Cymbidium sinense is a renowned ornamental orchid species appreciated for its captivating floral fragrance. To investigate the molecular mechanisms underlying floral scent formation, we performed an integrated analysis of transcriptomics and metabolomics across five developmental stages and three floral tissues. Metabolomic profiling revealed that (E)-β-ionone is the predominant volatile compound, with its levels fluctuating significantly during flower development and correlating with fragrance intensity. Notably, the sepals and petals were identified as the primary sources of floral scent, with their emission increasing as the flowers bloomed. Transcriptomic analysis revealed 1272 differentially expressed genes during the period of significant floral scent enhancement, with most genes, including CsCCD4, enriched in metabolic pathways and secondary metabolite biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified CsCCD4 as a central hub gene, closely associated with (E)-β-ionone biosynthetic pathways. Functional validation through stable transformation in tobacco and transient expression in Phalaenopsis petals confirmed that CsCCD4 catalyzes (E)-β-ionone production, promoting floral fragrance accumulation. Additionally, yeast one-hybrid screening, dual luciferase, electrophoretic mobility shift, and protoplast assays showed that CsKHZ1, a zinc finger transcription factor, binds the CsCCD4 promoter and activates transcription, reported here for the first time. These findings suggest that the CsKHZ1-CsCCD4 module regulates (E)-β-ionone accumulation and enhances floral fragrance in C. sinense. This study provides a deeper understanding of the molecular networks governing floral scent formation and offers valuable genetic resources for future breeding programs aimed at enhancing fragrance traits in orchids. Moreover, the identification of key regulatory genes holds potential for biotechnological applications in the production of high-value volatiles.

Polygala tenuifolia Willd. (P. tenuifolia) is one of the source plants of the traditional Chinese medicine ‘Yuanzhi’ and is widely used in clinical practice. As a meso-xerophytic medicinal plant with strong environmental adaptability, it is listed as a nationally protected wild medicinal species in China. However, the molecular mechanisms underlying its drought tolerance remain unclear. Therefore, a genome-wide identification of the ERF subfamily in P. tenuifolia was conducted to provide candidate genes for drought adaptation research and functional validation. Ethylene-responsive factors (ERFs) play important roles in plant responses to drought stress. In this study, 78 PtERF genes were systematically identified for the first time in P. tenuifolia. Phylogenetic analysis classified these genes into five subgroups (B1–B5), with members within the same subgroup exhibiting similar gene structures and conserved motifs. Collinearity analysis revealed that segmental duplication was the primary driving force underlying PtERF family evolution. Cis-acting element analysis revealed that PtERF promoter regions were enriched with drought-responsive cis-elements, including abscisic acid and methyl jasmonate (MeJA)-responsive elements. Transcriptome analysis combined with RT-qPCR verification identified five core drought-responsive genes, among which PtERF33 expression exhibited the highest level of upregulation. Further investigation showed that PtERF33 produced two alternatively spliced transcripts: the full-length PtERF33.1 transcript and the intron-retained PtERF33.2 transcript. These two transcripts exhibited opposite expression patterns under drought stress, suggesting that they may regulate drought responses through functional antagonism. These findings provide a systematic basis for identifying drought-resistant ERF genes in P. tenuifolia and establish a foundation for clarifying the role of alternative splicing in drought adaptation in this species.

Proanthocyanidins (PAs) are polyphenolic compounds widely distributed throughout the plant kingdom, playing critical biological and ecological roles, including in seed dormancy and defense. Owing to their powerful antioxidant, protein-binding, and antimicrobial properties, PAs also have broad applications in healthcare, the food industry, and animal nutrition. Here, we examine recent advances in PA research, focusing on their structural diversity, biosynthetic pathways, regulatory networks, and potential applications. All PAs are oligomers or polymers of flavan-3-ol monomers. PA biosynthesis begins with the phenylpropanoid pathway and the production of the starter units (-)-epicatechin and (+)-catechin. Polymerization proceeds by the addition of activated extension units through non-enzymatic mechanisms. PA biosynthesis is facilitated by metabolic compartmentation and precisely regulated by the MYB-bHLH-WD40 core transcriptional complex, which integrates signals from various phytohormones and environmental factors. Despite sharing common building blocks, PAs are structurally extremely complex, due to variations in their constituent monomers, degree of polymerization, linkage patterns, and chemical modifications. These structural features of PAs collectively determine their physicochemical properties and biological activities. Future PA research should focus on key knowledge gaps, including the site(s) of polymerization within the cell, the mechanisms that determine polymer structure, and the precise structure-activity relationships of PAs. Combined with advanced purification technologies and gene editing and synthetic biology strategies, this knowledge will allow the precise biomanufacturing of target PAs, thereby advancing both fundamental research and industrial applications.

