Polyploidization is a major driver of plant evolution and stress adaptation, yet its role in modulating biotic stress resistance through epigenetic mechanisms remains poorly understood. This study demonstrates that autotetraploidization in Chrysanthemum lavandulifolium significantly enhances resistance to Alternaria alternata , the cause of black spot disease. Whole-genome methylome and transcriptome analyses reveal that polyploidization induces locus-specific CHH hypomethylation in the promoters of a subset of WRKY transcription factors, leading to their transcriptional activation upon fungal infection. Functional characterization of CIWRKY103 , a key hypomethylated WRKY gene, confirms its critical role in conferring disease resistance. Chemical inhibition of DNA methylation (5-azacytidine treatment) in diploid plants mimics the tetraploid phenotype by activating WRKY103 expression and enhancing resistance. This epigenetic regulatory mechanism is conserved across diverse chrysanthemum species, highlighting the potential of targeting DNA methylation to modulate fungal disease resistance in polyploid crops. Our findings unveil a novel link between polyploidy, epigenetic reprogramming, and pathogen defense, offering strategic insights for sustainable crop protection.

Panax notoginseng is an important medicinal plant, and saponins are the primary active components that are the key determinants of pharmaceutical quality. Research has indicated that methyl jasmonate (MeJA) enhances the saponins accumulation in P. notoginseng, but the specific MeJA-responsive transcription factors (TFs) that regulate this process remains unidentified. Given the critical role of MYB TFs in the regulation of plant secondary metabolism, this study aimed to elucidate the regulatory mechanisms of the MYB TF family in P. notoginseng under MeJA treatment. Genome-wide screening led to the identification 110 MYB genes, followed by a comprehensive analysis of their phylogenetic relationships, conserved motifs, gene structures, cis-acting elements, chromosomal localization, and collinearity. Integrated transcriptomic and metabolomic analyses showed that MeJA treatment significantly altered the expression patterns of 84 MYB genes while also promoting saponin accumulation in P. notoginseng leaves. Co-expression network analysis revealed a significant correlation between PnMYB38 and saponin metabolites, highlighting the pivotal regulatory function of this TF. Subcellular localization experiments confirmed nuclear localization of PnMYB38. Yeast one-hybrid, electrophoretic mobility shift assay, and dual-luciferase assays demonstrated that PnMYB38 directly and specifically bound to the promoters of key saponin biosynthesis genes ( PnSE and PnDS), thereby inducing their expression. This study comprehensively characterized the functional role of PnMYB38 in regulating MeJA-mediated saponin biosynthesis in P. notoginseng, proposed a ‘MeJA- PnMYB38-saponin biosynthesis’ regulatory network that provided novel insights into the transcriptional regulatory mechanism of saponin biosynthesis, and established a foundation for molecular breeding targeting MYB TFs and metabolic engineering.

Early microbial seed priming is conceived to improve crop resilience, yet it remains unclear whether plants can discriminate among closely related beneficial strains and integrate dose-dependent microbial cues. We primed melon ( Cucumis melo) seeds with two phylogenetically similar Bacillus strains ( Bacillus subtilis NCIB3610 and B. velezensis FZB42) and combined transcriptomic, metabolomic, and physiological analyses across development. Despite comparable colonization, the strains provoked contrasting host programs and distinct dose responses. B. subtilis promoted radicle elongation, chloroplastic starch storage, and drought tolerance regardless of inoculum level, together with L-tryptophan and palatinose accumulation. By contrast, B. velezensis displayed a clear dose effect: low inoculum sustained normal radicle growth, whereas high inoculum transiently repressed it, coinciding with suppression of allene oxide synthase, genes related to proteasome complex, and enrichment of flavonoids and glutathione in leaves. Chemical assays showed that radicle inhibition depends on the synergistic action of surfactin, produced by both strains, and bacillomycin D, an iturin-type lipopeptide specific to FZB42. This synergy explains the strain-specific lipopeptide repertoire to the dose-dependent growth response. Although their early trajectories diverged, both primings converged on enhanced aboveground stress resilience. 3610-primed plants restricted Botrytis cinerea via caffeic and rosmarinic acid accumulation, whereas FZB42-primed plants curtailed jasmonate-sensitive Tetranychus urticae mites through jasmonic acid pathway modulation. Our results demonstrate that melon perceives inoculum dose and microbial identity, translating them into distinct metabolic and defense programs that converge on stress resilience. These mechanistic insights (linking lipopeptide fingerprints, sentinel metabolites, and defense transcripts) provide a framework for precision seed treatments in horticultural crops.

Apple Valsa canker (AVC), a disease instigated by Valsa mali (syn. Cytospora mali), poses a significant global threat to apple cultivation. Throughout its infection process, V. mali introduces an array of effector proteins into the host cells aimed at undermining the host immune defenses. The exact molecular mechanisms through which these effectors manipulate host transcription factors (TFs) to promote pathogenesis are not fully understood. This study identifies a ribonuclease T2-like effector, VmRnt2, that notably inhibits INF1-triggered cell death, chitin-induced reactive oxygen species bursts, and callose deposition. Knockout of the VmRnt2 gene markedly reduced the virulence of V. mali, without impacting fungal growth or spore production. Conversely, heterologous expression of VmRnt2 in Nicotiana benthamiana and apple markedly enhanced susceptibility to infections by Sclerotinia sclerotiorum and V. mali, respectively, highlighting its pivotal role in facilitating pathogenicity. VmRnt2 was found to interact specifically with an apple TF, MdMYB44, which belongs to the myeloblastosis (MYB) family of proteins. Further functional assays revealed that overexpression of MdMYB44 in apple enhances resistance to V. mali. Additionally, MdMYB44 was shown to bind specifically to the promoter of the defense-related gene MdPR1A, subsequently activating its transcription. Importantly, during V. mali infection, VmRnt2 disrupts the DNA-binding activity of MdMYB44. Collectively, our results elucidate how V. mali employs VmRnt2 to compromise MdMYB44-mediated immune regulation, thereby facilitating the pathogen’s colonization of apple trees.

