Phytohormones play a crucial role in regulating fruit ripening and quality, particularly in soluble sugar accumulation. Despite this, the molecular mechanisms behind hormone-induced sugar accumulation in grapes are not well understood. Our study shows that abscisic acid (ABA) enhances grape berry ripening and soluble sugar levels. We generated a transcriptome dataset from grape berries subjected to hormone treatment and constructed a potential regulatory network related to sugar accumulation using weighted gene co-expression network analysis (WGCNA). Furthermore, we identified five structural genes (SGs) and 44 transcription factors (TFs) responsive to ABA that potentially regulate sugar accumulation in grape berries. Notably, VvMYB44 was emphasized due to its highest expression in ABA-treated mature fruits among these TFs. It binds to the promoter of VvSPS4 and activates its expression, thereby influencing sucrose metabolism. Additionally, VvERF045 interacts with VvMYB44, further amplifying its transcriptional activation of VvSPS4. Overexpressing VvERF045 also increased the soluble sugar levels in tomato fruits. These findings underscore the role of the VvMYB44-VvERF045 complex in sugar accumulation and provide new insights into the molecular mechanisms underlying sugar accumulation in grapes.

Eggplant exhibits a diverse range of fruit colors, making it an excellent model for studying fruit pigmentation and its genetic regulation. While genes responsible for green and photosensitive purple fruit have been identified, the genetic basis of the nonphotosensitive (NPS) fruit trait in eggplant has remained elusive. In this study, we characterized a major quantitative trait locus (QTL), SmNPS10.1, on chromosome 10 using QTL-seq. By combining linkage-based gene mapping with progeny testing, we fine-mapped SmNPS10.1 to a 33.58-kb interval, within which we identified SmMYB113, an R2R3-MYB transcription factor that regulates anthocyanin biosynthesis, as the candidate gene. Sequence analysis identified a unique 725-bp tandem repeat in the SmMYB113 promoter, present in four copies in NPS eggplant variety 21E27 but only a single copy in photosensitive varieties. This suggests that increased copy number of the repeat may drive light-independent expression of SmMYB113. Transgenic complementation confirmed the additional three copies of the 725-bp repeat in the promoter of SmMYB113 contributes to light-independent anthocyanin regulation. Additionally, we validated the KASP markers 21QP381 (linked to anthocyanin-present fruit color) and 23QP715 (linked to NPS fruit color) across multiple populations, providing powerful tools for marker-assisted selection in eggplant breeding. Our findings offer new insights into the molecular mechanisms controlling fruit color in eggplant and lay the groundwork for the development of molecular markers to facilitate breeding for NPS and other fruit color variants.

Drought stress significantly threatens tea production and quality worldwide. To elucidate the genetic basis of drought tolerance in tea plant, we evaluated 11 physiological traits across 115 diverse tea accessions under drought conditions. A comprehensive drought resistance index (D-value) was constructed through principal component analysis and fuzzy membership function. Genome-wide association studies identified 67 significant SNPs and pinpointed four candidate genes associated with drought-responsive traits. Integrated transcriptome and qRT-PCR analyses revealed that three genes, including CsAGD6, were significantly upregulated under drought stress. Functional assays confirmed that CsAGD6, encoding a nucleus-localized ARF-GAP protein, positively regulates drought tolerance by modulating photosynthetic efficiency and membrane stability. Haplotype analysis identified favorable alleles Hap-P1 and Hap-C1 in the promoter and coding regions of CsAGD6, respectively. Moreover, an SNP-kompetitive allele-specific PCR marker targeting chr10:206216541 (C/T) was developed and validated in 104 accessions, demonstrating high efficacy for early selection of drought-tolerant genotypes. This study provides novel insights into the molecular mechanisms of drought tolerance in tea plant and offers valuable genetic resources and tools for marker-assisted breeding.

Osmanthus fragrans is a well-known ornamental tree species for its pleasing floral fragrance. Linalool, as the characteristic aromatic component of O. fragrans, holds significant potential for applications in the flavor and fragrance industry. Although jasmonic acid (JA) is well documented to regulate the biosynthesis and accumulation of various plant secondary metabolites, its role in linalool biosynthesis remains largely unclear. Here, we discovered a positive correlation between the endogenous JA levels and linalool accumulation during the flowering stage of O. fragrans. Exogenous JA treatment was shown to enhance linalool biosynthesis by activating the linalool synthase gene OfTPS2. Dual-LUC and EMSA assays demonstrated that the key protein in the JA signaling pathway, OfJAZ3, interacted with OfMYB21 and subsequently suppressed the transcriptional activation of OfTPS2 mediated by OfMYB21. Functional validation further revealed that overexpression of OfJAZ3 significantly inhibited linalool biosynthesis in O. fragrans, A. thaliana, and N. tabacum plants. In contrast, JA promoted the degradation of OfJAZ3, thereby disrupting the formation of the OfJAZ3-OfMYB21 complex and relieving its inhibitory effect on OfTPS2. Split-LUC, BiFC, and pull-down assays confirmed that OfJAZ3 interacted with the F-box protein OfCOI1 (a key component of the E3 ubiquitin ligase SCF COI1 complex), and JA treatment enhanced the strength of this interaction. Moreover, OfCOI1 was found to participate in OfTPS2 regulation by facilitating the ubiquitination and degradation of OfJAZ3. In conclusion, our findings elucidate the molecular mechanism by which OfJAZ3-OfMYB21 complex mediates JA signaling to regulate linalool biosynthesis in O. fragrans.

