Nucleotide-binding leucine-rich repeat receptors (NLRs) are central to plant immunity, yet the mechanisms regulating their homeostasis remain poorly understood. In this study, we identify StRWA2 as a susceptibility factor in potato (Solanum tuberosum) that negatively regulates NLR-mediated resistance to Phytophthora infestans. StRWA2 destabilizes NLR proteins R3a and Rpi-blb2 via the 26S proteasome, suppressing NLR-mediated hypersensitive responses (HR). Mechanistically, StRWA2 recruits the E3 ubiquitin ligase StSNIPER2 (SNC1-INFLUENCING PLANT E3 LIGASE REVERSE 2) and enhances its E3 ligase activity, enabling StSNIPER2-dependent ubiquitination and degradation of NLRs. Furthermore, we confirm the necessity of this partnership, where silencing NbSNIPER2a/b reduced StRWA2-mediated plant susceptibility, while expression of a ligase-dead StSNIPER2 variant (StSNIPER2^H123Y) restored NLR stability and plant resistance. Crucially, we obtained StRWA2-silenced potato plants via the RNA interference (RNAi), which conferred resistance to P. infestans with no observable growth penalties compared to wild-type controls. Together, this study identified a susceptibility factor RWA2 from potato that recruits the E3 ligase SNIPER2 to destabilize NLRs. Our findings reveal a critical NLR regulation mode and propose RWA2 as a promising target for engineering disease resistance in crops.

Apple (Malus domestica) is one of the most widely cultivated and consumed fruits worldwide, valued for its rich nutrition and health benefits. Low temperature (LT) significantly limits apple growth, productivity, and fruit quality. Understanding the intricate regulatory networks, underlying cold tolerance is crucial for developing resilient apple cultivars. In this review, we comprehensively summarize the molecular control enabling apple to withstand cold stress, encompassing transcription cascades, phytohormonal networks, reactive oxygen species (ROS) regulation, epigenetic modifications, and post-translational modifications (PTMs), as well as the crosstalk with drought, immune, and light signaling pathways. We also discuss the management strategies for enhancing apple cold tolerance, including the exploitation of wild germplasm resources, multi-omics-based network integration, gene editing, molecular marker-assisted breeding, rootstock grafting, and emerging bioinoculants approaches. This review provides a foundational framework for molecular breeding and gene regulatory strategies to improve cold resilience in apple.

Sunflower (Helianthus annuus L.) is one of the pioneer crops with extremely strong adaptability to adverse stresses, and its stress (such as high salinity) tolerance improvement will contribute to the utilization of abundant marginal land and promote sustainable development. However, the genetic determinants underlying response to salt stress are not fully understood. Here, we perform a genome-wide association study (GWAS) using 31 traits from a high-throughput platform in 342 oilseed sunflower accessions at the germination stage under salt stress conditions. We identify 359 significantly associated SNPs and 63 InDels corresponding to 424 and 83 candidate genes, respectively. One candidate gene, C-Repeat Binding Factor 4 (CBF4)-a member of the AP2/EREBP family transcription factor-directly binds to dehydration-responsive element in the promoter region of its downstream target gene, High-Affinity K⁺ transporter 11 (HAK11), thereby activating its expression. This regulator y mechanism contributes to enhanced salt tolerance in sunflower by modulating established salt-responsive genetic pathways. Collectively, our findings provide new insights into salt tolerance mechanisms and offer valuable genetic resources for breeding salt-tolerant sunflower cultivars.

Elucidating the genetic architecture of key quality traits and understanding population differentiation in walnut (Juglans regia) are critical for advancing molecular breeding and enhancing environmental adaptability. In this study, we performed whole-genome resequencing of 282 representative walnut accessions encompassing wild populations, ancient landraces, and modern cultivars. Walnuts in Xinjiang exhibit clear genetic differentiation and can be categorized into two main groups: wild walnuts from Yili and ancient landraces from Aksu, Kashi, and Hotan. The Yili region in northern Xinjiang, China, represents an independent center of walnut genetic diversity. In contrast, the ancient landraces and cultivated walnuts from other regions of Xinjiang are closely related to wild walnuts from the Middle East, suggesting a shared origin. Analysis of deleterious mutations uncovered contrasting accumulation patterns between Wild-Yili_China and Ancient Landrace-Xinjiang_China groups, likely shaped by demographic history and local environmental adaptation. Genome-wide association studies (GWAS) identified key loci and candidate genes, including JruL2x, JrCRK26, and JrRHF2A, that are associated with important quality traits. Furthermore, we functionally validated JrCYP98A2, which encodes a ferulate 5-hydroxylase, as a regulator of shell thickness. Together, these findings provide insights into walnut domestication and the genetic basis of quality trait variation, offering valuable genomic resources for future molecular breeding and genetic improvement of walnut.

Tomato (Solanum lycopersicum) is a nutrient-rich and flavorful vegetable, ranking among the most consumed globally. In recent years, consumers have increasingly demanded high-quality tomatoes, prompting the extensive research into the key factors and relevant molecular mechanisms regulating the formation of fruit quality. Coloration is a crucial aspect determining the appearance quality of tomato fruits and directly affecting their commercial value. This coloration is intrinsically linked to the composition and abundance of special chemical compounds in fruits, particularly chlorophyll and carotenoids. Chlorophyll is the predominant pigment accumulated in the early stages of fruit development and plays a vital role in photosynthesis. As the fruit ripens, chlorophyll undergoes gradual degradation, while carotenoids are abundantly synthesized, resulting in a striking color transition from green to red. Chlorophyll and carotenoids are essential natural pigments and antioxidants that are indispensable for both coloration and nutritional value of tomato fruits. This review presents a comprehensive overview of the metabolic pathways and regulatory mechanisms of these metabolites, aiming to provide novel insights and strategies for improving tomato quality to meet the growing consumer demand for fruits with appealing coloration and enhanced nutrients.

