Abstract The triterpenoid-rich Panax spp. possess notable allelopathic capabilities, yet current knowledge lacks comprehensive understanding of the biological mechanisms underlying these inhibitory effects. Here, we show that Zingibroside R1 (ZR1), a newly identified allelochemical from Panax spp., inhibits the adventitious root growth in ginseng and primary root elongation in Arabidopsis. Mechanistic analyses revealed that ZR1 disrupts auxin transport, as evidenced by monitoring DR5::GFP and PINs markers. The effect of ZR1 on auxin transport was further elucidated through synergistic effects observed with the auxin transport inhibitor NPA and in the auxin transport mutants aux1 and pin2. Additionally, ZR1 downregulates key root development regulators, including stem cell maintenance regulators PLT1/2, WOX5, SHR and SCR. Transcriptomic and biochemical data indicate that ZR1 triggers a ROS response in plants, which disrupts ROS scavenging—via altered peroxidase activities and GSH/GSSG balance—thereby impairing detoxification function and resulting in root shortening by regulation of auxin distribution and stem cell gene expression. Our results establish a mechanistic framework for understanding how ginsenosides mediate allelopathic effects on root development.

Chinese jujube (Ziziphus jujuba Mill., 2n = 2x = 24) is a drought-tolerant, nutrient-rich fruit crop. However, its genetic improvement is constrained by protandry, low fruit set, and severe embryo abortion. Interspecies hybridization between Chinese jujube and Indian jujube (Ziziphus mauritiana Lam., 2n = 4x = 48) is further hindered by asynchronous flowering. We developed a dual-regime protocol combining temperature control and strategic heavy pruning to advance the flowering time of Indian jujube (cultivar 'Niunaidaqingzao', N) by 2months, thereby synchronizing its anthesis with that of Chinese jujube ('Dongzao', D) and wild Chinese jujube ('Suanzao', S). In vitro artificial self-pollination (AS) and in vitro artificial cross-pollination (AC) were conducted to assess pollen tube elongation and ovary expansion. Triple AS (TAS) boosted pollen tube emergence to 59%-87% across the three genotypes, more than doubling in vitro spontaneous self-pollination (SSP) rates and outperforming single AS 1.4 to 2.7 times (P < 0.05). Ovary-swelling frequencies of TAS reached 68.52% in wild Chinese jujube S and 27.78% in Indian jujube N, indicating 2.85 and 2.14 times increases over SSP and 1.88-4.11 times increases over single AS. In ♀S × ♂D, ♀D × ♂S, and ♀S × ♂N crosses, triple AC (TAC) raised pollen tube emergence to 54%-72% (1.3-2.2 times of single AC) and ovary expansion to 26%-39% (1.4-1.9 times of single AC) (P < 0.05). These findings provide a practical and efficient strategy for overcoming asynchronous flowering and reproductive barriers of interspecies hybridization in genus Ziziphus, enabling the establishment of interspecies hybrid populations for downstream breeding programs.

Abstract The flowers of Osmanthus fragrans are widely appreciated for their distinctive fragrance, predominantly derived from monoterpenes and apocarotenoid volatiles. However, the transcriptional mechanisms coordinating the production of these scent compounds remain poorly understood. In this study, integrated transcriptomic and metabolomic analyses of five cultivars with varying scent profiles identified OfWRKY48, a Group II-c WRKY TF. Functional studies demonstrated that transient overexpression and virus-induced gene silencing (VIGS) of OfWRKY48 significantly altered the accumulation of key scent terpenoids, including linalool, its oxides, and the apocarotenoids β-ionone, α-ionone, and dihydro-β-ionone. Mechanistic investigations revealed that OfWRKY48 activated key genes in the methylerythritol phosphate (MEP) pathway, including OfDXS, OfCMK, OfTPS1, and OfTPS2, thereby promoting linalool synthesis. Furthermore, OfWRKY48 upregulated upstream carotenogenic genes (OfPSY, OfPDS2, and OfLCYb2) and, in parallel, enhanced the expression of the carotenoid cleavage gene OfCCD4, collectively boosting the production of ionone derivatives. DNA-binding assays, including yeast one-hybrid (Y1H), luciferase reporter (LUC), and electrophoretic mobility shift assays (EMSA), confirmed that OfWRKY48 bound to the promoters of OfTPS1, OfCMK, and OfLCYb2. These findings establish OfWRKY48 as a key regulator that orchestrates the biosynthesis of both monoterpene and apocarotenoid volatiles. Our work reveals a coordinated regulatory mechanism that synchronizes precursor supply in the MEP pathway with branching points in the carotenoid pathway, providing new insights into the complexity of floral fragrance regulation and suggesting a promising target for molecular breeding of aroma traits in horticultural crops.

