Ascorbate-glutathione (AsA-GSH) cycle genes are vital for plant processes like stomatal regulation, nutrient uptake, and stress responses. However, the relationships between the origin and expansion of the AsA-GSH cycle genes and the adaptive evolution of land plants are still unclear. To investigate their evolutionary origins and functional differences, we first used phylogenetic and expression analyses of 2424 AsA-GSH genes (1059 APXs, 364 DHARs, 629 MDHARs, and 372 GRs) derived from 127 green plants to investigate their evolutionary history and functional divergence in green plants. The results highlighted a strong linkage between plant AsA-GSH cycle genes and their adaptation to environmental stress. In grapevine (Vitis vinifera), 16 AsA-GSH genes were identified and analyzed for gene structure, motifs, cis-regulatory elements, and transcription factors network. Gene expression profiling demonstrated their involvement in growth, hormonal regulation, and responses to biotic (Plasmopara viticola infection) and abiotic (cold, heat, salt, and drought) stresses. Functional validation showed that some of these grapevine genes, such as VvAPX6/7/8, VvDHAR1, VvMDHAR2, and VvGR2, are localized in diverse cellular compartments effectively mitigate oxidative stress through ROS scavenging. This study enhances our understanding of the evolutionary dynamics and functional diversification of AsA-GSH cycle genes in green plants, and the stress resilience in grapevine.

Eggplant is one of the most important solanaceous vegetable crops worldwide. To explore its genomic diversity, we assembled two T2T-level reference genomes from the African eggplant ‘Y11’ (Solanum aethiopicum L.) and the cultivated variety ‘Gui5’ (Solanum melongena L.) with genome sizes of 1.10 and 1.13 Gb, respectively. The contigs N50 lengths are 94.2 and 93.9 Mb, with annotations of 37 324 and 40 300 protein-coding genes correspondingly. We also sequenced 238 germplasms, primarily local and cultivated varieties from China, Southeast Asia, Europe, and Africa, identifying 7 853 531 high-quality single nucleotide polymorphisms. Phylogenetic trees and population structures suggest that the domestication of Chinese eggplants occurred later than in Southeast Asia and subsequently diverged into northern and southern groups within China, evolving relatively independently with limited genetic flow between these two groups. Their diversity is significantly lower than that of Southeast Asia and Europe. By selecting 22 representative accessions and four chromosome-level genomes, we constructed an Asian-representative eggplant pan-genome, assembling 463.94 Mb of nonreference sequences. Of these sequences, 38.3% are core genes, 46.9% are dispensable genes, and 14.9% are unique genes. Presence/absence variation genes were found to be highly associated with stress resistance in eggplants. Genome-wide association studies identified 946 SNPs and 9605 genes significantly associated with 10 important traits. Notably, genes involved in zeatin biosynthesis closely linked to plant auxins significantly impact fruit size and shape attributes, playing a crucial role in eggplant yield. This high-quality reference genome alongside the pan-genome will provide valuable insights into eggplant breeding advancement.

Tanshinone accumulation serves as a critical determinant of medicinal value in Salvia miltiorrhiza cultivars. Precise fine-tuning of tanshinone biosynthesis while preserving elite agronomic traits remains a pivotal challenge in molecular breeding. Here, we report, for the first time, the successful application of CRISPR/Cas9-mediated upstream open reading frame (uORF) editing in medicinal plants to enhance the production of specialized metabolites. Five evolutionarily conserved uORFs identified in the 5′ leader sequence of the key diterpene synthase gene SmCPS1 were strategically edited to modulate post-transcriptional regulation. Homozygous mutants engineered through precision gene editing exhibited 1.19- to 1.81-fold enhanced tanshinone accumulation compared to the controls, correlating with coordinated transcriptional activation of core biosynthetic genes (SmHMGR1, SmKSL1, SmCYP76AH1, SmCYP76AH3). Integrative molecular analyses demonstrated unchanged SmCPS1 transcript levels and enhanced protein accumulation, mechanistically confirming uORF-mediated translational potentiation of the cognate main ORF. This study establishes uORF engineering as a robust platform for predictable metabolic engineering in S. miltiorrhiza plants. Future applications could expand this strategy to uORFs of rate-limiting enzymes or transcriptional regulators, enabling multidimensional optimization of high-value metabolites in medicinal species.