Grafting is widely used for asexual propagation and enhancing plant productivity; however, the molecular mechanisms underlying rootstock–scion interactions remain largely unclear. In this study, Populus × euramericana cv. ‘Neva’ (poplar 107) served as rootstock and Populus tomentosa ‘Yixian’ (P. tomentosa) as scion for grafting. By integrating physiological measurements, transcriptome sequencing [messenger RNA (mRNA) and long non-coding RNA (lncRNA)], widely targeted metabolomics, and mobile RNA identification revealed that heterografted scions had increased metabolites related to carbon fixation and metabolism, decreased metabolites associated with respiration and defense, and enhanced net photosynthetic rate, potentially promoting height growth; differential expression lncRNAs may represent an important molecular basis for accelerated scion growth; in scions, mobile mRNA-associated differential mRNAs primarily involved amino acid biosynthesis, while mobile lncRNA-associated ones focused on energy metabolism; no target mRNAs of mobile lncRNAs were found in the rootstock; both mRNAs and lncRNAs were transported in full-length and fragmented forms, and downward RNA transport showed a significant correlation with transcript abundance; in recipient tissues, mobile mRNAs were less abundant while mobile lncRNAs were more abundant than in donor tissues; the flavonoid biosynthesis pathway associated with mobile RNAs played an important role in rootstock-mediated scion growth, and kaempferol, as a key metabolite, reduced reactive oxygen species–induced damage, increased net photosynthetic rate, and promoted growth in Nicotiana benthamiana. This study provides an initial insight into the transport and regulatory patterns of mRNAs and lncRNAs in woody grafted plants, offering a theoretical basis for the rational application of grafting technology.

Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. In our previous work, we generated a high-throughput CRISPR library whereby a knockout collection was established for rapeseed breeding and functional genomics. However, the collection remains small and several promising candidate genes still await functional validation. Here, we report an update of this collection by constructing a small-scale CRISPR mutant library based on the elite commercial cultivar Zhongshuang 11 (ZS11). We first generated 326 independent T₀ lines using an optimized protocol for ZS11 transformation and regeneration with a high positive rate of 94.2%. Analysis of the editing outcomes revealed a mutagenesis frequency of 68.4%. We then phenotyped this new collection and unraveled possible key genes underlying the variations in seed oil content (SOC) and plant height. Finally, we functionally validated BnFAB1B and BnEDA32, two candidate genes identified from our knockout collection. The results confirmed that loss of function of BnFAB1B significantly increases SOC, indicating its great agronomic potential, whereas knockout of the nuclear-localized BnEDA32 severely disrupts seed oil accumulation. This study provides a valuable knockout collection of the elite cultivar ZS11 and new genes for creating superior rapeseed germplasm.

Alkaline salt stress is a key environmental factor restricting the sustainable development of the apple industry, significantly affecting the yield and quality of apple. In recent years, strigolactone (SLs) has been proven to play a central regulatory role in plant stress responses. However, its role and mechanism under alkaline salt stress remain unknown. Based on this, we found that exogenous application of the SL analog GR24^5DS can significantly enhance the adaptability of apple to alkaline salt stress. To elucidate the underlying molecular mechanisms, RNA sequencing (RNA-seq) analysis identified the key transcription factor MdbHLH1, whose expression was strongly induced by alkaline salt stress. Overexpression of MdbHLH1 conferred a salt-alkali tolerant phenotype. Further investigation demonstrated that MdbHLH1 directly binds to and activates the promoter of MdAT1 (Alkali Tolerance 1), a crucial alkali-tolerance gene. The MdbHLH1- MdAT1 module enhances alkaline salt stress resistance by promoting hydrogen peroxide (H₂O₂) efflux and alleviating oxidative damage. More in-depth studies revealed that MdbHLH1 interacts with MdD53 (MdDWARF53), a repressor in the SL signaling pathway. SL signaling induces ubiquitination and degradation of MdD53, thereby releasing MdbHLH1 to activate MdAT1 expression and ultimately improving alkaline stress tolerance in apple. This study elucidates a key SL–MdD53–MdbHLH1- MdAT1 regulatory pathway that enhances saline-alkali tolerance in apple by mitigating oxidative stress, thereby providing mechanistic insights into apple’s adaptation to saline-alkali environments.

Global warming is increasing the frequency of heat stress, a major abiotic constraint on crop growth and productivity. Hydrogen sulfide (H₂S), a novel gasotransmitter, has been reported to enhance crops’ heat tolerance, yet its underlying mechanism remains poorly understood. Here, we provide genetic evidence confirming that L-cysteine desulfhydrase (SlLCD1, Solyc01g068160) was the enzymatic source of endogenous H₂S in tomato heat adaptation. Dual activation of H₂S signaling through both SlLCD1 overexpression and exogenous application enhanced tomato heat tolerance. Conversely, CRISPR/Cas9-generated SlLCD1 mutants (cr-sllcd1), deficient in heat-induced H₂S production, displayed heightened heat sensitivity with accelerated wilting and increased oxidative damage, which was rescued by exogenous H₂S application. Compared to wild-type plants, the mutants showed a compromised heat-induced increase in antioxidant enzyme activities and levels. This defect, along with the concomitant ROS accumulation and oxidative damage, was reversed by H₂S pretreatment, underscoring the critical role of the SlLCD1-H₂S module in maintaining ROS homeostasis during heat adaptation. Additionally, cr-sllcd1 mutants exhibited attenuated heat-induced stomatal closure and increased stomatal density. H₂S pretreatment rescued both of these defects, thereby optimizing the trade-off among transpirational cooling, water conservation, and photosynthetic efficiency. Overall, the SlLCD1-H₂S module confers heat tolerance by a dual mechanism, coordinately enhancing antioxidant capacity and fine-tuning stomatal dynamics. Our study elucidates an important component of the H₂S signaling pathway in plant heat tolerance and offers a promising tractable target for developing heat-tolerant tomato cultivars.