Obligate parasitic plants, particularly members of the Orobanchaceae family, including Striga and Orobanche, greatly devastate crop production. Here, we synthesize recent advances in understanding the molecular and ecological dynamics underlying parasitic plant-host interactions, focusing on critical stages of parasitism: germination, host detection, haustorium formation, and resource extraction. Orobanchaceous parasites exploit host-derived strigolactones (SLs) to break seed dormancy, whereas Cuscuta species do not rely on SLs for germination. Instead, chemotropic responses to host-exuded compounds and light signals guide the directional growth of their seedlings. Haustorium morphogenesis, initiated through host lignin-derived quinones and redox-sensitive compounds, establishes vascular connectivity enabling nutrient diversion. Meanwhile, host organisms employ sophisticated multi-tier defense strategies encompassing SL biosynthesis, lignin deposition enhancement, hypersensitive cellular responses, and hormone-coordinated immunity. Key discoveries, such as receptor kinases and horizontal gene transfer events, highlight evolutionary arms races between parasites and hosts. Emerging technologies like CRISPR offer promising avenues for engineering resistant crops by disrupting parasitic signaling or enhancing host immunity. This review underscores the importance of integrating molecular insights with agricultural innovation to mitigate yield losses and addresses future challenges, including climate-driven parasite spread and the need for sustainable, genomics-driven solutions. By deciphering the silent dialogue between parasites and hosts, this work provides foundations for transformative strategies to safeguard global food security.

This study comprehensively characterizes the PEBP gene family in Cymbidium sinense, an orchid with a prolonged vegetative phase that limits its industrial production. Genome-wide analysis identified six CsPEBPs, classified into FT-like, TFL1-like, and MFT-like subfamilies. Evolutionary, gene structure, and collinearity analyses revealed both conservation and lineage-specific diversification of these genes. CsFTL3, a distinctive FT-like member, displayed notably high expression during the bud undifferentiated stage, followed by a sharp downregulation upon floral initiation. Functional studies identified CsFTL3 as a key floral repressor. Heterologous overexpression in Arabidopsis delayed flowering time from 32.0 days (wild-type) to 63.0-75.3 days (transgenic) and increased rosette leaf number from 12.6 to 33.0-34.5, while its knockdown via virus-induced gene silencing (VIGS) in C. sinense accelerated floral bud development and upregulated flowering-promoter genes. Phylogenetically, CsFTL3 falls within the flowering repressor FT-I clade, and multiple sequence alignment identified critical amino acid substitutions (Y134S, W138L, Q140E) that likely underpin its functional divergence from typical flowering promoters. Furthermore, promoter analysis revealed an enrichment of light-, hormone-, and stress-responsive cis-elements, and its expression was modulated by gibberellin (GA), abscisic acid (ABA), and low-temperature treatments. Predicted protein-protein interaction and transcriptional regulatory networks provide preliminary insights into its complex regulation. We conclude that CsFTL3 acts as a crucial floral inhibitor, integrating environmental and endogenous cues to repress flowering. These findings offer fundamental insights into the molecular mechanisms of flowering in orchids and provide a valuable genetic resource for molecular breeding programs aimed at achieving precise flowering time control.