Ethylene and abscisic acid (ABA) play crucial roles in the ripening and softening of persimmon fruit, and they can promote each other to accelerate the softening process. However, the underlying molecular mechanisms remain to be further elucidated. In this study, a transcription factor NAM ATAF1/2, CUC26 ( DkNAC26) induced by ethylene was identified. It could increase the content of ABA in persimmon fruit by promoting the expression of ABA synthesis-related gene DkNCED2+ 3′, thereby reducing fruit firmness. On the other hand, ABA could induce the expression of transcription factor DkNAC28, which binds to the promoter region of the ethylene biosynthesis gene DkACS1, leading to an earlier ethylene burst and consequently accelerating fruit softening. This study elucidates the functional roles of two transcriptional activators, DkNAC26 and DkNAC28, in regulating the biosynthesis of ethylene and ABA and reveals a molecular mechanism through which these two hormones interact to promote fruit softening, providing a new perspective for hormone crosstalk that drives rapid softening in persimmon.

The circadian clock enables plants to synchronize physiological and developmental processes with daily and seasonal light fluctuations. In horticultural crops, this endogenous oscillator interacts with photoperiod, light quality, and light intensity to coordinate flowering, growth, metabolism, and stress adaptation. Photoperiodic control, mediated largely by the conserved CONSTANS (CO)–FLOWERING LOCUS T (FT) module, governs flowering transitions and vegetative–reproductive balance in horticultural crops, such as strawberry, chrysanthemum, cucumber, tomato, and potato. Spectral composition, particularly red/far-red and blue light perceived through phytochromes and cryptochromes, reshapes circadian amplitude and phase to regulate photosynthesis, morphogenesis, and secondary metabolism. Meanwhile, light intensity adjusts oscillator robustness and energy allocation, influencing rhythmic stability under controlled-environment cultivation. The emerging research topics such as on species-specific clock diversity, circadian regulation of quality traits, and precision lighting strategies aligned with rhythmic principles were also discussed. Analyzing the interaction between light signals and the biological clock will help deepen our understanding of the time regulation mechanism in horticulture plants, and can provide a basis for designing optimized periodic cultivation systems in horticulture, thereby improving yield and quality of horticultural crops. In this review, we will summarize the research findings on how light environments regulate the circadian rhythms of horticultural plants, as well as their potential applications in horticulture.

Tomato ( Solanum lycopersicum) is one of the most economically important vegetable crops worldwide. Fruit quality is a critical determinant of consumer preference and market value, with color being the primary visual trait. While carotenoids impart red pigmentation, anthocyanins enable the accumulation of deep purple and blue hues. Although anthocyanins have been widely studied, a comprehensive understanding of their biosynthesis and regulation in tomato is still lacking. This review therefore synthesizes current knowledge to outline the molecular mechanisms underlying these processes. We highlight the central role of the MYB–bHLH–WD40 transcriptional activation complex. Additionally, we discuss the multilayered regulatory network involving other transcription factors, such as the bZIP family members SlHY5 and SlAREB1, BBX proteins, and others. Furthermore, we elaborate on post-transcriptional and post-translational regulatory mechanisms, which fine-tune anthocyanin accumulation. Finally, we outline current challenges and future directions for enhancing tomato anthocyanins. This review serves the dual purpose of providing an updated theoretical foundation for genetic improvement in tomato and offering a regulatory framework applicable to other horticultural crops.

Salvia miltiorrhiza, a medicinal plant of high value, faces significant yield and quality losses due to salt stress. Identifying salt tolerance genes is therefore essential for breeding resilient varieties. Gibberellin (GA) metabolism and signaling are modulated by diverse factors, with GA 2-oxidase (GA2ox) playing a key role in stress adaptation by inactivating GA and fine-tuning growth under adverse conditions. In this work, we identified 12 GA2ox genes in S. miltiorrhiza and generated an SmGA2ox4 transgenic line. Heterologous expression in Arabidopsis thaliana improved salt tolerance through enhanced germination, root growth, antioxidant activity, and stress-related physiological markers. Similar results were observed in transgenic hairy roots of S. miltiorrhiza. High-performance liquid chromatography (HPLC) analysis further showed that SmGA2ox4 overexpression promoted tanshinone accumulation but suppressed salvianolic acid biosynthesis, whereas RNA interference (RNAi)-mediated silencing had the opposite effect. Thus, SmGA2ox4 acts as a dual-function regulator, enhancing both salt tolerance and tanshinone production. This study establishes a novel link between GA2ox-mediated stress response and secondary metabolism in S. miltiorrhiza, providing a basis for engineering stress-resistant, high-quality varieties.

