, commonly known as pumpkin, is highly valued for its nutritional content, stress tolerance, fruit phenotypic diversity, excellent characteristics of easy-planting and transportation, and long shelf-life, which makes it recommended as an essential crop for the mitigation of food and nutritional challenges. However, the absence of a high-quality reference genome hinders genetic improvement studies on pumpkins. Here, we successfully assembled the telomere-to-telomere (T2T) genome of C. moschata L. (2 n = 40) with a total size of 289.6 Mb (Contig N50 = 11.2 Mb). It comprises all 40 telomeres, 8 gaps, and 29 901 protein-coding genes (BUSCO = 97.9%), and half of the chromosomes are composed of a single contig. Additionally, to investigate the genetic basis of fruit traits in pumpkin, we developed an F₂ genetic population consisting of 200 individuals and constructed a high-density genetic linkage map using the assembled genome as the reference. Quantitative trait locus (QTL) mapping of 20 fruit traits was applied. An AUX/IAA gene and a β-tubulin gene were identified as candidate genes regulating longitudinal flesh thickness and transverse/longitudinal diameter ratio, respectively. In summary, the genome assembly for C. moschata and QTL mapping results provide valuable resources for molecular breeding and functional genomics studies in the pumpkin.

Jasmonic acid (JA), a pivotal lipid-derived phytohormone, serves as a critical regulator in plant growth and defense mechanisms. However, the genetic mechanisms of OPR2 gene in JA-dependent biotic defenses of Camellia tachangensis have rarely been investigated. In this study, we performed a genome-wide association study to analyze 100,720 high-quality single nucleotide polymorphisms (SNPs) among 350 tea accessions from Guizhou province to identify genetic variations associated with JA. Analysis showed C. tachangensis displayed higher levels of JA content, further analysis identified 60 high-quality SNPs and nine candidate genes related to JA. Among them, CtOPR2 encoding 12-oxophytodienoic acid reductase 2 is responsible for catalyzing the conversion of 4,5-didehydro-JA (4,5-ddh-JA) to JA. The expression level of CtOPR2 in three tea accessions with different JA content was consistent with the dynamic changes of JA content. The expression level of synthetic (AOS, AOC, and ACX) and responsive (WRKY18 and MYC2) genes were significantly decreased and increased in asODN- CtOPR2-treated shoot tips and transgenic tobacco lines overexpressing CtOPR2, respectively, which were consistent with the JA content. These results further revealed that CtOPR2 gene played essential roles in promoting JA biosynthesis. A significant reduction in insect bite area was observed on transgenic tobacco leaves compared to wild-type leaves in feeding experiments with Spodoptera litura, highlighting that the positive regulatory function of CtOPR2 gene in JA-mediated immune responses. This study provides a robust theoretical foundation for marker-assisted selection breeding in tea, aimed at developing high-JA germplasm with potentially enhanced pest resistance for cultivation in Guizhou.

Plant aquaporin (AQP), one of the ancient protein superfamilies with high diversity, plays a canonical role as water channel transporters to regulate seed germination, stomatal movement, cell elongation, reproduction, and environmental adaptation. Previously, we have demonstrated that two AQPs colocalize within a quantitative trait locus (QTL) linked to the genetic regulation of rose prickles, which function as water reservoirs at their early developmental stages. Here, we systematically characterize the diversity of AQPs in all plant lineages taking the Rosaceae as one example and establish a genetic link between PIP2;1 expression and prickle development. We reveal the ancient origin and remarkable deep conservation in AQP protein structure, the increase of copy number following the diversification of plant lineages and a strong positive selection of the PIP2 and the SIP subfamilies within Rosaceae. Intriguingly, this is contrasted by substantial expression divergence, which is accompanied with regulatory divergence, particularly in cis-regulatory elements associated with hormone responses and developmental regulation. Spatial–temporal expression profiling demonstrates dynamic AQP expression patterns during development of prickle and the underlying cortical tissue in the prickly Rosa gigantea, while also differ substantially in shoots and leaves of the prickly Rosa chinensis and prickle-free Rosa wichuraiana. Silencing the expression of PIP2;1 within the prickle QTL region significantly attenuates the prickle production along rose stems. Our findings not only highlight both evolutionary conservation in AQP protein architecture and lineage-specific regulatory innovation in Rosaceae but also uncover a novel regulatory role of PIP2;1 in epidermal differentiation of the non-model roses, and of likely many other spiny angiosperms.