The branch crown is an important trait of the strawberry that influences plant architecture and yield. Strigolactones (SLs) are significant hormones involved in the plant growth response and are crucial for regulating branching. Previous studies have shown that SL signaling regulates branching by affecting abscisic acid (ABA) biosynthesis. In this study, we observed that the SL signaling pathway can affect branching by regulating ABA catabolism in strawberry. FveDAD2 in woodland strawberry was identified as the receptor for SL. Three FveDAD2-RNAi transgenic lines exhibited the phenotype of multibranched crowns and smaller fruits. Like the alpha/beta hydrolase DWARF14 (D14), the interaction of FveDAD2 with FveSMXL7 depended on SL. The FveSMXL7-RNAi transgenic plants exhibited a less branched phenotype compared to the control plant. In addition, FveSMXL7 binds to the promoter of FveHB7 and represses its transcription. FveHB7, a homeobox transcription factor, negatively regulates the transcription of the ABA 8′-hydroxylase gene (FveABA8'OH1). The expression of FveHB7 was up-regulated, while the expression of the FveABA8'OH1 was down-regulated in FveSMXL7-RNAi. ABA levels were reduced in the shoot tips of the FveDAD2-RNAi lines and increased in the FveSMXL7-RNAi lines. Treating wild-type plants with 20 μM ABA significantly suppressed the number of branch crowns, while 40 μM ABA rescued the phenotype of FveDAD2-RNAi. In conclusion, our research indicates that SL signaling may regulate branching by affecting ABA catabolism. These findings provide a theoretical basis for elucidating the mechanism of the development of branch crowns in the strawberry.

Grafting is extensively utilized in melon (Cucumis melo L.) cultivation to improve environmental tolerance and disease resistance. Our previous studies identified CmGH9B3, encoding β-1,4-glucanase, as a key factor promoting cell adhesion during graft union formation in melon scions grafted onto squash rootstocks. However, the upstream regulatory mechanisms controlling CmGH9B3 expression remained unclear. Here, we demonstrate that LED red light significantly enhances graft union healing by activating a transcriptional module involving CmHY5, CmWRKY23, CmWRKY69, and CmGH9B3. Specifically, the light-responsive transcription factor CmHY5 was induced by LED red light and activated the expression of CmWRKY23 and CmWRKY69. These WRKY transcription factors were directly bound to the CmGH9B3 promoter, promoting its expression to accelerate vascular reconnection and graft healing. Our findings establish a mechanistic link between light signaling and graft union formation via the CmHY5-CmWRKY23/69-CmGH9B3 regulatory module, offering practical targets to improve grafting efficiency in melon cultivation.

Tree peony (Paeonia section Moutan DC.) is a unique group of precious woody species with high ornamental, medicinal, and oil value. A drought environment severely restricts their yield and quality. However, the screening and identification of miRNAs in response to drought stress of tree peony has not been reported. In this study, Paeonia ostii ‘Fengdan’ were treated with mild drought, severe drought, and rehydration, respectively. The results of phenotypic observation and physiological characteristics showed that the cell membrane of P. ostii leaves was damaged by drought stress and had a self-regulation function. Combined with multi-omics analysis (transcriptomics, miRNA, and degradome), a total of 883 miRNAs with significant differential expression were identified, and the expression regulation networks of miRNAs and target genes were constructed. A set of 19 different miRNAs was found to regulate 189 different genes. Drought-responsive miRNA-mRNA-TF modules like miR172d-ARR (Arabidopsis Response Regulator), miR396g-STAT (Signal Transducer and Activator of Transcription), and miR168-DBB (Double B-Box) were discovered. By cloning the key miRNA PomiR172d and its target gene PoARR and conducting genetic transformation to verify its function, analyzing the permeability of cell membrane and enzyme activity of ROS in transgenic plants, the molecular regulatory mechanism of the PomiR172d-PoARR module of tree peony in response to drought stress was revealed. Our studies lay the foundation for future research on the regulatory mechanism of tree peony in response to drought stress and provide a theoretical basis for the improvement and cultivation of drought-resistant varieties of tree peony.