Horticultural crops, including fruits, vegetables, ornamental plants, and tea plants, are vital for economic and nutritional sustainability, yet their cultivation is severely hampered by abiotic stresses such as heat, cold, and salinity. The advent of the grapevine genome in 2007 initiated the genomic era for horticultural species. This milestone facilitated the use of genome-wide association studies (GWAS) to decode the complex phenotypic diversity of these crops. Unlike traditional methods, GWAS utilizes natural genetic diversity to identify quantitative trait loci linked to key traits, offering a high-resolution approach for dissecting traits such as stress resistance, quality, and yield. This review highlights the innovative workflows and technical advancements in GWAS applications for horticultural crops, covering aspects including population design, high-throughput phenotyping, sophisticated statistical modeling, and their applications in horticultural plants. Notably, the integration of multi-omics approaches has enhanced our understanding of the genetic mechanisms underlying critical horticultural traits. Future directions aim at harnessing technological innovations, cross-omics synthesis, and precision breeding strategies to optimize trait selection and expedite the development of resilient cultivars. Consequently, GWAS serves as a crucial bridge linking genomic variation to practical applications in horticultural improvement, enabling a paradigm shift toward predictive breeding and sustainable agricultural practices.

Fruit and vegetable browning is a complex physiological phenomenon responsible for substantial postharvest losses and profound economic consequences. While enzymatic oxidation mediated by oxidative enzymes has long been considered the core mechanism, emerging evidence highlights the flavonoid pathway as an alternative route, influencing pigmentation outcomes. Browning is governed by a multitiered regulatory network spanning molecular, biochemical, cellular, and physiological levels, which encompasses transcriptional, post-transcriptional, epigenetic, and hormonal controls. Notably, regulatory mechanisms exhibit both conserved features and species-specific variations, reflecting potential adaptive evolution that may underlie differential browning responses across species. Here, we provide a thorough review of current advances in the mechanistic understanding of browning, with emphasis on providing evidence on multilevel regulations, identifying conserved mechanisms versus species-specific variations, exploring their contributions to differential browning responses, and providing viable strategies for browning management through the application of exogenous hormones. Based on these, the current research landscape is critically assessed, and future research priorities are identified.

Dihydrochalcones (DHCs) are highly accumulated in tender leaves of Lithocarpus litseifolius but their biosynthetic pathway and accumulation mechanism remain unclear. In this study, candidate genes including one cinnamoyl-CoA reductase (LlCCR), two double bond reductases (LlDBR1 ~ 2), three aldehyde hydrogenases (LlALDH1 ~ 3), two 4-coumaroyl:CoA ligases (Ll4CL1 ~ 2) and four phloretin glycosyltransferases (LlP4′GT, LlP2′GT1~3) were comprehensively investigated. The substrate specificities and catalytic kinetics of these gene-encoded enzymes were achieved. Through successive catalysis of LlALDH1, Ll4CL2, and chalcone synthase 1 (LlCHS1) or combined action of LlCCR and LlCHS1, phloretin was biosynthesized from direct precursor dihydro-p-coumaraldehyde, which had been converted from initial precursor p-coumaroyl-CoA by LlCCR-mediated carboxylic acid reduction and LlDBR1-catalyzed α,β-double bond saturation. High accumulation of the DHCs in tender leaves of L. litseifolius was mainly driven by efficient catalysis of LlCCR toward p-coumaroyl-CoA and highly expressed genes in the pathway, especially the LlP4′GT and LlP2′GT1 which contributed to biosynthesis of trilobatin and phlorizin, respectively. Antisense oligodeoxyribonucleotide treatments against the LlCCR, LlDBR1, LlALDH1, Ll4CL2, LlP4′GT, and LlP2′GT1 significantly reduced transcripts of the target genes and content of DHCs, confirming these genes might be involved in the pathway. This finding provides insight into the biosynthesis and accumulation mechanism of DHCs in planta

Floral scent is a crucial quality trait in ornamental plants, yet research has been hampered by the lack of standardized sensory evaluation and the disconnect between genes, volatile compounds, and human perception. Hedychium is an excellent model for fragrance research due to its diverse fragrance types and rich volatile organic compound (VOC) profiles. This study establishes a sensory-omics framework to connect genetic pathways, VOC chemistry, and fragrance perception in Hedychium flowers. A multidisciplinary approach combined sensory panel analysis (developing a fragrance wheel), VOC profiling (HS–SPME–GC–MS and PTR–ToF–MS), transcriptomics, and functional characterization of key biosynthetic genes in 30 Hedychium accessions representing six fragrance types. Six distinct fragrance types were classified (e.g. strong floral, fruity), linked to specific VOC profiles (e.g. monoterpenoids, esters). PTR–ToF–MS validated rapid detection of key fragrance markers. Supervised partial least squares-discriminant analysis (PLS-DA) modeling of VOC signatures enabled fragrance-type classification and key variable selection. Transcriptomic analysis coupled with weighted gene co-expression network analysis (WGCNA) revealed two key gene modules-MEbrown (terpenoid-associated) and MEyellow (phenylpropanoid-associated)-that underlie fragrance variation. Functional validation through in vitro enzymatic assays and transient overexpression in tobacco leaves confirmed HcTPS1 as a eucalyptol synthase and HmBEAT1 as a benzyl acetate synthase. Collectively, these findings provide a comprehensive framework for Hedychium flowers, thereby elucidating the molecular and chemical basis of their sensory fragrance variation. The study delivers valuable genetic resources and a predictive model that establishes a foundation for the targeted breeding of floral fragrance in ornamental horticulture.