Volatile terpenes constitute a predominant class of floral scent emitted by Paeonia lactiflora. Despite their ecological and economical significance, the genetic blueprint of the underlying biosynthetic pathway remains poorly elucidated. Although a few terpene synthase (TPS) genes have been reported, the broader network of genes orchestrating terpene production in P. lactiflora is still largely unresolved. In this study, we attempted to address this gap by exploring the terpene biosynthetic pathway genes in P. lactiflora ‘Zifeng yu’. β-caryophyllene, geraniol, citronellol, and 1,8-cineole were identified as the dominant floral terpenes, and catalytic functions of key proteins-terpene synthase (PlTPS), Nudix hydrolase (PlNUDX), and prenyltransferase (PlPT) were comprehensively characterized. Briefly, biochemical analyses revealed that six of the nine identified PlTPS proteins utilized diverse prenyl diphosphates to generate both monoterpenes and sesquiterpenes, while their products specificity were determined by plastidic or cytosolic localizations in planta. In particular, PlTPS4, PlTPS5, and PlTPS9 catalyzed the production of β-caryophyllene, 1,8-cineole, and geraniol, respectively. Besides, two amino acid residues were found to drive catalytic activity and product profiles in PlTPS4 and PlTPS5. Markedly, PlNUDX hydrolyzed GPP and NPP to yield geraniol and nerol thereby providing a plastid-independent pathway for monoterpene biosynthesis, and prenyltransferases were further functionally characterized to clarify the supply of prenyl diphosphates feeding into volatile terpenes. Collectively, these findings not only provide a mechanistic framework for understanding floral terpene biosynthesis in P. lactiflora but also reveal alternative metabolic routes that enrich its volatile profiles that could be utilized in scent improvement of ornamental plants.

Botrytis cinerea is a broad host range fungal pathogen causing gray mold disease and crop losses worldwide. In blueberries, symptoms include blossom blight in the field and postharvest fruit rot, affecting the entire supply chain. With control options constrained by regulatory restrictions and fungicide resistance, the dissection of the genetic and molecular basis of blueberry response to B. cinerea can accelerate breeding for resistance. In this study, we phenotyped 354 blueberry selections using a high-throughput Botrytis infection fruit assay. The same population was genotyped by targeted sequencing for genome-wide association study (GWAS). In addition, we performed RNA-seq time-course (0–96 hours post-inoculation) for resistant and susceptible genotypes. Our results showed a continuum of tolerance levels and moderate narrow-sense heritability estimates for the disease-related traits (0.46–0.61). GWAS identified small-effect loci, consistent with quantitative resistance observed in other host plant species. Intersecting differentially expressed genes with GWAS intervals revealed eight candidate genes. Transcriptomic analyses showed that, at early stages, the resistant genotype upregulated components of basal innate immunity, including wax and cutin biosynthesis, responses to wounding and fungal-derived molecules, the MAPK cascade, and ethylene and jasmonate signaling. In contrast, susceptible genotypes displayed delayed activation of these defense pathways and altered cell wall-related processes. The moderate correlation between disease traits and wax bloom further supported a role for wax in disease response. Together, our findings provide molecular markers and candidate genes for Botrytis fruit rot resistance in blueberry with significant applications in breeding programs and opportunities to future validation studies.

Leaf chlorosis and senescence are key indicators of prolonged drought stress. In this study, we found that suppressing the chlorophyll b reductase gene (LpNOL) delayed drought-induced leaf chlorosis in perennial ryegrass (Lolium perenne). Through a yeast one-hybrid (Y1H) library screen, we identified a NAC transcription factor, designated chlorophyll b degradation regulator 1 (LpCbDR1), as a direct activator of LpNOL. Subcellular localization analysis confirmed that LpCbDR1 localizes to the nucleus, and its direct binding to the LpNOL promoter was validated by electrophoretic mobility shift assay (EMSA) and CUT&Tag-qPCR assays. Overexpression of LpCbDR1 accelerated leaf senescence, whereas knockdown of LpCbDR1 delayed leaf senescence. Notably, LpCbDR1’s expression was not only upregulated during leaf senescence but also induced by osmotic stress, promoting further investigation into its role and underlying mechanisms in regulating drought tolerance. Phenotypic analysis showed that LpCbDR1-overexpressing lines exhibited significantly higher drought tolerance compared to wild-type (WT) plants, while LpCbDR1- RNAi lines were drought-sensitive than WT. Integrated RNA-seq and CUT&Tag analysis identified LpPLA7 and LpERF1B as downstream targets of LpCbDR1. Directly binding of LpCbDR1 to the promoter of LpPLA7 and LpERF1B was confirmed by Y1H, EMSA, and CUT&Tag-qPCR assays. Both LpPLA7 and LpERF1B were drought-inducible, and functional validation revealed that overexpression of either gene enhanced osmotic stress tolerance in both WT and LpCbDR1- RNAi backgrounds. Collectively, this study demonstrates that LpCbDR1 regulates natural, dark-, and drought-induced leaf senescence by activating LpNOL, and improves drought tolerance at least partially through direct activation of LpPLA7 and LpERF1B in perennial ryegrass.