Chlorogenic acid is an important secondary metabolite in plants, and its antioxidant and antimicrobial activities confers its remarkable medical value. Ramie (Boehmeria nivea), an important fiber crop, riches numerous Chlorogenic acid in the root and leaf, making it used as a traditional Chinese medicinal herb and livestock feed. In this study, we report a high-quality telomere-to-telomere (T2T) and gap-free genome of ramie. The assembly length was ∼344 Mb, with all 28 telomeres and 14 centromeres. A total of 25 853 genes were identified, 90.5% of which were achieved functional annotation. Based on the T2T genome, we investigated the origin and evolution of the chlorogenic acid biosynthesis pathway and its production using comparative genomic and phylogenetic analyses. Subsequently, we identified five potential key genes involved in its biosynthesis via transcriptomic and metabolomic analyses, and characterized the metabolic pathway of chlorogenic acid biosynthesis in ramie through protease activity assays. Our T2T assembly represents the complete reference of genome and provides a valuable resource for genome and genetic studies in ramie; the proposed metabolic pathway of chlorogenic acid biosynthesis provided a basis for the improvement of chlorogenic acid content in ramie breeding.

Understanding how fruits ripen holds enormous potential for agro-industrial applications, enabling the development of healthier foods and plant-based medicines. Studying transcription factors (TFs) in nonconventional model species such as grapevine and strawberry remains challenging, yet offers strong translational value, as deciphering the regulatory mechanisms controlling ripening and the accumulation of health-beneficial compounds can support strategies to enhance fruit quality and also mitigate the impacts of climate change. Over the past decade, genome-wide studies in grapevine have applied systems biology approaches to reconstruct gene regulatory networks by integrating temporal transcriptomic and metabolomic data, revealing novel transcriptional relationships underlying berry ripening. Here, we review how these approaches have advanced grapevine research, with particular emphasis on DNA Affinity Purification followed by Sequencing (DAP-seq), a high-throughput method that maps TF binding sites using in vitro-expressed TFs and genomic DNA. DAP-seq provides a scalable and cost-effective alternative for TF characterization in grapevine, where stable genetic transformation remains difficult, enabling the rapid interrogation of large numbers of regulators. We further explore how integrating DAP-seq data with temporal transcriptomes from early- and late-ripening cultivars reveals novel regulatory targets and interconnections among known TFs controlling ripening-related processes. Within this framework, we highlight NAC60 as a high-hierarchy regulator of berry ripening, with a potential role in promoting sugar transport and signaling while modulating R2R3-MYB factors controlling specialized metabolite accumulation. Finally, comparative transcriptomic and network analyses in strawberry uncover conserved NAC-regulated ripening modules shared with grapevine, governing key physiological and metabolic transitions, including sugar transport, ABA biosynthesis, chlorophyll degradation, and flavonoid accumulation, supporting conserved regulatory principles across nonclimacteric fleshy fruits.

The induced capacity of plant growth-defense trade-offs under biotic stress is increasingly recognized. While many studies focus primarily on plants’ defense activation stage during insect attacks, limited attention has been given to poststress recovery. Herein, leaves from normal and postherbivory tea plants were collected during the compensation stage, and their microbiomes, metabolomes, and transcriptomes were used to dissect the mechanisms underlying growth-defense trade-offs. The results revealed that apart from altering the microbial community diversity, insect herbivory significantly enriched leaf-associated pathogens, particularly Alternaria spp. Network analysis and in-situ separation jointly revealed the role of Sphingomonas aquatilis in resisting pathogen invasion. Meanwhile, the restructured microbiota exhibited stronger network stability, indicating the enhancement of pathogen resistance among the endophytic community. Moreover, integrated transcriptomic and metabolomic analysis revealed that genes such as GSGT1, GolS4, and α-gal may regulate synthesis and degradation of growth-promoting and defense metabolites. The downregulated flavonoids were defense compounds against pathogens and the upregulated saccharides were plant growth-promoting compounds, which were verified in subsequent tests. Overall, tea plants compensate for reduced defense through restructuring of the endophytic microbiota, and prioritize growth over defense through metabolic resetting after insect herbivory. This study also revealed new biocontrol and growth-promoting resources for tea plants.