Pericarp browning of postharvest litchi is a significant obstacle to the industry’s high-quality development. Water loss from the pericarp is a key factor triggering browning, but the regulatory mechanism of water metabolism and its relationship with browning remain unclear. In this study, we found that aquaporin activity inhibitors (HgCl₂) can delay both water loss and browning in litchi. LcPIP2;4, a plasma membrane intrinsic protein (PIP) family member exhibiting high expression in the litchi pericarp and the greatest water transport activity, is significantly downregulated during water loss and browning. Further analysis revealed that HgCl₂) suppresses both the expression and water transport activity of LcPIP2;4, indicating a close association with the observed browning phenotype. By constructing transient overexpression fruits and transgenic callus tissues of LcPIP2;4 and measuring the water loss rate and browning index, we confirmed that LcPIP2;4 positively regulates water loss and browning in litchi. Through weighted gene co-expression network, LcPIP2;4 promoter sequence, and Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis, we identified 10 potential interacting transcription factors. Yeast one-hybrid, dual-luciferase reporter assay, chromatin immunoprecipitation analysis, and electrophoretic mobility shift assay confirmed that LcMYB306 specifically binds to the LcPIP2;4 promoter. In LcMYB306 overexpressing fruits and embryogenic callus, LcPIP2;4 expression was suppressed, resulting in delayed water loss and browning. In contrast, in CRISPR/Cas9-edited LcMYB306 callus, LcPIP2;4 expression was upregulated, and water loss and browning were accelerated, confirming that LcMYB306 negatively regulates this process. This study demonstrates that LcMYB306 delays postharvest water loss and browning in litchi by repressing LcPIP2;4 transcriptionally expression. It provides a theoretical foundation and key target gene for developing litchi varieties resistant to browning.

Cadmium (Cd) contamination in farmland soils poses a potential threat to crop safety and human health. Heavy metal-associated isoprenylated plant proteins (HIPPs), a unique group of proteins in vascular plants, play a crucial role in abiotic and biotic stress responses. However, their functional characterization remains limited. In this study, we identified a novel sweetpotato HIPP gene, IbHIPP7, and investigated its role in Cd transport and tolerance. Subcellular localization revealed that IbHIPP7 is localized to the plasma membrane. Functional domain analysis indicated that two conserved heavy metal-associated (HMA) domains, but not the C-terminal isoprenylation motif, are essential for Cd tolerance. Transgenic sweetpotato (cultivar Sushu33) overexpressing IbHIPP7 exhibited significantly enhanced Cd tolerance and reduced Cd accumulation in roots and shoots compared to wild-type (WT) plants. These results indicate that IbHIPP7 reduces Cd toxicity by decreasing Cd absorption and thereby enhancing Cd tolerance, providing a molecular basis for developing low-Cd-accumulating sweetpotato varieties to enhance agricultural safety.

Spring-type Brassicarapa L.isavaluablegeneticresourceforbreedingearly-maturingcrops,offeringadvantagessuchasearly flowering and rapid maturation. However, the genetic mechanisms governing flowering time in spring-type B. rapa remain insufficiently understood. In this study, we investigated the flowering-time trait of an extremely early-maturing landrace, ‘Haoyou 11’, originating from the Qinghai-Tibetan Plateau. Initial mapping was conducted using an F₂ population derived from the cross between Haoyou 11 and Dahuang (a late-flowering spring-type landrace of B. rapa). A major quantitative trait locus for flowering time, designated qFTA06, was identified within a 1.7-Mb interval on chromosome A06 using genotyping-by-sequencing and bulked segregant analysis sequencing (BSA-seq). The locus qFTA06 was subsequently fine-mapped to a 75.16-kb region with a set of near-isogenic lines (NILs), and BrCDF3, a gene encoding a Dof transcription factor, was identified as the causal gene underlying qFTA06. Virus-induced gene silencing experiments revealed that BrCDF3 acts as a negative regulator of flowering time under long-day conditions, with sequence variation contributing to the early-flowering phenotype in Haoyou 11. Phenotypic analysis of NILs showed that NIL-E, carrying the BrCDF3 allele from Haoyou 11, flowered ∼7 days earlier than NIL-L, which harbors the BrCDF3 allele from Dahuang. By employing CRISPR/Cas9 technology, we further validated that the homologous gene BnCDF3 also functions as a negative regulator of flowering time in Brassica napus L., and analyzed natural variations in the CDF3 gene across natural populations. This study provides new insights into the genetic basis of flowering time in spring-type B. rapa, advancing early-maturity breeding efforts in crops.

Salt stress, with Na⁺ being the most dominant harmful ion, is a significant environmental constraint on crop growth and yield worldwide. The plant Bile Acid Sodium Symporter (BASS) family encodes a class of sodium/solute symporters found on the chloroplast envelope. However, the role of BASS family members in tomato salt stress response is uncertain. We found SlBASS4, a chloroplast envelope-located transporter in tomato (Solanum lycopersicum L.), and explored its role in salt stress response. High salinity activated the SlBASS4 gene, which in turn positively regulated tomato salt tolerance. Under salt stress, SlBASS4 overexpression (OE) lines outperformed wild-type (WT) plants, with increased fresh weight, more chlorophyll and osmolyte, improved antioxidative enzyme activity, and lower reactive oxygen species (ROS) accumulation. In contrast, the performance of RNAi lines of SlBASS4 was the inverse. Following salt treatment, the chloroplasts of OE lines collected less Na⁺, protecting the photosynthetic apparatus from Na⁺ toxicity, but the photosynthetic apparatus of RNAi lines was damaged due to excess Na⁺. The western blot results indicated that SlBASS4 may sustain the content of D1 protein levels during salt stress. Furthermore, SlBASS4 upregulated the expression of genes encoding sodium-potassium ion transporters. In conclusion, SlBASS4 positively regulates salt tolerance in tomatoes via modulating ion homeostasis, accumulating osmolyte, and scavenging ROS.