Ginkgo biloba is a singular and relict gymnosperm indigenous to China. Its distinctive fleshy episperm is rich in unique metabolites, ginkgolic acids, which protect the developing seed from biotic stresses. The unique nature of the tissue and its metabolites has made it highly challenging to elucidate the molecular and cellular mechanisms governing ginkgolic acid biosynthesis and regulation. In this study, we performed the mass spectrometry imaging of G. biloba seed, revealing that ginkgolic acids primarily accumulate in the secretory cavities of the episperm. We constructed a single-cell expression atlas of the G. biloba episperm and identified seven cellular types: meristem cells, subepidermal cells, lignified cells, trancheid cells, parenchymal cells, secretory cavity cells, and epidermis cells. Based on the analysis of upregulated gene expression in secretory cavity cells, pseudotime analysis of cell differentiation, and gene expression trajectory analysis, we precisely identified the key enzyme-encoding genes highly associated with ginkgolic acid biosynthesis. This approach elucidated the cellular and molecular mechanisms underlying secretory cell differentiation, secretory cavity formation, and ginkgolic acid biosynthesis and accumulation in response to exogenous jasmonic acid induction. By constructing a molecular interaction network, it was determined that the GbWRKY35, encoded by Gb_25334, is the core transcription factor. We further identified the signaling proteins that interact with GbWRKY35, confirming its central positive regulatory role in ginkgolic acid biosynthesis. As a core transcription factor, GbWRKY35 regulates ginkgolic acid biosynthesis through stimulating the expression of GbAAE16. This study provides the first spatially resolved investigation into the molecular and cellular regulatory mechanisms of ginkgolic acid biosynthesis in the episperm under jasmonic acid induction.

Lilies ( Lilium spp.) are globally important ornamental crops which are constrained by their narrow thermal tolerance range. However, tiger lily ( Lilium lancifolium), a wild lily species, exhibits remarkable cold tolerance. Based on our previous findings, we proposed that LlR3MYB, an R3-MYB transcription factor (TF), confers cold tolerance via transcriptional regulation of flavonoid metabolism in tiger lily. Here, we revealed that LlR3MYB represents a unique CPC-type R3-MYB TF exhibiting a bifunctional role in flavonoid metabolism. Specifically, LlR3MYB suppresses anthocyanin biosynthesis while promoting non-anthocyanin flavonoid accumulation (i.e. flavonols, flavones, and chalcones) responding to cold stress. Overexpression of LlR3MYB in tobacco and tiger lily increased total flavonoid content but reduced anthocyanin levels, consistent with the upregulation of early biosynthesis genes (e.g. CHS and FLS) and repression of late biosynthesis genes (e.g. DFR and ANS) in the pathway. In contrast, silencing LlR3MYB in tiger lily reduced total flavonoid production, enhanced anthocyanin accumulation, and compromised cold resistance. Mechanistically, LlR3MYB can directly bind to the AC-I element (ACCTACC) and MBSI motif (CAACGGTT) in the LlCHS2 promoter and activating its transcription, with enhanced activation under low temperature conditions. Mutations of critical residues within the C1/C2 repressor motifs may endow LlR3MYB with this transcriptional activation function. Furthermore, LlDREB can directly bind to the DRE motif (ACCGAC) in the LlR3MYB promoter and activating its transcription in a low-temperature-dependent manner. Our findings uncover a branch-specific regulatory mechanism by which MYB TFs fine-tune flavonoid biosynthesis, highlighting their essential role in plant cold stress responses.

Nucellar apomixis is truly clonal and is a powerful tool for broadening the genetic base of crops. Black pepper ( Piper nigrum L.), the ‘King of Spices’ is difficult to improve through conventional breeding. Although transgenesis and genome editing are prime strategies for rapid crop improvement, recalcitrance hinders genetic modifications. Here, we report a highly efficient Agrobacterium-mediated procedure for generating genetically modified black pepper plants using nucellar apomixis-derived embryos of the varieties Sreekara and Karimunda, with a 99% survival rate. Both Agrobacterium tumefaciens and Agrobacterium rhizogenes were efficient in transformation, and the AGL1 strain harboring the plasmid with mgfp achieved >90% frequency following 20 min in the infection medium, 30 s sonication, 10 min vacuum infiltration, and 4 days of cocultivation. Sugar type determined embryonal taproot development and soil establishment. Glucose-supplemented medium produced plantlets with well-developed root systems that displayed a high expression of PnPIN2. Transgenic plantlets survival ex vitro from glucose-supplemented liquid medium was 99%. The genome-editing efficiency of Pds using CRISPR/ Cas9 was 89%. Agroinfiltration of black pepper in this study is useful for high-throughput screening of disease resistance. Composite plants of black pepper generated at >60% efficacy is an easy strategy to develop plants expressing disease-resistant genes in roots to reduce yield loss, especially by root-rot. This study demonstrates that black pepper is an easy-to-transform crop, which reinforces speedy trait development through genetic modifications. Scale-up using temporary immersion bioreactors in this study fast-track high throughput accomplishment of untransformed/transformed/genome edited plants empower the market demand for black pepper.