Homogalacturonan (HG) methyl-esterified modification pathway genome-wide expression analysis in two texture types of oriental melon fruits ‘HDB’ (crisp) and ‘HPM’ (mealy) at different developmental stages revealed that the Golgi S-adenosyl-L-methionine transporter gene CmGoSAMT1 and the pectin methyltransferase genes CmPMT1 and CmPMT15 were critical functional genes for HG methyl-esterification in melon. However, overexpression of CmGoSAMT1 cannot significantly alter fruit hardness, whereas overexpression of CmPMT1 and CmPMT15 appears to cause the fruit to synthesize more highly methyl-esterified HG, which are separated from each other due to the ‘steric effect’ of methyl groups on the C-6 carboxyl of D-GalA, and cannot be cross-linked by Ca²⁺ to form an ‘egg-box’ matrix making it more accessible to de-methylating and degrading enzymes (CmPMEs, CmPGs, and CmPLs), thus fruit susceptible to softening. In addition, a transcription factor CmbZIP11 co-expressed with CmPMT1 and CmPMT15 was verified, which could activate the expression of CmPMT1 and CmPMT15 to regulate the methyl-esterification of HG, thereby affecting fruit softening.

Oriental melon, a climacteric fruit prized for its superior quality, faces limited shelf life. Although knockout NON-RIPENING (CmNOR) prolongs storage duration at the expense of quality loss, the potential of its direct agricultural application to reconcile this conflict remains uninvestigated. Through crossing homozygotes Cmnor and wild-type (WT) plants, we created CmNOR/Cmnor heterozygotes. These heterozygotes exhibited a 6-day ripening delay accompanied by reduced sucrose and β-carotene levels, yet ultimately attained WT quality parameters. Exogenous ethylene treatment accelerated fruit softening but failed to restore key quality parameters in both heterozygotes and homozygotes to WT levels. Transcriptomic and quantitative polymerase chain reaction (qPCR) analysis revealed that homozygotes displayed >10-fold expression differences versus WT in quality-associated genes (e.g. involved in carotenoid biosynthesis and sucrose metabolism). These expression disparities diminished to approximately 2-fold in heterozygotes. Furthermore, heterozygotes extended shelf life by 3-5 days during storage at 20°C while maintaining fruit quality. Storage-phase differential genes clustered in water regulation and cell wall modification pathways, with heterozygous-WT expression disparities gradually decreasing over time. The CmNOR dosage effect dynamically modulates interconnected quality and preservation networks, proposing an editing-based solution to overcome the storability-quality dichotomy in climacteric fruits.