Sorghum (Sorghum bicolor), the fifth most important cereal crop worldwide, serves as a staple food in arid and semi-arid regions and is a critical resource for livestock forage, bioenergy production, and industrial applications. Owing to its relatively small genome and strong tolerance to abiotic stresses such as drought, salinity-alkalinity, and heat, sorghum has emerged as an important model crop for abiotic stress research. This Perspective article synthesizes recent advances on sorghum genomics, including the development of gapless reference genome assemblies, pan-genome analyses of extensive structural variation, and population resequencing studies that have uncovered domestication signatures and loci associated with stress adaptation. We also summarize the progress in sorghum genetic resource collection, selection strategies, and breeding improvement. Functional genetic studies have identified key genes regulating yield-related traits, quality attributes, and tolerance to both abiotic and biotic stresses. In molecular breeding, notable achievements include the establishment of efficient transformation systems, CRISPR/Cas9-mediated genome editing enhanced by morphogenic regulators, and the development of mutagenized populations for gene function validation. Nevertheless, major challenges remain, particularly in functional dissection of complex quantitative traits, the integration of multi-omics datasets, and genotype-dependent transformation efficiency. Future research directions emphasize the exploitation of wild germ-plasm, in-depth analysis of structural variation, population-scale transcriptomics, investigation of plant-microbiome interactions, and the application of AI-driven intelligent breeding approaches. Together, these strategies are expected to accelerate the development of climate-resilient sorghum varieties, thereby enhancing global food security and supporting sustainable bioenergy production.

Low temperature is a key environmental cue governing floral transition and inflorescence development in nobile-type Dendrobium, and chilling treatments are routinely applied in horticultural practice to manipulate flowering time. Nevertheless, a robust genetic strategy for modulating flowering independent of temperature signals has yet to be established in this genus. To elucidate the molecular framework through which plants perceive and respond to chilling, we integrated cytological analyses with RNA sequencing (RNA-seq) to characterize transcriptional dynamics and chilling-responsive pathways under different low-temperature regimes. Continuous exposure to chilling markedly hastened floral induction, advancing flowering by nearly 1 month relative to plants maintained under standard growth conditions. Comparative transcriptomic analysis identified 13,708 differentially expressed genes (DEGs) between chilled and control plants. KEGG enrichment revealed strong overrepresentation of pathways related to photosynthesis and plant hormone signal transduction. Further analyses indicated that chilling triggered extensive reprogramming of hormone-related, cold-responsive, and floral-developmental genes. Specifically, low temperature reshaped hormonal homeostasis by elevating transcripts associated with CK and ABA catabolism, stimulating GA biosynthetic enzymes, and repressing JA biosynthesis. Concurrently, chilling suppressed FRI expression, while activating key cold-responsive genes, floral integrators, and meristem identity regulators, including LEA, FT, LFY,AP1, and CAL, collectively accelerated floral transition and organ initiation. These results not only offered actionable insights for horticultural control of flowering time, but also provided a valuable genetic resource for understanding chilling-induced flowering in nobile-type Dendrobium.

The endosomal sorting complex required for transport (ESCRT) is a conserved molecular machinery that plays fundamental roles in the cellular endomembrane network. Functioning as a core mechanism, ESCRTs recognize and sort ubiquitinated membrane proteins, which are subsequently sequestered into vacuoles (lysosomes in other eukaryotes) for degradation by luminal proteases or recycled from endomembranes to the plasma membrane for functional reuse. Through these processes, the ESCRT machinery acts as a critical regulator of plant development and stress adaptation. Recent studies on plant ESCRT components, particularly VPS23A and FREE1, have identified their key roles in abiotic stress responses, with a focus on their modulation of abscisic acid (ABA) signaling pathways. Additionally, post-translational modifications including ubiquitination and phosphorylation have been shown to play pivotal roles in these regulatory processes. Notably, FREE1 has been identified to mediate endosome membrane bending and scission independently of the ESCRT machinery, a mechanism crucial for plant responses to osmotic stress. This review summarizes and discusses recent advances in ESCRT-mediated signaling in plant abiotic stress responses, aiming to highlight the fundamental roles of ESCRTs in plant biology and provide key targets for molecular breeding of abiotic stress-tolerant crops.