Safflower is featured with time-honored medical and economic values and developing into diverse phenotypic and genetic variations. In this study, to explore the critical genes associated with color phenotypes and flavonoid derivatives biosynthesis of safflower, BSA-seq, conflated with transcriptomic and metabolic methods were performed in two extreme colors (yellow and white) in the population of ‘ZHH0119’ and ‘XHH007.’ After crossing two parent plants reciprocally, the F₄ generation of two accessions were used to construct near-isogenic gene pools for the two extreme traits of yellow and white safflower. BSA-seq results located five QTLs regions on chromosomes 2, 8, 9, 10, and 12 including 6 CtPALs, 3 CtC4Hs, 2 Ct4CLs, 1 CtCHS, 32 CtUGTs, and 70 CtCYPs, which tied to the yellow color phenotype of safflower. Through transcriptome analysis of two accessions and at different flowering stages, 1 CtPAL, 5 CtC4Hs, 4 CtCHSs, 3 CtCHIs, 3 CtFLSs, 48 CtUGTs, 51 CtCYPs, and 75 transcription factors were revealed as significantly upregulated in the yellow accession compared to the white. Integrated analysis identified eight CtUGTs ( CtUGT50-57) that exhibited significant positive correlations with chalcone glycosides of yellow safflower. Based on functional characterization, CtUGT52 was found to boost Hydroxysafflor yellow A (HSYA) content in yellow safflower which possessing substrate promiscuity (chalones, flavonols, and flavonoids) and catalytic promiscuity (flavonols and flavonoids), revealing its vital role in the HSYA biosynthesis through transgenic overexpression. Combining catalytic mechanism verification of CtUGT52 towards phloretin, kaempferol, and luteolin, our study to some extent, elucidated the modification function of CtUGTs for flavonoid aglycones in the flavonoid biosynthesis pathway of safflower.

Chilling requirement (CR) is a key determinant for bud dormancy release in peach [ Prunus persica (L.) Batsch]. To examine the genetic basis of CR and facilitate the breeding of climate-resilient varieties, we conducted a genome-wide association study (GWAS) on a diverse panel of 213 peach accessions with their CR phenotypes. The CR phenotypic data collected over 3 years demonstrated high heritability ( H² = 0.86), indicating a strong genetic component. The GWAS analysis identified 52 SNPs associated with CR traits, with major loci clustered on chromosome 1 (17.3–21.2 and 43.7–47.3 Mb) and chromosome 2 (5.2–13.9 Mb), thereby both confirming established loci in the DAM cluster and identifying novel genetic regions. By focusing on regions exhibiting stable CR associations across years and which could be successfully validated by Kompetitive Allele Specific PCR (KASP) assays, 13 candidate CR-related genes were identified. Two highly robust KASP markers derived from loci in chromosome 1 were developed and validated. These markers effectively discriminated between low (<400 h) and high (≥900 h) CR phenotypes. The combined use of these two markers achieved 95.5% accuracy in identifying extreme low-CR phenotypes (CR < 300 h) in peach accessions. The identification of genes linked to these robust markers of CR-related loci and the analysis of their expression during dormancy identified three potentially related with CR trait modulation: a receptor-like protein kinase, a protein kinase and a BED-type zinc finger domain-containing protein. This study provides useful molecular tools for marker-assisted breeding for low-CR peaches and new insights into the complex regulatory network of CR.

Drought tolerance is a pivotal trait for tomato ( Solanum lycopersicum) genetic improvement, and enhancing the root/shoot ratio (R/S) serves as a core adaptive strategy for plants to cope with water deficit. While trehalose-6-phosphate phosphatase (TPP) genes are implicated in plant drought responses, their role in modulating R/S remains unclear. Here, we characterized SlTPP1 as a key positive regulator of drought tolerance in tomato. We found that drought stress dynamically induces SlTPP1 expression in roots while suppressing it in leaves. Mechanistically, SlTPP1 overexpression increases root soluble sugar content and upregulates night-specific expression of cell wall biosynthesis genes in roots to promote root growth, while concurrently suppressing the ethylene signaling pathway in leaves to increase R/S. Furthermore, we identified the transcription factor SlERF4 as a direct upstream repressor of SlTPP1. SlERF4 binds to the CE1 element (CACCG) in the SlTPP1 promoter and inhibits its transcription. CRISPR/Cas9-mediated knockout of SlERF4 results in enhanced drought tolerance, elevated SlTPP1 expression, increased R/S, and upregulation of root cell wall biosynthesis genes. Additionally, drought enhances ethylene biosynthesis in tomato leaves while concurrently reducing that in roots. Collectively, our study unveils a novel SlERF4–SlTPP1 regulatory module that enhances drought tolerance in tomato through the regulation of R/S, providing strategic targets for breeding drought-tolerant crops.

Plant growth-promoting rhizobacteria (PGPR) interact with host plants through chemical signals. However, the specific signals in citrus–PGPR interactions remain unclear. Here, we show that a predominant and growth-promoting Burkholderia strain (Burk_2H3) isolated from citrus rhizosphere promotes plant growth by secreting N-(3-oxo-octanoyl)-L-homoserine lactone (PGPHL). Metabolomic analysis revealed that PGPHL abundance in Burk_2H3 secretions was 9.7- to 17.2-fold higher than that in three non-promoting Burkholderia strains. Exogenous application of PGPHL, but not other secretory metabolites, increased citrus seedling dry weight by 43.12%. Transcriptomic analysis showed that Burk_2H3, its cell-free supernatant, or PGPHL consistently upregulated key nutrient transporter genes in roots. Consistently, ionomic analysis confirmed higher root concentrations of nitrogen, phosphorus, and potassium. Field trials further demonstrated that PGPHL increased biomass by 21% in pepper, 15% in celery, and 18% in mustard. Together, these findings identify PGPHL as a candidate for developing plant growth stimulants and biofertilizers.