Flavor-related compounds, particularly γ-decalactone—the key contributor to the characteristic ‘peach-like’ aroma—serve as essential indicators of peach fruit quality and strongly influence consumer purchasing decisions. However, excessive application of N fertilizers has led to a significant decline in the flavor quality of peaches, posing a major obstacle to the sustainable development of the peach industry. Although this remains a critical challenge, the molecular mechanisms linking N to flavor compound biosynthesis are still not well characterized. In this study, we discovered that excessive N application reduced the biosynthesis of γ-decalactone in peach, based on multi-year field observations. Correlation analysis and expression profiling under N treatments revealed that two NAC (NAM-ATAF1/2-CUC2) transcription factors (TFs), PpNAC6 and PpNAC36, were involved in regulating γ-decalactone biosynthesis in response to N signaling. Genetic analyses indicated that PpNAC6 and PpNAC36 positively regulated the accumulation of γ-decalactone. Both yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays consistently showed that PpNAC6 and PpNAC36 directly interact with the promoter regions of γ-decalactone biosynthesis-related genes (PpAAT2, PpAAT3, PpLOX1, PpLOX6, and PpFAD3) and significantly enhance their transcriptional activity. Furthermore, transgene verification demonstrated that the α subunit of peach SNF-related Kinase 1 (PpSnRK1α) suppresses γ-decalactone biosynthesis. Notably, we found that PpSnRK1α interacts with PpNAC6/PpNAC36 and selectively phosphorylates PpNAC36 in response to N, thus regulating γ-decalactone production. Our study uncovers the transcriptional regulatory network involved in PpSnRK1α-mediated phosphorylation of PpNAC6/PpNAC36, linking N signaling to γ-decalactone synthesis in peach, and provides insights for molecular breeding and precision fertilization to enhance peach flavor.

Acer palmatum ‘Duocai’ is an excellent ornamental cultivar maintained through asexual propagation. In spring and autumn, it exhibits red leaves, and in summer, it displays green leaves. To investigate the genetic and epigenetic regulation underlying these seasonal pigmentation shifts, we implemented a comprehensive multi-omics approach. Metabolomic profiling identified cyanidin-3-O-glucoside as the predominant biochemical factor governing seasonal leaf color transitions. RNA-seq, ATAC-seq, Hi-C, and WGBS were utilized to examine transcriptomic and chromatin remodeling dynamics. Multi-omics regulatory network analysis identified ApMYB2 as a key transcription factor (TF) affecting anthocyanin accumulation by regulating ApF3'H2 expression. Functional analyses demonstrated that the TF ApWRKY26 positively modulates ApMYB2 expression, while ApERF4 exerts an inhibitory effect on its expression. These regulatory interactions were corroborated by seasonal RNA-seq-based correlation analyses. Genetic manipulation experiments, including overexpression and silencing of these genes in A. palmatum, provided empirical evidence supporting their functional roles in the anthocyanin biosynthetic pathway. Together, our study elucidates the molecular mechanism by which ApWRKY26 and ApERF4 coordinate the activity of ApMYB2 to govern seasonal anthocyanin synthesis in A. palmatum foliage.

Lettuce (Lactuca sativa) is a globally cultivated leafy vegetable with leafy morphology critically influencing consumer preference and market value. Despite the agronomic importance of leaf traits, the genetic basis underlying their diversity remains poorly characterized. To address this, we resequenced 811 accessions collected from major lettuce production areas as well as the relative wild species, and developed a publicly accessible core collection of 268 accessions that captures 99.4% of the total genetic variation. Phenotypic evaluation of 16 leaf morphological traits across two growing seasons identified significant correlations, including negative associations between plant width and anthocyanin content, and positive correlations between apical margin incision and multiple traits. Population structure analysis revealed frequent introgression events from looseleaf type into domesticated varieties (butterhead, crisphead, romaine, and stem lettuce), highlighting dynamic gene flow during breeding. Genome-wide association studies (GWAS) pinpointed 13 robust quantitative trait loci (QTLs) and candidate genes regulating leaf morphology, including a validated anthocyanin biosynthesis regulator (ANS). Notably, we pinpointed the causal gene genotypes responsible for leaf anthocyanin coloration. Leveraging these findings, we successfully aggregated favorable alleles through genomic design breeding to develop a novel high-anthocyanin variety binfen5 with desirable leaf morphology. This integrative approach demonstrates the value of core germplasms and genomic tools for accelerating lettuce improvement.