A single recessive gene, Multi-Grain Spikelet 1 (MGS1), governs the multiple-grain spikelet trait in sorghum. The natural variants mgs19E and mgs1BA45 trigger adjacent double-pistil primordia, significantly boosting grain numbers per panicle, suggesting potential strategies for breeding high-yield sorghum.

Gaseous phytohormone ethylene regulates various aspects of plant development. Ethylene is perceived by ER membrane-localized receptors, which are inactivated upon binding with ethylene molecules, thereby initiating ethylene signal transduction. Here, we report that a novel E3 ligase RING finger for Ethylene receptor Degradation (RED) and its E2 partner UBC32 ubiquitinate ethylene-bound receptors for degradation through an ER associated degradation (ERAD) pathway in both Rosa hybrida and Solanum lycopersicum. The depletion of RED or UBC32 leads to hypersensitivity to ethylene, which is manifested as premature leaf abscission and petal shedding in roses, as well as the dwarf plants and accelerated fruit ripening in tomatoes. Disruption of the conserved ethylene binding site of receptors prevents RED-mediated degradation of the receptors. Our study discovers an ERAD branch that facilitates the ethylene-induced degradation of receptors, and provides insights into how the plant's response to ethylene can be controlled by modulating the turnover of ethylene receptors.

The aromatic plant Ocimum basilicum var. pilosum, a Lamiaceae family member, is renowned for volatile organic compounds (VOCs), which have diverse applications in the culinary, medicinal, and aromatic industries. Despite its high economic and aromatic value, the biosynthetic pathway of VOCs is not well understood. This study employed metabolomic and transcriptomic approaches to explore the biosynthesis of VOCs in O. basilicum var. pilosum. Volatile metabolome analysis identified 151 compounds, with leaves serving as the primary source of VOCs. Phenylpropanes were identified as the major components, accounting for approximately 50% of the total VOC content in leaves, with methyl cinnamate and anethole being the predominant constituents. Illumina and PacBio sequencing identified 7,843 novel genes and 20,405 differentially expressed genes. Correlation analyses indicated that several transcription factors, including AP2/ERF-ERF, bHLH, and MYB families, are involved in the biosynthesis of methyl cinnamate and anethole. Additionally, the study identified 2,889 long non-coding RNAs and 10,427 instances of alternative splicing. Importantly, the biosynthetic pathways for methyl cinnamate and anethole were reconstructed. Two CBG genes (TCONS_00000475 and PB.4387.1) and two ACT genes (TCONS_00055847 and TCONS_00064938) were found to correlate with methyl cinnamate biosynthesis, whereas no gene expression showed a positive correlation with anethole content. This study elucidates the metabolic pathways and regulatory mechanisms underlying the biosynthesis of aromatic compounds in O. basilicum var. pilosum. The findings provide a foundation for enhancing the quality and yield of essential oils, offering valuable insights into the molecular breeding and cultivation strategies of aromatic plants.

Mediator25 (MED25) has been ascribed as a signal-processing and -integrating center that controls jasmonate (JA)-induced and MYC2-dependent transcriptional output. A better understanding of the regulation of MED25 stability will undoubtedly advance our knowledge of the precise regulation of JA signaling-related transcriptional output. Here, we report that Arabidopsis MED16 activates JA-responsive gene expression by promoting MED25 stability. Conversely, two homologous E3 ubiquitin ligases, MED25-BINDING RING-H2 PROTEIN1 (MBR1) and MBR2, negatively regulate JA-responsive gene expression by promoting MED25 degradation. MED16 competes with MBR1&2 to bind to the von Willebrand Factor A (vWF-A) domain of MED25, thereby antagonizing the MBR1&2-mediated degradation of MED25 in vivo. In addition, we show that MED16 promotes hormone-induced interactions between MYC2 and MED25, leading to the activation of JA-responsive gene expression. Collectively, our findings reveal a multiprotein regulatory module that robustly and tightly maintains MED25 homeostasis, which determines the strength of the transcriptional output of JA signaling.