Plant grafting is a horticultural technique used to join different plants with desirable traits. However, graft incompatibility limits its application, especially in agriculturally important Fabaceae species. To enhance grafting efficiency, we conducted chemical screening utilizing an in vitro grafting (IVG) system in Fabaceae. In this study, we screened 3000 artificial chemical compounds and identified a compound, designated graft-promoting molecule 1 (GPM1), which enhanced graft adhesion in Fabaceae species-including Phaseolus coccineus, Vigna unguiculata, Vigna angularis, and Glycine max-as well as in V. unguiculata/ G. max hetero-IVGs at 5 days after grafting (DAG). Notably, GPM1 also increased adhesive force in Nicotiana benthamiana IVGs and improved survival rates in Arabidopsis thaliana micrografting, indicating that its activity is not restricted to Fabaceae. Transcriptome analysis of P. coccineus IVGs at 1 DAG revealed that application of GPM1 induced the upregulation of cell wall modification genes, including PvEXPA5, PvEXPA22, and PvEXPA25. In contrast, treatment with 2,4-dichlorophenoxyacetic acid (2,4-D) induced a broader transcriptional response, predominantly upregulating genes related to cell division. In G. max stem grafting, GPM1 enhanced scion growth and promoted the formation of larger callus cells at the graft junction. Moreover, qRT-PCR analysis revealed that GPM1 significantly upregulated Glyma.07G229000, a homolog of PvEXPA5. The upregulation of cell wall-associated genes by GPM1 is consistent with a role in early graft union formation, potentially by facilitating tissue adhesion at the graft interface. Collectively, this study identifies GPM1 as a chemical regulator that enhances graft adhesion and provides insight into molecular processes associated with early graft adhesion.

Loquat (Eriobotrya japonica Lindl.), a subtropical evergreen species of the Rosaceae family, faces industry constraints in industrial development due to its sensitivity to freezing temperatures and low photosynthetic efficiency. Polyploid loquats, particularly triploids, exhibit enhanced stress resistance, vigorous growth, and seedless fruit production. In this study, triploid F1 progeny (B431 × GZ23) was obtained through hybridization between diploid (GZ23) and tetraploid (B431) parents. Under − 3^◦ C stress, the triploid lines exhibited significantly improved freezing tolerance and photosynthetic performance, as evidenced by chlorophyll fluorescence parameters and ultrastructural integrity. Lipidomics profiling across all B431 × GZ23 lines revealed that phosphatidylcholine (PC), particularly the abundant unsaturated PC species 18:2/18:2, played a key role in these adaptive advantages. Compared to the parental lines, EjFAD2 expression was specifically upregulated in triploid loquats under freezing stress. Consistent lipidomic and gene expression patterns across three B431 × GZ23 lines ruled out line-specific mutations. Heterologous expression of EjFAD2 in Arabidopsis increased freezing tolerance. Co-expression analysis identified EjMYBS3 as a regulator that binds to the EjFAD2 promoter, and its overexpression in transgenic Arabidopsis enhanced freezing tolerance. Transient expression of EjFAD2 and EjMYBS3 increased the content of PC 18:2/18:2 in loquat, which contributed to the maintenance of photosystem activity under freezing stress, thereby enhancing the freezing tolerance of loquat. Collectively, these findings provide preliminary insights into the molecular mechanisms underlying cold resistance in polyploid loquats and highlight the regulatory role of EjFAD2 and EjMYBS3 in freezing stress response.

Chitooligosaccharides, such as chitin, are essential components of fungal cell walls and have thus naturally been selected as microbe-associated molecular patterns detected by plants to initiate defense mechanisms. These molecules are typically recognized by the lysin motif receptor-like kinases (LysM RLKs) at the plasma membrane. While chitin perception is well elucidated in Arabidopsis thaliana and other plant species, the recognition mechanisms of its deacetylated form, chitosan, remain poorly investigated despite its use as a biocontrol strategy to protect crops against pathogens. Here, we investigated the role of the two grapevine orthologs of AtLYK4, which participate in the tripartite complex for chitin perception in A. thaliana. Using a dual approach consisting of the functional complementation of the atlyk4/5 double mutant and CRISPR-Cas9 genome editing in Vitis vinifera, we showed that VvLYK4-2 is involved in both chitosan- and chitin-induced immune responses, encompassing MAPK phosphorylation and defense gene expression. Furthermore, grapevine in vitro plantlets lacking VvLYK4-2 exhibited a significantly reduced response to chitosan while retaining a low-intensity response to chitin, potentially due to the presence of VvLYK5-1. Finally, VvLYK4-2 produced in a heterologous system showed binding to chitosan oligomers and, to a lesser extent, to chitin oligomers. These findings indicate that this pattern recognition receptor plays a crucial role in the perception of chitosan oligomers and has thus potential for selective breeding purposes. This discovery may also help to better understand the partial lack of efficacy of chitosan-based plant defense stimulants used in viticulture.

Camellia sinensis (L.) O. Kuntze exhibits severely restricted growth at low temperatures, resulting in reduced tea leaf yield and quality. BRI1-EMS-suppressor (BES) transcription factors, as key components of the brassinosteroids (BR) signaling pathway, are highly homologous to BZR and jointly regulate plants’ adaptation to environmental stress. In this study, the CsBES1-14 gene was successfully cloned and identified from the transcriptome database of tea plant. Biochemical analyses identified CsBES1-14 as a nuclear localized transcriptional activator, and BR and low temperature induced its expression. Arabidopsis thaliana plants overexpressing CsBES1-14 exhibited increased chilling tolerance by promoting root growth and increasing the expression of cold responsive genes. Conversely, the suppression of CsBES1-14 through virus-induced gene silencing (VIGS) in tea plant notably impaired cold tolerance. Transcription Factor-centered Yeast One-Hybrid screening identified CsCOR413 as a downstream target, and electrophoretic mobility shift assays confirmed the direct binding of CsBES1-14 to specific cis-elements in the CsCOR413 promoter. Exogenous application of brassinazole (BRZ) and VIGS silencing experiments verified that the ICE-CBF cold response pathway could regulate the low-temperature-regulated protein CsCOR413. In summary, these findings elucidate that CsCOR413 expression is modulated not only by the classic ICE-CBF signaling pathway but also directly regulated by CsBES1-14. These findings outline the key components of the cold resistance network in tea plant and provide novel molecular targets for genetic improvement strategies in perennial crops.