Cornus officinalis is a traditional medicinal plant known for producing loganin, a bioactive iridoid glycoside with potential anticancer properties. However, the absence of a high-quality reference genome has limited insights into its biosynthetic pathways. Here, we present a chromosome-level genome assembly of C. officinalis with a size of 2.85 Gb. Comparative genomic analysis revealed that the genome expansion and longer gene structures, relative to other Cornales species, are primarily due to a recent expansion of transposable elements. In this study, we identified unique biosynthetic gene clusters coding multiple core enzymes, including loganin acid O-methyltransferase (LAMT), secologanin synthase (SLS), and cytochrome P450, all of which catalyze sequential steps leading to loganin formation. LAMT enzymes from C. officinalis capable of catalyzing the C-9 hydroxylation of loganin acid were identified, whereas the homolog (CoLMAT) was not found to possess this activity. Additionally, molecular docking studies revealed critical residues in CoLAMT that govern substrate positioning, providing insights into the mechanism of C-9 regioselective hydroxylation. Further characterization of 7-deoxyloganicacid hydroxylase, LAMT, and SLS enzymes allowed us to elucidate the complete biosynthetic pathway of major loganin derivatives in the medicinal plant C. officinalis. Finally, we introduced CoLAMT and its upstream genes into Nicotiana benthamiana and successfully achieved the de novo biosynthesis of a series of loganin derivatives. This work reveals key evolutionary and molecular mechanisms in loganin biosynthesis, providing insights into biotechnological applications in anticancer drug development.

Mango is the second most important tropical fruit crop. Due to ever-changing environmental conditions, world mango production is facing challenges such as diseases (anthracnose and mango malformation), physiological disorders (alternate bearing), low fruit setting, poor fruit quality, short shelf life, and climate change adaptation. Breeding efforts are hindered by the long juvenile period, outdated breeding system, and high heterozygosity, resulting in a slow pace of mango improvement programs. However, over the last decade, significant advances in high-quality genome assemblies, pangenomics, genetic mapping, multiomics data, and phenomics of large populations have accelerated crop genetics and breeding. Here, we summarize recent progress on the origin and domestication of mango, advancements in genome assemblies, development of genetic maps, functional and comparative genomics, evolutionary insights, and assessments of global phenotypic and genotypic diversity, including species at risk. We also discuss the integration of multiomics approaches with quantitative genetics for crop improvement. Furthermore, we highlight the key research gaps that limit breeding efficiency and propose integrative strategies combining pangenomics, multiomics, and machine learning with improved transformation protocols and multienvironment testing to accelerate the development of climate-resilient, high-quality mango cultivars.

γ-Aminobutyric acid (GABA), a four-carbon non-protein amino acid functions as a key signaling molecule in plants. As a signature bioactive compound in tea, GABA plays a crucial role in determining both flavor profile and health-promoting properties. Despite its importance, the molecular regulation of GABA accumulation in tea plants—especially its metabolic crosstalk with key quality determinants like flavonoids—remains elusive. While amino acid transporters are known to mediate source-sink allocation in plants, the functional characterization of GABA transporters in Camellia sinensis has been lacking. In this study, we identified and functionally characterized the bidirectional amino acid transporter CsBAT in tea plants. Through a comprehensive multiplatform validation system encompassing yeast heterologous expression, Arabidopsis genetic transformation, and tea transgenic system, we revealed that CsBAT shows vascular-specific expression and facilitates directional amino acid transport from source (mature leaves) to sink (young shoots), thereby significantly boosting GABA accumulation in buds and young leaves. Importantly, we discovered that CsBAT functionally interacts with key flavonoid biosynthetic enzymes (LAR, 4CL, C4H) within secondary metabolic networks. Our findings provide the first mechanistic link between CsBAT-mediated amino acid transport and tea quality formation, establishing both theoretical frameworks and practical tools for molecular breeding of premium tea cultivars.

Fire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of genes effectively involved in resistance to E. amylovora have been identified. Seeking new resistance candidates, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as Malus domestica agglutinins (MdAGGs). When loss-of-function editions were introduced into MdAGG genes, the plant’s ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora.