Plasmopara viticola, the causal agent of grapevine downy mildew, exhibits substantial intraspecific variation in pathogenicity and genetic diversity, yet the genomic features underlying this variation remain incompletely characterized. Here, we sequenced and assembled two P. viticola isolates, PvH (from Vitis vinifera) and PvS (from V. amurensis), using PacBio HiFi sequencing, and performed comparative genomic analysis. Two complete genome assemblies (17 chromosomes) of P. viticola (PvH: 115.3 Mb; PvS: 113.0 Mb) were generated and revealed that nearly 90% of the putative effectors exist as local duplicated gene clusters. Comparative genomics uncovered distinct intraspecific expansion, deletion, and diversification of putative effectors driven by local segmental, tandem, and proximal duplication events in P. viticola. Specifically, PvH exhibited a ~1.4-fold increase in CRNs (PvH: 237; PvS: 183; PV221: 169) and harbored 35 strain-specific CRNs. These differential effectors were predominantly clustered in complex structural variation hotspots (SVs, duplication and inversion). Notably, 104 putative effectors-including 21 RxLRs, 59 CRNs, and 24 CAZymes-were located within inversion regions. Together, our results highlight a highly dynamic genome architecture in P. viticola, in which SV and local gene duplication are closely associated with effector diversification. This study provides a genome-resolved comparative framework for understanding intraspecific genomic diversity in P. viticola and establishes a foundation for future population-level and functional investigations.

Solanaceous vegetables are continuously threatened by Fusarium wilt disease, which is mainly caused by Fusarium oxysporum ( Fo), a fungal species complex comprising many devastating soil-borne pathogens, resulting in severe yield losses worldwide. Over the past decade, significant and numerous advances have been made in dissecting the molecular and genomic basis underlying the interaction between solanaceous vegetables and Fo, particularly owing to the emergence of the tomato- Fo pathosystem as a powerful model system for studying the molecular basis of resistance and susceptibility in solanaceous vegetables against vascular wilt pathogens. In this review, we summarize recent advances driven by improvements in genome sequencing and assembly of Fo infecting solanaceous vegetables, the virulence strategies and diverse arsenals employed by Fo to modulate and suppress host immunity, as well as the identification and functional characterization of race-specific resistance genes in solanaceous vegetables and their corresponding Fo determinants. We address the potential downstream signaling pathways involved in activating solanaceous vegetable immunity against Fo. In addition, we explore emerging insights into microbiome-based strategies for disease control, emphasizing the potential use of beneficial and synthetic microbes in the sustainable management of Fusarium wilt in tomato. Collectively, this review provides an integrated perspective on pathogen genomics, pathogenesis, host resistance, and microbiome-driven control of Fusarium wilt in tomato, offering promising avenues for developing durable and broad-spectrum resistance against various Fo strains in solanaceous vegetables.

Drought stress profoundly impacts plant productivity worldwide. The roles of basic helix–loop–helix (bHLH) transcription factors are critical in processes of plant growth, development, and stress management. However, roles of specific bHLH genes in tomato, particularly in relation to drought tolerance, remain poorly understood. This research identified SlbHLH70 as a factor that enhances drought tolerance in tomato. Transgenic lines overexpressing SlbHLH70 exhibited enhanced drought tolerance and improved post-stress recovery, whereas SlbHLH70 knockout mutants showed increased sensitivity to drought stress. Further study showed that SlbHLH70 directly regulated genes associated with abscisic acid (ABA) synthesis, ABA-mediated signal transduction, and root development. Our research identified SlbHLH70 as an important regulator of drought resistance in tomato, offering a valuable genetic target for enhancing crop resilience to water shortages.

Comprehensive 3D genome maps are essential for understanding transcriptional regulation, yet such resources remain limited for perennial woody crops. Here, we present a high-resolution, tissue-resolved 3D genome atlas of kiwifruit ( Actinidia chinensis). Using in situ Hi-C, we generated chromatin contact maps from leaf and fruit tissues and integrated these data with epigenomic and transcriptomic datasets, including chromatin accessibility, whole-genome DNA methylation, seven histone modifications, and RNA-seq profiles spanning multiple tissues and fruit developmental stages. This integrated dataset enables systematic annotation of genome architecture across multiple spatial scales, including A/B compartments, hierarchical subcompartments, TAD-like domains, and chromatin loops. Global features of 3D genome organization are broadly similar between tissues, while quantitative variation is observed at finer scales, such as subcompartment rank, domain insulation strength, and loop detection frequency. Integration with genomic and epigenomic features reveals consistent associations between chromatin states and spatial organization, providing a reference framework for interpreting plant genome architecture in a perennial context. We further map tissue-specific gene sets onto the 3D genome landscape and describe their spatial distributions relative to compartments, domains, and loop anchors, offering a view of how transcriptional programs relate to higher-order chromatin organization. Together, this work establishes an integrative, high-resolution 3D genome resources for a woody perennial fruit crop, and supports future functional, evolutionary, and applied research in kiwifruit and other perennial species.