Mycoheterotrophic plants rely entirely on fungal symbionts for nutrients, yet the role of intraspecific genomic variation in shaping symbiotic adaptation remains unclear. Gastrodia elata is a mycoheterotrophic orchid with multiple cultivated varieties. Here, we generated a chromosome-level genome of G. elata Bl. f. glauca. Comparative genomic analyses with published G. elata assemblies revealed extensive intraspecific variation, characterized by transposon-mediated inversions occurring in 26% of syntenic regions. Notably, these regions frequently harbored orphan genes. Population genomic analysis of 150 individuals identified three genetically distinct clades: two cultivated (Clades E and G) and one hybrid (Clade I). Transcriptomic profiling uncovered clade-specific expression patterns in symbiosis-related genes, particularly within strigolactone signaling pathways. Molecular dynamics simulations and protein interaction assays demonstrated that polymorphisms in the M domain of the suppressor protein DWARF53 (GeD53) modulate strigolactone signaling by altering the stability of its interaction with the receptor (GeD14). Specifically, a Clade G-specific haplotype enhanced signaling through stabilized protein interactions, thereby influencing tuber development genes, whereas GeD14 variants had minimal functional impact. Further co-expression networks identified LOL5 , RNP1 , and MTHD as downstream effectors correlating with clade-specific tuber phenotypes and carbohydrate allocation. These findings demonstrate how intraspecific variation in strigolactone signaling components drives functional divergence in G. elata , providing both mechanistic insights into mycoheterotrophic adaptation and genomic resources for future research.

Fruits and vegetables are key components of the human diet, valued for their unique textures and flavors. In recent years, numerous studies have demonstrated that individual transcription factors (TFs) can simultaneously regulate two biological processes; these TFs are defined as bifunctional TFs. However, systematic reviews on these bifunctional TFs in fruits and vegetables remain limited. This review systematically summarizes current knowledge on bifunctional TFs in fruits and vegetables, focusing on three themes: (i) molecular mechanisms (cis-element diversity, partner switching, posttranslational); (ii) network topology (hubs vs bottlenecks); and (iii) agronomic trade-offs. Meanwhile, the functional conservation and divergence of homologous TFs in different fruits and vegetables have also been investigated. In addition, we elaborate how key TF families, including MYB, bHLH, WRKY, ERF, and NAC, regulate diverse physiological processes in fruits and vegetables via dual mechanisms. We also identify several limitations in the existing literature, such as insufficient understanding of bifunctional regulatory mechanisms, incomplete identification of target genes, and inadequate exploration of crop applications.

Cucurbit powdery mildew, predominantly caused by Podosphaera xanthii, poses a major threat to global cucurbit production due to the pathogen’s rapid adaptability and resistance to conventional fungicides. This growing challenge highlights the urgent need for alternative, sustainable disease management strategies. As the primary interface between the fungus, host plant, and environment, the fungal cell wall emerges as a strategic target for development of innovative control approaches. This study focuses on ECM33, a glycophosphatidylinositol (GPI)-anchored protein believed to play a role in cell wall architecture and integrity, although its specific biochemical function remains undefined. In silico structural modeling revealed that PxECM33 resembles leucine-rich repeat proteins and contains potential carbohydrate-binding motifs. Recombinant PxECM33 exhibited binding affinity for chitin, β-glucans, and mannans, the main glycosidic components of the P. xanthii cell wall, supporting these structural predictions. Molecular docking analyses uncovered distinct ligand-specific interactions with these carbohydrates, further implicating PxECM33 in cell wall dynamics. Silencing PxECM33 via RNA interference significantly impaired fungal growth and caused pronounced cell wall disorganization. Notably, dual silencing with the melon immune receptor gene CmCERK1 mitigated these defects, suggesting that PxECM33 may function in masking immunogenic oligosaccharides to evade host detection. Furthermore, spray-induced gene silencing (SIGS) targeting PxECM33 effectively reduced disease symptoms in melon plants, highlighting its potential as a sustainable and nontoxic biocontrol strategy. Given the high-sequence conservation of ECM33 among ascomycete fungi, these findings support its candidacy as a broad-spectrum molecular target for managing powdery mildew in cucurbits and potentially other crops.

Potato (Solanum tuberosum L.) is a globally important tuber crop and a vital component of the food system. Tuber skin texture is a key quality trait that influences market appearance and is closely associated with resistance to biotic and abiotic stresses as well as tolerance to mechanical damage. However, the genetic basis and regulatory mechanisms underlying this trait remain poorly understood. In this study, we investigated the genetic and molecular mechanisms underlying potato tuber skin texture. A quantitative trait locus (QTL) for tuber skin texture was mapped to a 1.94-Mb interval on chromosome 4 using bulked segregant analysis of a segregating population derived from a cross between russet-skinned variety Innovator and smooth-skinned variety Zhongshuzao43 (Z43). The tuber skin of Innovator contained more cell layers than Z43 and developed progressive cracking during tuber expansion. Innovator also exhibited lower suberin content but higher lignin accumulation in tuber skin compared to Z43. Transcriptome profiling across multiple developmental stages identified a distinct gene expression cluster enriched in pathways related to lignin and suberin biosynthesis. Integrating genes within the QTL with this expression cluster revealed StPXG4 , which encodes a peroxygenase, as strongly correlated with skin texture. StPXG4 showed significantly higher expression in commercial smooth-skinned varieties than in russet-skinned varieties. Co-expression analysis further identified two potential upstream regulators of StPXG4 , namely StMYB103 and StMYB58 . These findings provide key insights into the genetic regulation of tuber skin texture and identify candidate genes that could be targeted to improve tuber appearance and stress tolerance through molecular breeding.