The control of fruit quality is of major scientific, nutritional, and commercial importance. In addition to being influenced by the intrinsic characteristics of each fruit species, fruit quality development is largely modulated by environmental factors. The environmental modulation of fruit quality primarily involves a signal transduction process that links environmental perception to the transcriptional or post-transcriptional regulation of key enzymes participating in fruit quality-associated metabolisms. Over the past decades, the effects of environmental factors on fruit quality traits have been extensively studied, and increasing attention has been directed toward elucidating the signaling mechanisms that govern this environmental modulation. However, knowledge in this research area has not yet been systematically summarized. In this review, we first provide an overview of the physiological and molecular bases underlying the modulation of fruit quality development by the three major environmental factors: water deficit, salinity, and temperature stresses. We then summarize recent advances in understanding the signaling mechanisms that mediate the environmental modulation of fruit quality development. Finally, we propose several perspectives to facilitate comprehension and guide future research endeavors.

Abstract 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 ‘Zifengyu’. 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 which could be utilized in scent improvement of ornamental plants.

Citrus Huanglongbing (HLB), caused by the phloem-restricted bacterium Candidatus Liberibacter asiaticus (CLas), is a devastating disease threatening global citrus production. CLas infection triggers excessive accumulation of phloem proteins (PPs) that obstruct sieve pores, a dual-edged process potentially restricting pathogen spread while impairing phloem transport. Despite its pathophysiological significance, systematic identification and functional characterization of PPs in citrus, particularly their roles in CLas defense, remain unclear. Here, we performed a genome-wide analysis of the PP2 gene family in the HLB-susceptible sweet orange (Citrus sinensis) and identified 26 CsPP2 genes. Phylogenetic and structural analyses uncovered evolutionary divergence and regulatory complexity among CsPP2 family members. Using promoter-driven GUS gene expression assays in transgenic hairy roots, we identified three phloem-specific paralogs, CsPP2-3, CsPP2-5, and CsPP2-18, and delineated core regulatory regions conferring tissue specificity. Overexpression of each gene significantly enhanced phloem protein deposition. Notably, although virus-induced silencing of individual CsPP2s did not affect resistance to Xanthomonas citri subsp. citri, overexpression of any of the three genes substantially enhanced resistance against this apoplastic pathogen, demonstrating functional redundancy. However, the three paralogs exhibited marked functional divergence in response to CLas: CsPP2-3 and CsPP2-18 conferred enhanced resistance, whereas CsPP2-5 increased susceptibility. Distinct defense-related gene expression profiles further supported their specialized immune roles. Our study provides the first systematic identification of PP2 genes in citrus and reveals the functional differentiation of CsPP2-3/5/18 as key regulators of phloem-mediated defense. These findings provide crucial insights into phloem defense regulatory networks and identify novel genetic targets for HLB resistance breeding.

Abstract 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 (DRE) in the promoter region of its downstream target gene, High-Affinity K+ transporter 11 (HAK11), thereby activating its expression. This regulatory 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.

Abstract 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 (ROS) 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.

Abstract 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.

Clinacanthus nutans is a traditional medicinal plant widely used in Southeast Asia for treating inflammation, viral infections, and cancer. However, its molecular basis remains poorly understood. In this study, the first chromosome-scale genome of C. nutans (731.61Mbp) was assembled, with 93.76% anchored to 18 pseudochromosomes. Repetitive elements constituted 69.05% of the genome, predominantly long terminal repeat retrotransposons. Phylogenomic and synonymous substitution rate analyses revealed a Lamiales-wide whole-genome duplication event, followed by extensive chromosomal rearrangements. Gene family expansion analysis showed that segmental and dispersed duplications were the primary drivers of enzyme-coding genes (EGs) expansion involved in the flavonoid and triterpenoid pathways. Integrated transcriptomic and metabolomic analyses across five organs revealed distinct organ-specific expression and metabolite profiles. Genes exhibited pronounced differential expression between leaves and roots, with enrichment in flavonoid and triterpenoid biosynthetic pathways, highlighting functional divergence and metabolic specialization. Flavonoids were enriched in aerial tissues, whereas triterpenoids accumulated in roots. Weighted gene co-expression network analysis identified key EGs (e.g. CHS, CHI, OSC) and core transcription factors (e.g. MYB, bHLH, WRKY) potentially involved in organ-specific metabolic regulation. These findings suggest a coordinated transcriptional-metabolic regulatory framework underlying the specialized functions of different tissues. This work provides valuable genomic resources and mechanistic insights into the biosynthesis and regulation of bioactive compounds in C. nutans, thereby facilitating future research and molecular breeding of this important ethnomedicinal plant.