Arnebia tschimganica is a vulnerable species within the Boraginaceae (Boraginales), which has long been taxonomically debated due to inconsistent molecular and morphological characteristics. Shikonin and its derivatives, which are found in the roots of Boraginaceae species, possess significant pharmacological and industrial potential; however, the regulatory mechanisms underlying their biosynthesis are not yet fully comprehended. The lack of reference genomes for Arnebia species has hindered further research in these fields. Here, this study sequenced and assembled the chromosome-level genome of A. tschimganica, revealing that Boraginales is sister to Lamiales within the lamiids and suggesting that the taxonomic status of A. tschimganica should be regressed from Arnebia to Lithospermum. Arnebia tschimganica has undergone a recent whole-genome duplication that is shared with other Boraginaceae species, and this event has driven the evolution of shikonin biosynthesis. Multi-omics analysis revealed significant differences in shikonin production between A. tschimganica and Lithospermum erythrorhizon, attributing reduced shikonin productions in A. tschimganica to low transcript levels of key biosynthetic genes postdivergence. Furthermore, AtsDSH1, the enzyme responsible for catalyzing the hydroxylation of deoxyshikonin to shikonin in A. tschimganica, was identified and functionally characterized. Two ERF transcription factors were identified as conserved regulators of the dehydroshikonin hydroxylase gene DSH1, potentially regulating shikonin biosynthesis. These findings provide a chromosome-level genomic perspective to clarify the taxonomy of this controversial swing species and advance valuable insights for shikonin biosynthesis regulation.

The delayed flower bud opening of Lonicera japonica ‘Huajin 6’ extends its harvest window and enhances agricultural value, yet the underlying molecular basis remains unclear. Here, we assembled a chromosome-level genome of ‘Huajin 6’ using PacBio sequencing and high-throughput chromosome conformation capture scaffolding (824.72 Mb, scaffold N50 = 91.2 Mb). Comparative genomic analyses revealed a subfamily-specific contraction of lipoxygenase ( LOX) genes, particularly within the 9-LOX clade, which is associated with a reduced jasmonate biosynthetic capacity during floral development. Transcriptomic and hormone profiling showed coordinated suppression of jasmonic acid (JA) biosynthesis-related genes and a marked reduction of JA and its bioactive derivatives during the transition from the complete white stage to flower opening. A JA-responsive co-expression module enriched in cell wall modification genes exhibited attenuated activation in ‘Huajin 6’. Functional assays further demonstrated that exogenous JA restored timely flower bud opening in both ‘Huajin 6’ and L. macranthoides, while heterologous expression of Lonicera LOX genes enhanced jasmonate accumulation in Arabidopsis. Together, these findings are consistent with a jasmonate threshold model in which LOX gene contraction constrains JA accumulation during floral transition, contributing to delayed flower bud opening and highlighting how genome structural variation influences hormone-dependent flowering dynamics.

Green flowers are uncommon in nature, yet they present a unique opportunity to explore the molecular, developmental, and evolutionary principles underlying floral pigmentation. While most species undergo petal degreening during maturation, some retain chlorophyll through suppressed degradation, sustained synthesis, or altered plastid differentiation. Here, we synthesize recent advances in understanding the molecular basis of green flower formation, integrating evidence from plastid biology, chlorophyll metabolism, transcription factor regulation, and floral organ identity genes. Research across diverse taxa reveals that chlorophyll homeostasis in petals is shaped by the interplay of light and hormonal signals, and orchestrated by transcriptional networks. In certain instances, homeotic transformations result in leaf-like characteristics. Naturally occurring variants, as well as engineered lines, offer powerful systems to dissect how developmental programs governing organ identity intersect with pigment metabolism. Green flowers also hold distinct ornamental and cultural value, expanding their relevance beyond ecological function. By tracing progress from morphological observations to multi-omics analyses, we highlight how this field is beginning to uncover shared regulatory frameworks and lineage-specific innovations. In the future, targeted manipulation of key regulatory nodes could enable the precise breeding of stable green blooms, while comparative studies promise deeper insights into how pigment pathways evolve and integrate with broader developmental networks. Understanding these processes will not only enrich floral biology but also enhance our ability to intentionally design and diversify plant phenotypes.

Astragalus membranaceus var. mongholicus (AMM) is the principal botanical source of Huangqi, a traditional medicinal herb whose therapeutic value primarily stems from the accumulation of isoflavones and other bioactive compounds in the roots. In this study, field surveys across major AMM production regions revealed pronounced natural variation in stem coloration. Chemical analysis showed that the roots of the red-stemmed type contained significantly higher levels of four bioactive isoflavones and volatile organic compounds than those in green-stemmed plants. Metabolomic profiling further revealed a specific enrichment of cyanidin-based anthocyanins in the red stems, establishing the metabolic basis of the red stem phenotype. Both transcriptomic and metabolomic analyses indicated an overall upregulation of the flavonoid and phenylpropanoid biosynthetic pathways in the stem and root tissues of red-stemmed AMM. Weighted gene co-expression network analysis (WGCNA) identified six key genes ( AmC4H, AmCHS, AmCHI, AmF3H, AmF3′H, and AmBZ1) that were strongly associated with the red stem phenotype, all of which were specifically highly expressed in red stems. Functional assays confirmed their roles in anthocyanin biosynthesis. Molecular modeling provided further insights into the substrate specificity of AmBZ1. This study proposes stem color as a visible phenotypic reference for early-stage germplasm selection in AMM, and characterizes the molecular basis underlying red stem formation, providing a foundation for elite germplasm development and molecular breeding.