Low-temperature environments cause chilling injury in horticultural crops and accelerate quality deterioration after rewarming, which is closely related to epigenetic modifications. Epigenetic regulation is widely involved in various aspects of cold responses in horticultural crops, including the expression of cold-tolerant proteins, dynamic changes in cell membranes, energy metabolism, and reactive oxygen species metabolism. With the emergence and development of new scientific technologies, uncovering the secrets of epigenetic regulation in horticultural crop quality is becoming possible. Therefore, this paper reviews the types, roles, and potential mechanisms of epigenetic modifications involved in cold stress responses in horticultural crops, summarizes the dynamic changes and effects of exogenous treatments on epigenetic modifications, and discusses the feasibility of new editing technologies in epigenetic research and applications. This review aims to elucidate the complex regulatory mechanisms of epigenetic control in cold responses in horticultural crops, providing a theoretical foundation for developing novel strategies to control quality decline in horticultural crops.

Chinese cabbage production faces critical mechanization challenges due to traditional plant architectures that limit mechanical harvesting efficiency. Traditional breeding prioritized short-hypocotyl varieties to prevent damping-off, but long hypocotyls are now critical for mechanical harvesting. We identified BrHB52, an HD-Zip transcription factor, as a key regulator of hypocotyl elongation through quantitative trait locus (QTL) mapping, RNA-seq, and haplotype analysis. BrHB52 expression was significantly higher in the long-hypocotyl variety R031L than in the short-hypocotyl variety R032S. Overexpression of BrHB52 in both Chinese cabbage and Arabidopsis led to elongated hypocotyls. The silencing of BrHB52 in R031L resulted in a reduction of hypocotyl length. Sequence alignment revealed a 251-bp insertion in the BrHB52 promoter of the long-hypocotyl variety R031L, which introduced the light-responsive GT-1 motifs. The upstream transcription factors Phytochrome-interacting factor4 (PIF4) and B-box zinc finger 24 (BBX24) were identified through yeast one-hybrid screening using the BrHB52 R031L promoter sequence. PIF4 were found to bind to the both BrHB52 R031L and BrHB52 R032S promoters and activate their expression through G-box, while light-induced factor BBX24 only bind to the BrHB52 R031L promoter and activate its expression by light-responsive element GT-1. Our findings elucidate a BrPIF4/BrBBX24-BrHB52 regulatory module that controls plant architecture through hypocotyl elongation. These findings not only provide critical genetic targets for developing mechanization-compatible Chinese cabbage, but also develop transgenic prototypes with elongated hypocotyls, offering practical resources for mechanized breeding.

Floral organ formation plays an essential role in Cymbidium sinense reproductive development and serves as a key deter-minant of their ornamental traits. During the domestication and natural evolution of C. sinense, numerousfloralorgan variant cultivars have emerged, among which many floral morphological variations arise from abnormal development of the gynostemium, a reproductive organ. These gynostemium variant (GV) cultivars not only exhibit enhanced commercial appeal but also provide a unique model for investigating floral morphogenesis and evolutionary diversification. In this study, we identified single nucleotide polymorphisms (SNPs) in the promoter region of CsSEP4 closely linked to GV through genome-wide association studies. Functional analyses of CsSEP4 revealed that it played a crucial role in the development of gynostemium. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays indicated that the CsbZIP26 transcription factor binds to the CsSEP4 promoter and activates its expression in normal flowers, whereas the SNP mutations from ACGTG to ATGTG or ACGTA of the CsSEP4 promoter were detected in GV lines, which resulted in the inability of CsbZIP26 to bind and regulate the expression of CsSEP4. Furthermore, DNA affinity purification sequencing (DAP-seq) and Y1H experiments identified CsSPL18 as a direct downstream target of CsSEP4. Genetic evidence also demonstrated that CsSEP4 orchestrates gynostemium development by positively activating CsSPL18 expression. Collectively, our results revealed that the CsbZIP26–CsSEP4–CsSPL18 regulatory module governs the development of stamen gynostemium to regulate flower morphology in C. sinense. These findings provide insight into the molecular mechanisms underlying gynostemium development in orchids and establish amolecular framework for further elucidating orchid diversity and evolution.

Apple sweetness is primarily attributed to the high content and perceived sweet taste of fructose. A previous study used an F1 hybrid population of Malus × domestica [‘Honeycrisp’ (HC) × ‘Qinguan’ (QG) (2n = 34)] to identify quantitative trait loci (QTLs) for fructose content in fruit, revealing a stable QTL on linkage group (LG) 03 in the HC genetic map. In this study, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses of genes within this interval in combination with RNA-sequencing identified a cell wall invertase gene MdCWINV1, whose expression was highly associated with the dynamic changes in fructose content in parental fruits. The coding sequences were conserved between the two cultivars, while the promoters carried 73 single nucleotide polymorphisms (SNPs). Based on transcriptional regulatory element prediction, a unique SNP, CWINV1pro-1080 (A/C), located at −1080 bp upstream of the ATG start codon in the HC-P1 haplotype, was identified and predicted to affect the binding of the transcription factor MdWRKY20. β-glucuronidase (GUS) assays, chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR), dual-luciferase assays, and genetic transformation confirmed that MdWRKY20 specifically binds to the CWINV1pro-1080 (A) haplotype and significantly suppresses MdCWINV1 expression, reduces CWINV activity, and consequently decreases fructose accumulation. This study elucidated the functional role of MdCWINV1 as a key gene regulating fructose content and clarified how natural mutations in its promoter influence gene expression and sugar composition.