Monk fruit (Siraitia grosvenorii, Cucurbitaceae) is globally renowned for its triterpenoid glycoside mogroside V, a high-intensity, non-caloric natural sweetener. However, its domestication and mogroside biosynthesis remain largely unknown. Here, we report a haplotype-resolved telomere-to-telomere (T2T) gapless genome for monk fruit, consisting of 14 chromosomes with genome sizes of 316.21 Mb (Hap1) and 316.07 Mb (Hap2). Comparative genomic analyses of the haplotypes revealed that structural variations and transposable elements have significantly contributed to genomic variation and architecture in monk fruit. Population genomic analyses based on 173 re-sequenced genomes indicated that cultivated monk fruit was mainly domesticated in situ from local wild populations in northern Guangxi of China, and that it likely experienced a mild domestication bottleneck, while exhibiting low genetic diversity. Demographic inference further revealed that the low genetic diversity is largely attributed to demographic changes driven by historical climate shifts. Selective sweeps were identified across all chromosomes of cultivated monk fruit, among which are genes exhibiting diverse putative functions and involved in various biosynthetic processes and secondary metabolism. This pattern of selective sweeps demonstrates the joint role of artificial selection and demographic changes in shaping the genomic landscape of cultivated monk fruit. Furthermore, comparative transcriptome analyses showed a pronounced temporally specific expression pattern among mogroside biosynthesis genes during fruit development and delineated additional candidate genes potentially involved in mogroside biosynthesis. This study not only provides insights into the domestication and mogroside biosynthesis of monk fruit but also lays a valuable genomic foundation for its molecular breeding and mogroside-targeted synthetic biology.

Long-read sequencing and pangenomics are revolutionizing crop research by providing more complete genome information and revealing crucial structural variations (SVs) linked to important agricultural traits. Building on recent advances in intraspecific pangenome construction, this study addresses the challenge of creating broader, cross-taxon pangenomes, using the Armeniaca taxonomic section as a model. Leveraging a diverse panel of genome assemblies as well as completing it with seven more genome assemblies generated for this study, we constructed a pangenome graph and cataloged the associated genetic variation, identifying approximately 25 million single nucleotide polymorphisms and over 537 000 structural variants. We characterized the diversity of these variants and assessed the extent to which different taxa contribute to overall pangenome expansion. Additionally, we evaluated the performance of low-depth sample mapping to the graph-based reference, highlighting key technical limitations that may affect the quality of downstream analyses. We further identified specific subsets of SVs that exhibit associations with particular classes of transposable elements (TEs). We showed that TEs are a major driver of SV, particularly insertions and deletions, with distinct size and distribution patterns (peaking in the 200- to 400-bp indel bin). They are also nonrandomly positioned in the genome, showing a tight concentration near coding genes, which suggests a role in gene regulation. As a case study illustrating the potential functional relevance of graph-derived SVs, we examined the genomic configuration of the Dormancy-Associated MADS box locus within the Armeniaca pangenome. These findings provide a framework to investigate adaptation in perennial fruit trees of the Armeniaca section.

The GOLDEN2-LIKE (GLK) gene family, known for its role in chloroplast development, has recently been implicated in involvement of anthocyanin biosynthesis in kiwifruit (Actinidia spp.), but the underlying regulatory mechanism remains unclear. Here we report the characterization of a kiwifruit GLK homolog AcGLK2 in regulating anthocyanin accumulation. We found that expression of AcGLK2 is much higher exclusively in the red pigment-accumulated fruit tissue. Overexpression of AcGLK2 in Arabidopsis and kiwifruit significantly enhanced anthocyanin content, whereas its RNAi-mediated silencing compromised anthocyanin accumulation. RNA-Seq analysis revealed significant upregulation of many structural genes and transcription factors (TFs) associated with the flavonoid pathway in AcGLK2-overexpressing kiwifruit. ChIP-Seq analysis indicated that AcGLK2 directly binds to AcMYB5 and AcTRY. We showed AcMYB5, an R2R3-MYB TF, promotes anthocyanin accumulation by interacting with the bHLH protein AcbHLH42, while AcTRY, an R3-MYB protein, competitively inhibits the interaction between key MYBs and AcbHLH42, thereby repressing anthocyanin biosynthesis. Transgenic and molecular assays in tobacco, tomato, and kiwifruit demonstrated that AcGLK2 positively participates into regulation of anthocyanin accumulation through transcriptionally activating AcMYB5 expression and concomitantly suppressing AcTRY expression. This study reveals the dual regulatory mechanism of AcGLK2 in anthocyanin biosynthesis, broadening the understanding of GLK gene functions and providing a valuable genetic resource for molecular breeding of nutritional quality in kiwifruit and other crops.

High-throughput genotyping has revolutionized horticultural breeding, yet the efficient utilization of genomic data remains a bottleneck for germplasm curation and downstream selection. Translating complex genomic information into cost-effective and readily applicable tools for clonally propagated crops requires a shift from maximizing marker density to optimizing information content. Here, we reinterpret cacao (Theobroma cacao L.) genotyping as an information-allocation problem and introduce an information-theoretic framework for designing minimalist, trait-enriched single nucleotide polymorphism (SNP) barcodes. Using a diverse international collection from Trinidad (ICGT) and an independent field trial in Puerto Rico (USDA-ARS Tropical Agriculture Research Station), we compress a 500+ SNP panel into a 32-marker ‘CacaoCipher’ barcode that preserves pairwise genetic distance structure at coarse resolution while retaining trait-aligned signal for pod index and related yield components. Barcode–space axes correlate with agronomic traits measured across environments in a limited overlap subset, supporting the portability of key signals beyond the training setting. We further quantify a heuristic ‘genomic bit budget’, showing how information is allocated across unique identification, ancestry structure, and trait variation. Together, this framework converts cacao germplasm from an analog collection of names into a compact digital code and provides a general template for designing low-cost, high-information marker panels for germplasm quality control and stratified screening in clonally propagated crops.