Banana, a globally important staple fruit, is naturally deficient in anthocyanins; however, successful engineering of anthocyanin-enriched banana has not been reported to date. Herein, a regulator y network of five R2R3-MYBs ( MusaUP1 , MusaUP2 , MbaMA2 , MusaMA4 , and MusaMA8 ) differentially synchronizing anthocyanin biosynthesis in banana bract is reported. RNA-seq data of red bract revealed a web of regulator y and structural genes fine -tuning anthocyanin accumulation through amalgamation of MYBs and bHLHs activities. Yeast one -hybrid (Y1H) demonstrated differential affinities of these MusaMYBs to banana TT8, CHS, ANR, UFGT, FLS, ANS, and LAR, revealing an intricate pattern of layered regulation in bract pigmentation. Functional competence of this MYB network resulted in intense anthocyanin accumulation in whitish onion and restoration of pigmentation in myb90/ tt8 Arabidopsis seedlings. Hierarchical regulation in this MYB network stemmed from contrasting control over early and late flavonoid structural genes as revealed by disparate orange fluorescence of myb90/ tt8 Arabidopsis seedlings after DPBA staining. In banana, a distinctive requirement of TT8 for pigmentation was observed for MbaMA2 and MusaMA8 , while MusaUP1 , MusaUP2 , and MusaMA4 were self-competent, although co-expression of MusaTT8 augmented the ectopic pigmentation effect. Transcript abundance of flavonoid structural genes in transgenic banana is in coherence with Y1H data, thus catalysing pigmentation up to 500-fold over control. This regulator y MYBs hierarchical framework manifested flux in a spectrum of distinct pigment metabolites, viz peonidin-3,5-diglucoside in MusaUP1 and MusaUP2 , dalbergiodin in MbaMA2 /TT8 lines (FLS -mediated pathway), leucodelphinidin and leucopelargonidin in MusaMA4 lines (DFR to ANS flux), and prodelphinidin B4 in MusaMA8 lines. This study will be a step forward towards metabolic engineering for bio-fortification of banana and development of functional foods, as evident by strong antioxidant activities of these MYB lines.

Understanding the genetic and regulatory mechanisms underlying wood traits and secondary cell wall (SCW) development in Ginkgo biloba is crucial for improving wood quality. We identified key genes related to wood traits and SCW development through integrated genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and weighted gene co-expression network analysis (WGCNA). Cellulose biosynthesis in the SCW is catalyzed by the CesA4–CesA7–CesA8 complex encoded by GbCesA4, GbCesA7, and GbCesA8A/ 8B. These CesA genes form a co-expression network with TUBA/ TUBB and EG, indicating coordination among cellulose synthesis, cytoskeletal guidance, and cell wall remodeling. Additionally, loss of function of GbCesA8B caused only a slight reduction in cellulose content, supporting potential functional redundancy between GbCesA8A and GbCesA8B. For hemicellulose biosynthesis, GbCSLA9A/ 9B and IRX9/ IRX14 were major contributors to mannan/glucomannan and xylan synthesis, respectively, and formed a co-expression network with UXS, UXE, IRX7, GXMT, and URGT, spanning nucleotide sugar supply, transport, and polymer elongation and modification. Moreover, MYB46 may regulate mannan/glucomannan biosynthesis in the SCW by activating CSLA9 transcription. For lignin biosynthesis, TWAS identified multiple genes involved in phenylalanine biosynthesis, phenylpropanoid metabolism, and lignin monomer polymerization, including ADT/ PDT, PAL, and PER, as well as MYB91 and several bHLH genes that may positively regulate lignin accumulation. Furthermore, several transcription factors potentially involved in SCW development were identified, including GATA9 as a putative positive regulator, WRKY12 and HB15 as potential negative regulators, and ELF6, which may facilitate tracheid expansion. Our findings provide valuable insights into the genetic regulation of wood traits and SCW development in Ginkgo.

The evolutionary history of the ANA-grade angiosperms provides a crucial window into the transition of early flowering plants. Within this group, the Nymphaeales (water lilies) are pivotal, yet a lack of gapless genomic resources has hindered research into their complex developmental and adaptive programs. In this study, we present a telomere-to-telomere (T2T), gap-free genome assembly of Nymphaea minuta, a miniature water lily endemic to Madagascar. Utilizing PacBio Revio HiFi and Hi-C technologies, we generated a 382-Mb assembly anchored to 14 chromosomes. Comparative analysis reveals a compact genome with lower levels of ancient polyploidization than other Nymphaeaceae. By integrating a comprehensive transcriptome atlas of 15 organs and developmental stages, we identified seven primary developmental trajectories and 1179 organ-specific genes. Our analysis uncovered two critical regulatory models: Sequential Dual-Module Relay: In leaves, water fluctuation triggers an initial MAPK-signaling stress response, followed by a post-transcriptional ‘transcriptome reset’ mediated by the RNA degradation pathway (LSM1/2 and ENOC) during severe drought. Energy-Program Coordination: Seed development is governed by a three-phase transition where the glyoxylate cycle (MLS) drives energy mobilization, while an ERF1-centered hub integrates ethylene, ABA, and JA signaling to balance rapid germination with immune defense. These findings provide a definitive genomic reference for basal angiosperms and elucidate the molecular networks enabling the survival and rapid development of these ancient aquatic herbs.