Citrus reticulata ‘Chachiensis’ contributes its fruit peel to the raw material of ‘Guangchenpi’, is renowned for its distinctive medicinal and aromatic properties, and has been utilized for hundreds of years. However, the molecular and metabolic mechanism underlining the properties remains unknown. In this study, dimethyl anthranilate was uniquely detected in ‘Chachiensis’ fruit peel compared to other mandarin cultivars and was further validated as the characteristic metabolic biomarker based on orthogonal partial least squares discrimination analysis analysis. Two SAMTs genes, CreSAMT1 and Cre-SAMT2, were screened by combined volatile profiling and transcriptome sequencing. CreSAMT1 could catalyze the methylation of N-methyl-2-aminobenzoic acid to synthesize dimethyl anthranilate, and its constant expression contributes to the specific accumulation of dimethyl anthranilate in ‘Chachiensis’, which was activated by CreERF35 and CreZAT11. While CreSAMT2 is highly expressed in citrus flowers and is responsible for catalyzing anthranilate to form methyl anthranilate, the main floral volatiles. Moreover, the involvement of transcription factors such as ERF were speculated in regulating its volatiles biosynthesis. The study provides a theoretical basis to elucidate the volatile metabolism, and to improve the aromatic citrus industry.

Rose (Rosa spp.) is a high-value ornamental plant cultivated worldwide for its aesthetic and commercial importance. However, rose production is frequently challenged by a wide range of biotic and abiotic stresses that impair growth, development, and floral quality, ultimately reducing the yield and economic returns. Recent advances have clarified the molecular pathways that govern stress responses in roses, with particular emphasis on transcriptional regulation, post-translational protein modifications, and epigenetic control. Transcription factors such as the WRKY, NAC, MYB, and AP2/ERF families regulate stress-responsive gene expression. Post-translational modifications, including phosphorylation and ubiquitination, together with epigenetic mechanisms such as DNA methylation and chromatin remodeling, establish molecular ‘stress memory’ and resilience. In response to biotic stress, roses defend against major pathogens, including black spot (Marssonina rosae), gray mold (Botrytis cinerea), and powdery mildew (Podosphaera pannosa) through integrated hormonal signaling and transcriptional regulation. Aphid herbivory triggers calcium fluxes, phosphorylation cascades, and the synthesis of secondary metabolites that strengthen defense. Emerging biotechnological tools, particularly genome editing using clustered regularly interspaced short palindromic repeats/Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9, marker-assisted selection, and virus-induced gene silencing, provide promising approaches for breeding rose cultivars with improved tolerance to environmental and pathogenic stresses. This review synthesizes recent advances in understanding the molecular mechanisms underlying both biotic and abiotic stress adaptation in roses and outlines strategies for developing resilient cultivars capable of maintaining productivity and ornamental value under adverse conditions.

Citrus Huanglongbing (HLB), caused by the phloem-restricted bacterium Candidatus Liberibacter asiaticus (C Las), is a devastating disease threatening global citrus production. C Las 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 C Las 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 C Las: 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.

The efficiency of carbon and nitrogen uptake in apple trees is co-regulated by plant genotype and rhizosphere microbial communities. However, the mechanisms by which different scion varieties modulate microbial structure and function under varying nitrogen levels remain poorly understood. In this study, Malus sieversii was used as the rootstock, onto which three scion cultivars (M. sieversii, Malus domestica cv. Hanfu, and Malus domestica cv. Red Fuji) were grafted under two nitrogen regimes. A combination of ¹³C/¹⁵N isotope labeling, Illumina MiSeq amplicon sequencing, and metagenomic analysis was employed to elucidate how scion-rootstock interactions and nitrogen availability affect carbon and nitrogen acquisition. Under nitrogen-deficient conditions, Red Fuji exhibited stronger root activity and larger root surface area, indicating enhanced nutrient foraging capacity. Conversely, under nitrogen application, Hanfu showed significantly greater ¹³C and ¹⁵N uptake, with 5.7-fold and 1.6-fold higher ¹³C accumulation in roots and stems, respectively, and markedly higher ¹⁵N utilization efficiency in roots and leaves compared with M. sieversii. In parallel, Hanfu under nitrogen input showed enrichment of beneficial microbial taxa and more complex microbial co-occurrence networks. Metagenomic analysis and random forest analyses revealed that the relative abundance of specific functional genes related to carbon and nitrogen transformation (rbcL, abfA, napB/C, nasA) was significantly higher under specific scion-nitrogen combinations, contributing to enhanced microbial carbon fixation and nitrogen reduction. Collectively, these results demonstrate that scion genotype modulates rhizosphere microbial structure, physiological root traits, and carbon-nitrogen distribution patterns, thereby improving nutrient uptake efficiency under different nitrogen inputs.