Spuriopimpinella brachycarpa (2 n = 2 x = 22), a perennial Apiaceae herb traditionally consumed in Northeast China, is rich in bioactive compounds such as flavonoids and terpenoids and possesses both medicinal and comestible value. However, the metabolic mechanisms underlying these traits remain unclear due to the lack of genomic resources. Here, we present the first chromosome-level genome assembly of S. brachycarpa (4.12 Gb; scaffold N50 = 358.95 Mb; 11 chromosomes). Comparative genomics analysis revealed two postdivergence whole-genome duplication (WGD) events in Apiaceae and a close phylogenetic relationship between S. brachycarpa and Daucus carota (carrot). Metabolomic profiling indicated that flavonoids, dominated by flavanols and flavones, are most actively synthesized in leaves, with their biosynthesis likely regulated by the MYB transcription factor SbraChr11G00348720.1. Terpenoids, primarily monoterpenes and sesquiterpenes, accumulated predominantly under cultivated conditions, demonstrating habitat-specific patterns. Transcriptomic analysis further identified two key terpene synthase genes- SbraChr6G00204720.1 (TPS-a subfamily) and SbraChr3G00078100.1 (TPS-b subfamily)-associated with sesquiterpene and monoterpene biosynthesis, respectively. By integrative genomic, transcriptomic, and metabolomic data, this study systematically elucidates the biosynthesis basis of major secondary metabolites in S. brachycarpa and provides a valuable genetic resource for comparative genomics and molecular breeding in Apiaceae crops.

Salicylic acid (SA) is a central phytohormone in plant immunity and stress responses, yet the evolutionary dynamics of its phenylalanine ammonia-lyase (PAL)-mediated biosynthetic route remain poorly understood despite recent biochemical advances. As the original source of SA, Spiraea (Rosaceae) holds historical and evolutionary significance for studying SA biosynthesis. Here, we generated a chromosome-level genome assembly of Spiraea chinensis and integrated comparative genomics, transcriptomic, and targeted metabolite profiling to investigate the evolutionary diversification of SA biosynthesis across Rosaceae. Phylogenomics places S. chinensis in the subfamily Amygdaloideae, diverging from other genera ~57.8 Mya. Extensive chromosome fission–fusion events and lineage-specific whole-genome duplication (WGD) have driven karyotype diversification across Rosaceae. Comparative analyses revealed the PAL-mediated route as the dominant SA biosynthetic pathway across Rosaceae, with WGD-driven expansion in Amygdaloideae and combined WGD- and small-scale duplication (SSD)-derived origins in Rosoideae. WGD-derived PAL-route genes largely retained synteny and stable high expression, whereas lineage-specific SSD-derived paralogs exhibited reduced synteny and variable expression, consistent with post-duplication regulatory divergence and subfunctionalization. Transcriptome analyses revealed pronounced tissue-specific expression of PAL-route genes across Rosaceae, and UPLC–MS/MS profiling further demonstrated differential SA accumulation in S. chinensis, with the highest levels in branches (606–1038 ng/g FW), followed by leaves (183–432 ng/g FW) and flowers (42–56 ng/g FW), supporting active SA biosynthesis in both vegetative and reproductive tissues. Collectively, our results establish the PAL-mediated pathway as the primary and evolutionarily conserved route of SA biosynthesis in Rosaceae and demonstrate how genome dynamics and regulatory diversification jointly drive the evolutionary innovation within this pathway.

Sugars are not only metabolites but also signals that gate plant growth, fruit ripening, and stress responses. Carbon-sensing pathways (HEXOKINASE 1, TOR-SnRK1, and the sucrose Trehalose-6-phosphate pathway) reprogram gene expression by engaging DNA methylation, histone modification, chromatin remodeling, regulatory RNAs, and RNA modifications. Cutting-edge quantitative epigenomic and epitranscriptomic methods, integrated with novel bioinformatics tools, are driving unprecedented resolution in epigenetic landscape analysis. Benefitting from state-of-the-art technologies, we summarize epigenetic control points for pigmentation, softening, sugar–acid balance, and stress acclimation (e.g. SlDML2, PH5, RdDM-ABA modules). This synthesis underscores that decoding the sugar–epigenome interplay is key to understanding plant phenotypic plasticity and improving crop performance. Finally, we explore how leveraging epigenetic regulation via CRISPR-based epigenome editing, transgenerational inheritance patterns, and epigenomic biomarker-based (epibreeding) approaches holds promise for improving crop resilience and productivity.

Broccoli (Brassica oleracea var. italica) is a widely cultivated cruciferous vegetable valued for its abundant bioactive compounds and nutraceutical properties. Among these, anthocyanins are not only important secondary metabolites contributing to nutritional and medicinal benefits, but also influence stress tolerance and the commercial quality of broccoli through purple pigmentation. However, the molecular mechanisms regulating anthocyanin biosynthesis in broccoli remain poorly understood, partly due to the incomplete genomic resources currently available. In this study, we constructed a telomere-to-telomere gap-free assembly of the broccoli genome using a combination of Oxford Nanopore Technology ultralong reads, PacBio high-fidelity reads, and Hi-C datasets. The resulting genome is 633.61 Mb in length, with an N50 of 60.36 Mb, and comprises gap-free assemblies of all 18 chromosomes, including complete telomere-to-telomere assemblies for nine chromosomes. Using this high-quality reference, we identified BoF3’H, a key gene regulating anthocyanin accumulation, which controlling the purple coloration of broccoli buds. To validate the function of the BoF3’H gene in anthocyanin biosynthesis, we used CRISPR-Cas9 gene editing to target and knock out the BoF3’H gene. The bof3’h mutant exhibited an 81.4% reduction in cyanidin and delphinidin derivative levels compared with those in the control. Metabolomic and transcriptomic profiling showed that the expression of 12 anthocyanin-related genes, including PAL, C4H, CL3, CHS, F3’H, and ANS, was downregulated. These findings elucidate the molecular basis of anthocyanin regulation in broccoli and provide a foundational genomic resource for evolutionary studies, gene discovery, and future breeding.