Parasitism with Striga poses a major threat to global food production. Striga germination and growth rely on strigolactones (SLs) exuded by crop roots under phosphate (Pi)-deficient conditions, although the mechanism of this host-parasite interaction remains elusive. In this study, transcriptomic and functional analyses of sorghum treated with Pi deficiency or the SL GR245DS identify two ABC transporter G (ABCG) transporters of SL, Sorghum biocolor strigolactones transporter 1 (SbSLT1) and SbSLT2. Using AlphaFold2 and amino acid conversion mutants, we identify highly conserved amino acids in SL transport channels essential for transport function. Sorghum lines with single or double knockouts of these transporters exhibit significantly reduced SL secretion from roots, leading to decreased Striga germination and parasitism in field experiments and consequently reducing the grain loss under Striga infestation. This study thus describes the mechanism of SL exudation in monocots and defines conserved residues essential for SL transporter function, offering a potential strategy for enhancing crop resistance to Striga parasitism.

Wheat (Triticum aestivum L.) is the widest cultivated crop in the world. Abiotic stress, such as drought and high salinity, dramatically impacts the growth and development of wheat and leads to remarkable yield loss. Understanding the underlying mechanisms of abiotic stress tolerance is of great importance to develop high yield varieties with wide adaptability. Ubiquitination is a major type of post-translational modification in eukaryotes. The plant U-Box (PUB) protein is the smallest family in the E3 ligase superfamily, and involved in the responses to various environmental stimuli. Currently, TaPUB57 has been cloned from wheat. It was induced by multiple abiotic stresses and phytohormone. Its ectopic expression increased grain size and drought tolerance, but caused hypersensitive to salt stress in rice. TaPUB57 interacted with and ubiquitinated TaEXPB3. Constitutive expression of TaEXPB3 resulted in small grain size and remarkably enhanced salt tolerance. Moreover, TaPUB57/TaEXPB3 co-expressing rice plants exhibited phenotypes of salt sensitivity and larger grain size relative to TaEXPB3 transgenic lines. Therefore, it is speculated that TaPUB57 acts on grain size and the salt tolerance by ubiquitinating TaEXPB3.

The Orchidaceae family, with its unparalleled species diversity among angiosperms, is integral to ornamental, medicinal, cultural, and ecological value. Multi-omics techniques have proven invaluable for the identification of candidate genes and the advancement of functional genomics research. Nevertheless, the application of these technologies in Orchidaceae remains severely limited due to the lack of effective platforms that can integrate and analyze multi-omics data, especially in understanding the mechanisms underlying key traits such as distinctive floral morphology. In this study, we present OrchidMD, the Orchid Multi-omics Database (www.orchidcomics.com), a resource platform that integrates data from five omics layers: genomics, transcriptomics, proteomics, metabolomics, and phenomics, encompassing a total of 213 species. OrchidMD is equipped with 18 specialized statistical and analytical tools, and features a user-friendly interface that facilitates efficient gene mining, multi-omics data exploration, and integrative interactive analysis. A case study on the comprehensive identification of the pan-ARF gene family across Orchidaceae species demonstrates the effectiveness and convenience of OrchidMD. Furthermore, experimental validation further shows that transgenic overexpression of CsiARF04 promotes the differentiation and budding of orchid rhizomes. In addition, another case study using gene editing in orchids, CRISPR Design was employed to predict the CsiPDS target site in Cymbidium sinense. Effective editing was subsequently achieved via Agrobacterium-mediated delivery of the CRISPR/Cas9 vector into leaves. These results underscore OrchidMD's formidable capacity to discern candidate genes associated with salient traits and elucidate their regulatory mechanisms. Thus, OrchidMD serves as a pivotal platform advancing multi-dimensional biological research and functional genomics in orchids.