Quercetin glucosides are important phytopharmaceutical metabolites in Descurainia sophia seeds, which are widely used in traditional herbal medicine. However, the key genes involved in quercetin glucoside biosynthesis in D. sophia have not been characterized. Herein, we present the telomere-to-telomere genomes of a tetraploid D. sophia, which accumulates high levels of quercetin glucoside, and a diploid D. sophia, which accumulates only trace amounts. Multiomics analyses and uridine diphosphate glucosyltransferase (UGT) enzyme assays revealed that the gene duplication and functional evolution of Dscd6AG01520, an UGT gene, led to high quercetin-3- O - β - D -glucoside and quercetin-3,7- O - β - D -diglucoside accumulation in tetraploid D. sophia seeds. Further UGT enzyme assays with the point mutations of Dscd6AG01520 showed that S213 was a critical amino acid for the enzymatic activity of Dscd6AG01520. In addition, we found that diploid D. sophia evolved from an ancestral crucifer karyotype through chromosome fusion and rearrangement. Collectively, our findings illuminate the mechanism of high quercetin glucoside accumulation in tetraploid D. sophia, clarify the origin of the diploid D. sophia genome, and provide valuable genomic resources for comparative genomics and research into polyploid evolution.

Regulating floral induction (FI) through the application of gibberellin (GA) biosynthesis inhibitors is a critical agricultural practice to prevent yield loss in fruit trees. We observed that mepiquat chloride (MC), a highly safe plant growth retardant, enhanced FI in mango. Nevertheless, the molecular mechanism by which MC facilitates FI remains elusive. Using two distinct treatments and varied stages during FI in mango (Mangifera indica L. ‘Tainong No.1’), 24 dynamic transcriptome profiles were constructed. Through pairwise comparisons and weighted gene co-expression network analysis (WGCNA), a regulatory network centered on the hub gene FLOWERING LOCUS T3 (MiFT3 ) was established. We further discovered MC-induced floral transition was associated with the decreases of GA 20 and GA 3 levels and the upregulation of MiGA2oxs (GA2 OXIDASES ) expression, alongside the increase of abscisic acid (ABA) content and the upregulation of MiNCED1 (9-cis-epoxycarotenoid dioxygenase 1 ) and MiABI5-like7 (ABSCISIC ACID-INSENSITIVE 5-like7 ). Furthermore, biochemical assays and stable transgenic experiments were applied to confirmed that MiABI5-like7 activated the expression of MiFT3. Moreover, silencing MiABI5-like7 in mango buds delayed floral transition, while ectopic expression of MiABI5-like7 promoted early flowering. Additionally, exogenous ABA accelerated the floral transition induced by MC, whereas an ABA inhibitor delayed floral transition, which were associated with the expression levels of MiABI5-like7 and MiFT3. This study clarified the mechanism by which MC induced floral transition by inhibiting GA biosynthesis that activate MiABI5-like7-mediated signaling pathway, which provides novel insights into the regulatory network of FI in plants and offers a solution for solving the issue of insufficient flowering in warm winter climates.

The mechanisms underlying plant root response to mechanical environmental stimuli are crucial for plant growth, development, and environmental adaptation. In this review, we examine the mechanical environments encountered by plant roots, including the different types of mechanical stimuli they experience. We describe in detail the mechanisms that enable roots to perceive these stimuli and their modes of action. Unfavorable mechanical stimuli can cause roots to alter their growth patterns and rates. Morphologically, roots become thicker, enhancing their stress resistance. Mechanical stimuli influence the activity of hormones, including auxin and ethylene, which jointly regulate root growth. Auxin promotes cell elongation in roots, whereas ethylene can inhibit root growth under certain conditions. Plants modulate antioxidant enzyme activity and osmoregulatory substance accumulation to cope with environmental stress. We explored the molecular regulatory mechanisms underlying plant root adaptation to mechanical stimuli, including those involved in regulating genes and signal transduction pathways. Finally, we suggest future research directions, including an in-depth study of the multi-signal integration mechanism of roots and gene editing technology for improving plant adaptability. This review provides a basis for studying the interactions between plants and mechanical environments for plant adaptation and agricultural production.

Coptis species are rich in protoberberine-type benzylisoquinoline alkaloids (BIAs). However, the differential BIA accumulation between Coptis chinensis and C. teeta, two primary botanical sources of traditional Chinese medicine ‘Huanglian’, remains mechanistically poorly understood. Here, we combined widely targeted metabolomics, matrix-assisted laser desorption/ionization mass spectrometry imaging, histological characterization, and transcriptomic analyses to investigate the mechanisms underlying the specialized BIA accumulation in C. chinensis versus C. teeta. Clearly, we observed significantly elevated BIA accumulation in C. chinensis rhizomes compared to C. teeta, in particular, the preferential BIA localization within the cortical tissues of C. chinensis rhizomes, consistent with the anatomically expanded cortical and xylem regions. This structural specialization facilitates BIA compartmental distribution patterns. Integrated transcriptomic-metabolomic analysis further constructed a BIA biosynthetic regulatory network, identifying key transcription factors that synergistically promote BIA accumulation in C. chinensis rhizomes, establishing their roles as speciation-associated regulators of medicinal quality divergence between C. chinensis and C. teeta. Overall, this study provides the first integrated anatomical and transcriptional framework explaining interspecies differences in BIA accumulation, enabling the development of quality improvement strategies for medicinal plants.