Jasmonic acid (JA) and its derivatives, including methyl jasmonate, are well-known plant growth regulators that mediate a wide range of physiological and developmental processes. Although the role of JA in regulating fruit trichome density has been recognized, the specific mechanisms underlying this remain to be fully understood. This study investigated the effects of various JA concentrations on trichome density at different developmental stages in cucumber (Cucumis sativus L.). Our findings revealed a dose-dependent increase in trichome density following exogenous JA application, with 1.5 mM JA showing the most significant effect at all stages. Conversely, the use of a JA biosynthesis inhibitor resulted in reduced trichome density, further highlighting the pivotal role of JA in trichome formation. Through transcriptomic analysis, we identified the allene oxide synthase CsAOS gene, which encodes an allene oxide synthase, as a key regulator of the JA biosynthesis enzyme preferentially expressed in trichomes. To investigate its functional role, we used CRISPR/Cas9-mediated knockout and overexpression strategies. Knockout of CsAOS in wild-type plants lead to a significant reduction in trichome density, whereas CsAOS overexpression in wild-type plants resulted in an enhanced trichome phenotype. These results provide novel insights into the molecular mechanisms governing trichome development in cucumbers, establishing CsAOS as a critical mediator of JA signaling in regulating trichome density. This study not only sheds light on the intricate relationship between JA and trichome development but also paves the way for future applications in plant breeding and genetic modification to improve pest resistance and herbivore defense.

Enzymatic browning significantly affects the processing and quality maintenance of a wide range of horticultural produce. Identifying key regulators of browning is essential for elucidating its underlying mechanisms and developing effective mitigation strategies. In this study, transcriptomic comparison between potato cultivars with contrasting browning sensitivities identified a small auxin-up RNA, StSAUR31, as a potential regulator of auxin-mediated browning inhibition in potato. Functional analyses showed that overexpression of StSAUR31 markedly reduced browning intensity and PPO activity, whereas knockout of StSAUR31 produced the opposite phenotype. Correspondingly, StuPPO1 protein abundance decreased in StSAUR31 overexpression lines and increased in knockout lines. Mechanistically, StSAUR31 physically interacted with StuPPO1 in an auxin-enhanced manner, partially altering its subcellular localization and reducing its accumulation in plastids. Additionally, StSAUR31 downregulated StuPPO1 expression, reduced endogenous free tyrosine levels, and enhanced antioxidant capacity. Collectively, these findings indicated that StSAUR31 coordinately regulated PPO activity, substrate availability, and antioxidant capacity, thereby integrating multiple mechanisms to suppress enzymatic browning in potatoes. These results advance our understanding of the crosstalk between auxin signaling and enzymatic browning, providing new insights into the role of hormone signaling in postharvest quality regulation.

Actinidia eriantha, a kiwifruit species endemic to China, produces fruits with notable nutritional, medicinal, and economic value, particularly due to its high L-ascorbic acid (L-AsA) content. However, the regulatory mechanisms underlying L-AsA accumulation in its fruit remain poorly understood. This study meticulously measured L-AsA levels of fruits in 216 A. eriantha accessions from natural populations and performed a genome-wide association study, through which we identified significantly associated lead single nucleotide polymorphisms and insertion deletions, and characterized a key candidate gene AebHLH89, AePPR, AePP2Ab, and AePHL1 involved in the positive regulation of L-AsA accumulation. Functional experiments showed that overexpression of AebHLH89 significantly enhanced L-AsA accumulation, while its silencing via virus-induced gene silencing markedly decreased L-AsA levels. Yeast one-hybrid assay and dual-luciferase assay preliminarily revealed that AebHLH89 could bind to the AeGMP1 promoter and activates its transcription, thereby upregulating the L-AsA biosynthesis pathway and promoting L-AsA synthesis and accumulation. These findings provide valuable genetic resources for molecular marker-assisted breeding in kiwifruit and contribute to germplasm innovation. Simultaneously, the identification of key regulatory genes enhances our understanding of L-AsA metabolism and lays a theoretical foundation for the genetic improvement of kiwifruit.

Andrographolide (AD) is the major bioactive component in the Chinese medicinal plant Andrographis paniculata (A. paniculata), which is widely used for its anti-inflammatory and antiviral properties. In this study, we observed that light is a critical environmental factor for AD biosynthesis and identified a potential transcription factor, ApTrihelix1, as a regulator of AD biosynthesis via RNA-seq combined with co-expression analysis. ApTrihelix1 is light-induced, and knocking down its expression downregulates AD content as well as the expression of several AD biosynthesis-related genes (ADRGs). Furthermore, through high-throughput sequencing methods (e.g. ChIP-seq) and molecular experiments (e.g. Yeast One Hybrid assay), ApTrihelix1 was found to bind to the promoter of ApCPS2 (a key ADRG) to activate its expression. Taken together, these data strongly support that light upregulates the expression of certain transcription factors (e.g. ApTrihelix1), thereby activating key ADRGs (e.g. ApCPS2) and promoting AD accumulation in A. paniculata.

The stem, a crucial organ that connects the root and aboveground parts, is responsible for transporting water and nutrients. This review synthesizes the current understanding of stem development in ornamental plants. We first outline the morphological and physiological characteristics of stem elongation and stem thickening. Subsequently, we examine the roles of key genes, plant hormones, and cell wall components in regulating stem growth, mechanical strength, and overall plant architecture. We also analyze how environmental factors (e.g. temperature, light, water, and nutrients) and hormonal and genetic networks modulate stem development. Particular emphasis is placed on the functions of auxin, gibberellins, and brassinosteroids. Recent studies in ornamental plants such as Prunus, Chrysanthemum, and Paeonia have illuminated the advances in cultivation techniques and gene identification associated with cellular processes, cell wall synthesis, hormone biosynthesis, and signal transduction. Looking forward, we highlight emerging research directions, including the use of advanced imaging and artificial intelligence for phenotypic analysis, and the integration of multi-omics data within a ‘Breeding 5.0’ framework. Ultimately, this review aims to support the targeted breeding of ornamental plants with optimized stem traits, enhancing both aesthetic value and production efficiency.