Endoplasmic reticulum-associated degradation (ERAD) is an important mechanism for degrading misfolded proteins, and is mediated by different complexes containing several conserved ER-localized ubiquitin ligases, such as Hrd1, Doa10, and gp78. Recent studies have shown that the ERAD machinery is conserved in eukaryotes. However, it remains unknown whether plants have gp78 homologs. We report a functional study of Arabidopsis homologs of gp78 and their involvement in ERAD. T-DNA insertion mutations in Arabidopsis gp78 genes, AtGP78A and AtGP78B, increased degradation of mutated brassinosteroid (BR) receptors, bri1-5 and bri1-9, leading to lower activation of the signaling protein BES1, and thereby enhancing the dwarf phenotypes of bri1-5/9. This is different from the effects of knockout in known ERAD components, which suppress the dwarf phenotypes of bri1-5/9. AtGP78s interacted with and affected the stability of AtOS9, but not other components in the AtHRD1 complex. AtOS9 accumulated in atgp78a-1 atgp78b bri1-5/9, and knockout of AtOS9 rescued the enhanced-dwarf phenotypes of atgp78a-1 atgp78b bri1-5/9. We determined that AtGP78s were involved in plant ERAD by modulating the stability of AtOS9. Taken together, our results not only reveal AtGP78s as new ERAD components but also reveal a relationship between AtGP78s and the AtHRD1 complex in plants.

This study aims to identify and evaluate the phosphate-solubilizing ability of endophytic bacteria isolated from roots of Chinese Cymbidium and to assess their impact on phosphorus uptake and plant growth. Thirty strains of endophytic bacteria were isolated from six orchid varieties. Molecular identification based on 16S rRNA gene sequencing revealed that the most frequently isolated strains belonged to the genera Pseudomonas and Burkholderia. Among them, 10 bacterial strains exhibited the capacity to solubilize inorganic and organic phosphorus. Two strains, designated X1 (Paraburkholderia sp. Beta-32) and X13 (Rhizobium freirei PRF81 (X13), were identified as the most effective phosphate-solubilizing bacteria (PSB). Gluconic acid was the dominant organic acid secreted, driving inorganic phosphorus solubilization, while alkaline phosphatase activities facilitated organic phosphorus mineralization. Inoculation with phosphate-solubilizing bacteria (PSB) resulted in increased plant growth and phosphorus content in both leaves and roots as compared to the control plants. PSB treatments also increased available phosphorus content in soil, reduced total phosphorus content, and increased exopolysaccharide and alkaline phosphatase activities. Real-time q-PCR analysis showed that PSB inoculation significantly upregulated the expression of phosphorus transport-related genes, including PDR2, PHF1, PHR1, PHT1;9, and PHT4;4, thereby enhancing phosphorus absorption. Moreover, strains X1 and X13 not only exhibited strong phosphate-solubilizing capacity but also demonstrated stable colonization in both roots and root rhizosphere soil of orchids over extended periods. In conclusion, the endophytic PSB identified with phosphate-solubilizing abilities increased phosphorus availability and its uptake in Chinese Cymbidium, thereby promoting plant growth and development. This is the first attempt to characterize endophytic PSB from roots of Chinese Cymbidium orchids. These findings provide a basis for selection of PSB that are efficient in P uptake for application in microbial fertilizers for orchid cultivation.

Parasitic weeds of the Orobanchaceae family cause substantial economic losses and pose significant threats to global agriculture. However, management of such parasitism is challenging, and very few resistance genes have been cloned and characterized in depth. Here, we performed a genome-wide association study using 152 tomato accessions and identified SlABCG45 as a key gene that mediates host resistance to Phelipanche aegyptiaca by affecting the level of strigolactones (SLs) in root exudates. SLs are synthesized and released by host plants and act as germination stimulants for parasitic weeds. We found that SlABCG45 and its close homolog SlABCG44 were membrane-localized SL transporters with essential roles in exudation of SLs to the rhizosphere, resistance to Phelipanche and Orobanche, and upward transport of SLs from roots to shoots. As a predominant environmental stimulant exacerbates parasitism, phosphorus deficiency dramatically induced SlABCG45 expression and weakly induced SlABCG44 expression via the transcription factors SlNSP1 and SlNSP2. Knockout of SlABCG45 in tomato had little effect on yield traits in a broomrape-free field, but conferred increased resistance to different Phelipanche and Orobanche species, resulting in an ∼30% yield increase in a Phelipanche-infested field. Our findings reveal that targeting a single gene by genome editing can confer broad-spectrum parasite resistance in tomato, providing an effective strategy for the sustainable control of parasitic plants in agriculture.