Green mold caused by Penicillium digitatum significantly impacts the citrus industry economically. Enhancing postharvest disease resistance in citrus fruit remains challenging due to the complex pathogen-citrus interaction. Previous researches have indicated that PgSCP, a cysteine-rich secretory protein derived from Pichia galeiformis, activates resistance responses in citrus fruit. However, the precise molecular mechanisms underlying this effect remain unclear. This study showed that PgSCP enhances disease resistance gene expression and substance accumulation in citrus fruit. Additionally, potential citrus proteins that may interact with PgSCP was identified. Among these, four candidate transcription factors were identified: CsFAR1, CsMIKC, CsLBD, and CsGRAS. Subsequent validation demonstrated that PgSCP interacts with the citrus transcription factor CsFAR1. Transient overexpression analysis demonstrated that CsFAR1 positively regulates resistance to green mold, and CsFAR1 also enhances the disease resistance gene expression in citrus fruit. The CsFAR1 protein enhances resistance by activating DHAPS-1, GSH1, ACO1, INVA, PAL6, OMT, CYP73A16, CCOAOMT1, CYP73A4, and PER16. These findings suggest that the yeast-secreted protein PgSCP may act as an elicitor that interacts with citrus transcription factors CsFAR1 to enhance host defense responses, thereby contributing to improved postharvest resistance to green mold.

Phalaenopsis orchids are one of the most important ornamental crops, prized for their beautiful flowers and long flowering phase. Hundreds of commercially available cultivars display a remarkable range of variation in key horticultural traits, including inflorescence type, floral size, and color patterning. While most current cultivars have been developed through cross-breeding or mutation breeding, genetic homogenization has become a growing concern. This is largely due to extensive hybridization among existing cultivars, which are predominantly derived from a limited number of parental species. Additionally, trait linkage in Phal. can hinder the integration of desirable characteristics in progeny. Therefore, there is an urgent need to decipher the genetic programs governing key horticultural traits to facilitate both conventional and molecular breeding. Despite significant research efforts, progress has been hampered by several resource limitations. These include a scarcity of high-quality genome assemblies, the lack of stable genetic transformation systems, and insufficient materials for molecular biology studies—a challenge exacerbated by the plant’s relatively long life cycle. Consequently, the molecular mechanisms underlying the formation and diversity of most important horticultural traits in Phal. orchids remain largely unexplored. This review summarizes recent research advances, with a primary focus on the key floral traits in Phal. orchids, including inflorescence type, flowering time, floral organ organization, color patterning, size, longevity, scent, organ shape, cuticle production, and wax biosynthesis. Furthermore, we offer perspectives on future research directions aimed at elucidating the genetic basis for the remarkable diversity of these traits and advancing molecular breeding in Phal. orchids.

Cucumber is an important vegetable crop with thermophilic but heat-sensitive growth characteristics. Heat stress threatens cucumber growth and development, leading to a decline in both quality and yield. However, the evaluation system and molec- ular mechanism of long-term heat tolerance remain unclear. Here, an evaluation system in response to long-term heat stress was established, and chlorophyll a content and catalase(CAT) activity were identified as key evaluation indices for determining the heat tolerance of cucumber seedlings. Transcriptomic and physiological analyses revealed that sugar metabolism played a pivotal role in the heat response. Notably, the expression of CsIAGLU (Indoleacetic Acid glucosyltransferase) was significantly upregulated in heat-tolerant genotype PS76, whereas it was not induced in the heat-sensitive genotype PWRG. Loss of function of CsIAGLU by gene editing resulted in increased sensitivity to heat stress along with higher sugar contents, accelerated stomatal closure, and chlorophyll degradation. Furthermore, CsDREB2C.L, a positive regulator of heat stress response, directly bound to the CsIAGLU promoter to enhance its expression. Overexpression of CsDREB2C.L and CsIAGLU maintained stable sugar contents, thereby keeping stomatal opening and sustaining leaf greening to resist heat stress. Taken together, our findings provide valuable insights into the mechanism of heat resistance in cucumber.

Roses (Rosa sp.) are highly valued ornamental plants, with over 25 000 cultivars created by breeders, among which cut roses dominate the global flower market. Flowers of these cultivars can last up to 20 days in a vase from the moment they are cut, which is not the case for garden roses. This review examines whether the vase life of cut roses resembles or differs from natural flower senescence, focusing on the phytohormonal processes involved in both scenarios. We first compare petal senescence with other senescence phenomena and then examine genes related to hormone action. Finally, we show the similarities between senescence in cut roses and that of standing roses. We conclude that, despite the existence of similarities, including the involvement of ethylene in petal senescence, comparative studies between cut and uncut roses would be useful, both for basic research and to improve the selection of varieties with long vase life.

Jujube (Ziziphus jujuba Mill.) is a fruit crop of high economic value, renowned for its distinctive flavor and wide range of phenotypic diversity. Despite major advancements in jujube genomics, the role of genetic variants in underlying agronomic trait formation is still poorly understood. Here, we used seven high-quality jujube genomes to construct a pan-TE (transposon element) map and investigated how TEs shape genome evolution and agronomic traits. We found that TEs constitute 29.05%-30.38% of the genome, predominantly long terminal repeat (LTR) retrotransposons such as Copia and Gypsy. A positive correlation (R² = 0.76) between TE content and genome size underscores their role in genomic expansion. TE insertions within gene bodies significantly reduce gene expression, particularly for genes involved in cell wall biosynthesis and glucose metabolism. Population scale analysis of 1041 accessions identified 4176 transposable element insertion polymorphisms (TIPs) that distinguish wild and cultivated groups. Wild jujubes harbor stress-related TIPs (e.g. in peroxidase genes), whereas cultivated accessions carry TIPs linked to fruit development. Notably, a Gypsy insertion upstream of the cellulose synthase gene ZjCESA4 is associated with reduced expression and thinner pericarp in ‘Dongzao’ compared to ‘Huizao’. Similarly, a downstream LTR/Gypsy insertion near the MADS-box transcription factor gene ZjAGL18 correlates with suppressed expression, highlighting the recurrent targeting of key regulatory genes by TEs during domestication. Our findings demonstrate that TIPs are a major source of genetic variation in jujube, providing molecular markers for breeding programs that aim to balance fruit quality and stress resilience.

Chinese yam (Dioscorea polystachya) is extensively cultivated for nutritional and medicinal applications. However, the lack of a high-quality reference genome has hindered molecular genetic analysis and breeding advancements. Here, we present a haplotype-resolved chromosome-level assembly for this autotetraploid species, featuring a 1.56-Gb genome anchored to 80 chromosomes across four haplotypes and comprising 95 668 protein-coding genes. Following divergence from Dioscorea alata about 4.64 million years ago (Mya), D. polystachya underwent a specific whole-genome duplication ∼1.42 Mya, resulting in an autotetraploid species without subgenomic dominance. Notably, the biosynthetic pathway genes of dioscin, an important steroidal saponin primarily accumulating in tubers, were generally over-retained in D. polystachya compared to the diploid species D. alata. Of these genes, 7-dehydrocholesterol reductase (Dp7-DR) promoted the accumulation of dioscin, exhibiting tuber-specific expression and strong inducibility by abscisic acid, based on transcriptome and gene function analyses. We determined that the transcription factor DpbZIP12 activates Dp7-DR transcription, as supported by yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays. Notably, overexpressing Dp7-DR or DpbZIP12 resulted in lower cholesterol levels and elevated dioscin levels, while silencing either gene produced opposite metabolic profiles. These findings delineate promising targets for manipulating dioscin content and expand genetic resources for enhancing yam nutritional quality.

Complex traits are controlled by many unknown genes, making it difficult to elucidate a global picture of the genotype-phenotype map. Here, we develop a statistical mechanics model to contextualize all possible genes into informative, dynamic, omnidirectional, and personalized idopNetworks. This model, derived from the combination of functional mapping and evolutionary game theory, can visualize and trace how genes act and interact with each other to shape the genetic architecture of complex traits. The model can estimate changes in the genotypic value of one gene due to the influence of other genes, specifically on individual subjects, surpassing traditional quantitative genetic studies that can only capture the marginal effect of a gene at the population level. We reconstruct growth idopNetworks from a genome-wide mapping data in a woody plant, mei, identifying unique genetic interaction architecture that distinguishes between fast-growing trees and slow-growing trees. We perform computer simulation to validate the statistical power of the model. IdopNetworks can disentangle the genetic control mechanisms of complex traits and provide guidance on how to alter phenotypic values of specific individuals by promoting or inhibiting the expression of interactive genes.

Global climate change and widespread unsustainable agricultural practices increasingly impose both biotic and abiotic stresses on the production of horticultural plants. Lilies (Lilium spp.) are globally renowned ornamental plants, with some species also possessing medicinal, edible, and cosmetic value. However, their quality and yield are often negatively affected by various stresses. Conventional breeding methods are often inefficient due to the long juvenile phase, complex genetic background, and large genome size of lilies. While numerous emerging technologies provide opportunities for resistance breeding in lilies, their successful application relies on a thorough understanding of the resistance response mechanisms. This review systematically summarizes recent advances in lily stress resistance research, delineating the physiological and molecular response mechanisms of lilies under abiotic stresses (extreme temperature, drought, high salinity), biotic stresses (pathogens, pests), and continuous cropping obstacles. Furthermore, it discusses current challenges and limitations, and explores the potential applications of emerging technologies in improving the stress adaptability of lilies. These findings provide important insights for advancing stress resistance research and breeding stress-tolerant lily cultivars.

ASMT/COMT, as a key rate-limiting enzyme regulating melatonin biosynthesis, has garnered significant attention. This study investigates the evolutionary mechanisms of the ASMT/COMT gene family in melatonin biosynthesis. A total of 28 010 ASMT/COMT genes from 1052 species were identified through an integrated approach combining large-scale identifications and analyses. At the pan-genome level, we identified 5186, 336, 2137, and 1814 ASMT/COMT genes respectively in Triticum aestivum, Aegilops tauschii, diploid and tetraploid Solanum tuberosum haplotype genomes (247, 86, 670, and 96 orthologous gene groups). Expansion patterns of the ASMT/COMT gene family were explored through synteny networks in 104 Poaceae and 88 Solanaceae plants. Further investigation of copy number variation (CNV) in the 1052 species, along with a focused analysis of hexaploid wheat and its diploid progenitor Ae. tauschii, indicated a functional divergence linked to gene dosage. The catalytically efficient COMT is maintained at low-copy conditions, whereas the less active ASMT is amplified under high-copy conditions. Intriguingly, in polyploid potatoes, the total ASMT/COMT copy number was lower in tetraploids than in diploids, suggesting a distinct dosage balance mechanism operating in polyploids. In contrast, the melatonin receptor CAND2 consistently remained in a low-copy state, with no significant correlation to ASMT/COMT copy number. Expression analysis revealed that COMT is generally expressed at higher levels than ASMT, highlighting a compensatory relationship between gene dosage and transcriptional regulation. Collectively, our findings uncover a dosage balance mechanism that fine-tunes melatonin biosynthetic homeostasis through coordinated CNV and expression regulation, offering a new perspective on the evolution of metabolic enzymes.

Breeding perennial fruit trees like apple is constrained by long generation times and limited population sizes, which often lead to repeated use of a few elite cultivars and consequently narrow genetic diversity. To better understand how such selection processes have shaped the current genetic structure, we applied gene-drop simulations—a pedigree-based method using known parentage and genetic maps—to a curated set of 185 apple cultivars used in Japanese breeding programs, genotyped with 11 786 genome-wide single nucleotide polymorphism markers. This approach enabled us to quantify the expected distribution of founder haplotypes and identify genomic regions where observed founder haplotype frequencies significantly deviated from expectation, suggesting potential selection. Notably, biased regions overlapped with loci associated with key fruit traits, such as fructose content, exemplified by an increase in haplotypes from “Golden Delicious.” Furthermore, Gene Ontology analysis revealed enrichment for regions containing genes involved in stress-related and developmental functions, pointing to broader physiological traits under selection. Unlike traditional methods requiring phenotype data, our approach does not depend on trait measurements and can thus uncover cryptic selection signals, including traits that were not explicitly targeted during breeding. This method offers a framework for identifying overlooked genetic regions and underutilized founder alleles, which can be reintroduced to broaden the genetic base and improve breeding outcomes. Furthermore, the approach is adaptable to other perennial crops with available pedigree and genomic data. Our findings demonstrate the power of integrating pedigree structure with genomic information to reveal both historical and ongoing selection in structured breeding populations.

Horticultural and medicinal plants are important for their economic and pharmacological value; however, their quality traits are severely affected by abiotic stresses. The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signaling module that links abiotic stress signals to the regulation of plant quality traits. While the roles of MAPKs in growth, phytohormone signaling, and immunity are well established, a comprehensive review that integrates MAPK functions in abiotic stress responses and secondary metabolism, particularly in horticultural and medicinal plants, is still lacking. In this review, we systematically summarize (i) the composition, classification, and phylogenetic relationships of MAPKs in horticul- tural and medicinal plants; (ii) their mechanistic involvement in abiotic stress responses, particularly to salt, drought, and extreme temperatures; (iii) recent advances in understanding how MAPK-mediated signaling governs secondary metabolite accumulation; and (iv) a unified framework that presents MAPKs as a key bridge between stress responses and metabolic reprogramming. These insights provide a foundation for MAPK-targeted breeding and engineering strategies that enhance stress tolerance and improve quality traits in horticultural and medicinal plants through precise pathway manipulation.

Fruit ripening is a highly coordinated developmental process that transforms immature fruits into edible organs adapted for seed dispersal and human consumption. Although transcriptional regulation has long been acknowledged as a fundamental mechanism underlying ripening control, accumulating evidence now indicates that post-translational modifications (PTMs) function as master regulatory switches that precisely control protein activity, stability, and interactions. PTMs such as phosphorylation, ubiquitination, acetylation, redox modifications, and methylation establish dynamic regulatory networks that integrate hormonal signals, metabolic fluxes, and environmental signals to control the complex biochemical and physiological changes during fruit ripening. This review summarizes current understanding of PTM-mediated regulation in both climacteric and nonclimacteric fruits, emphasizing how modification cascades control key processes including ethylene signaling, cell wall remodeling, pigment accumulation, and stress responses. We explore emerging crosstalk networks in which multiple PTMs target important proteins to form complex molecular switches and discuss recent methodological advances that facilitate systems-level analysis of PTM. Integrating PTM research with precision agriculture and biotechnology offers promising approaches for improving fruit quality, extending shelf-life, and enhancing stress tolerance in the context of global climate change.

Camellia sinensis Fuding Dahaocha, a triploid white tea cultivar widely cultivated in south China, exhibits distinctive traits including dense leaf trichomes, early sprouting, and robust stress resistance. Here, we present the first high-quality chromosome-level genome assembly of this triploid variety, resolved through integrated PacBio long-read sequencing and Hi-C scaffolding. The genome assembly spans 45 chromosomes with a scaffold N50 value of 182 Mbp. A total of 149 455 gene models were annotated and mapped to chromosomes, among which 30 568 were identified as protein-coding genes. The genome features high repetitiveness (65.9% transposable elements), heterozygosity, and three distinct haplotype sets with substantial allelic variation (17 601 triallelic genes), with the retained haplotype-specific genes potentially contributing to regulatory complexity through dosage effects. Genome completeness assessment revealed a BUSCO completeness of 99.0% (2303 out of 2326 conserved core genes identified), which included 40 single-copy (1.7%) and 2263 duplicated (97.3%) genes. Evolutionary analyses indicated conserved relationships among the three homologous chromosome sets. We also performed single-nucleus RNA sequencing on a sufficiently large pooled sample of leaf tissues to study trichome development, overcoming technical limitations posed by secondary metabolites and low protoplast isolation efficiency. This yielded a single-cell atlas for woody plants, identifying 35 trichome-specific marker genes and modeling developmental trajectories during epidermal differentiation. Functional validation identified CsCUT1 as a suppressor of trichome branching and CsMYB4 as a negative regulator of trichome initiation. Cell cycle analysis showed G2-phase dominance in developing trichomes. These findings provide a genetic framework for trichome development and offer resources for tea breeding.

The female flower gives rise to the fruit/seed and thus directly affects crop yield in unisexual plants. Both ethylene and auxin promote femaleness in cucurbits. However, how auxin regulates sex determination has been an open question over half a century. The recent publication identified auxin response factor CsARF3 as a crucial player in auxin-promoting femaleness, and revealed a reciprocal relationship between auxin and ethylene during female flower determination.