Xiangru, with Mosla chinensis (Mc, 2n = 18) and its considered cultivar M. chinensis ‘Jiangxiangru’ (McJ, 2n = 18) as original plants, is an annual herb of the Lamiaceae family, and is widely used as medicinal and edible plant due to its spleen strengthening function. However, absence of genomic resource impedes in-depth research towards Xiangru. In this study, the morphological characteristics and volatile organic compounds (VOC) contents of Mc and McJ were analyzed, showing higher trichome density and monoterpenoid accumulation obtained in Mc, whereas McJ possessed higher biomass. We assembled high-quality Mc, McJ, and their adulterant Mosla soochowensis (2n = 18) genomes of 426.1, 408.8, and 412.8 Mb, respectively, containing the repeat sequences of 57.17%, 56.33%, and 55.83%. Comparative genomics analysis indicated Mosla radiated ~13.3 Mya, supporting McJ initially as a natural naturally formed resource. Five monoterpene synthase genes were identified through comparative transcriptome and were responsible for catalyzing production of diversified monoterpene skeleton, in which TPS1 mediated formation of γ-terpinene, accompanied by CYP71D179 and SDR2, leading to the final production of carvacrol and thymol. We further explored correlation between monoterpenoids biosynthesis and trichome development, indicating MIXTA and WIN1 jointly regulate both trichome formation and VOC accumulation by directly binding promoters of TPS1 and CYP71D179, respectively. Our study fills vacancy of genus Mosla genomes, improving the biosynthetic and regulatory mechanism of volatile compounds in aromatic Traditional Chinese Medicine, also offering novel targets for quality-directed breeding in Xiangru.

Citrus Huanglongbing (HLB) is the most destructive disease in citriculture, mainly caused by Candidatus Liberibacter asiaticus (CLas). However, the immune response of citrus to CLas at the cellular level remains to be elucidated. In this study, the first single-cell atlas of rough lemon (Citrus jambhiri Lush.) root apexes were generated using single-nucleus RNA sequencing at 20 weeks postinoculation with CLas. According to gene expression patterns, the single-cell atlas was partitioned into 20 transcriptionally distinct clusters, and five cell types were identified within these clusters. A significant number of defense-related genes were co-upregulated across the five cell types following CLas infection, whereas genes involved in signal transduction pathways, such as tubulin beta-6 chain (TUBB1) and the phospholipase D alpha 1 (PLD1), were concurrently downregulated. Based on pseudotime trajectory analysis, the key pathways and genes involved in the coordination of cell differentiation and resistance in citrus under CLas infection were characterized. Following CLas infection, the development of phloem cells was significantly delayed, and the differentiation of cambium cells into xylem cells was evident. The expression of genes associated with lignin synthesis was significantly upregulated in these cells. The reduction in phloem cell differentiation and the enhanced differentiation of cambium cells into defense-related xylem cells may represent the primary vascular immune mechanisms exhibited by citrus plants in response to CLas infection. Additionally, DNA-binding one zinc finger transcription factor DOF2.4 was found to potentially serve dual roles in regulating vascular cell development and inducing plant resistance against CLas. In conclusion, this study collectively provides insights into the cellular innate immunity responses of citrus to CLas infection. These findings hold significant implications for the sustainable development of citriculture amidst the ongoing global HLB epidemic, and offer novel insights into vascular immunity and plant defense responses.

Allopolyploids have successfully overcome ‘genome shock’, yet how their subgenomes adapt to coexistence remains largely unclear. Here, we constructed high-resolution epigenomic maps for the diploids Brassica rapa (ArAr) and Brassica oleracea (CoCo), and examined epigenomic variation in the allotetraploid Brassica napus (AnAnCnCn) relative to its putative progenitors. We discovered that coordinated genomic and epigenomic reprogramming in B. napus drove convergence of sequence and epigenomic features between An and Cn, significantly reducing expression divergence in homoeologs. Convergent homoeologs were functionally enriched in pathways related to genome stability and abiotic stress responses. Notably, Cn in B. napus exhibited greater sequence conservation and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) affected by genomic variation in An showed convergent regulatory changes toward Cn, indicating that allopolyploids mitigate subgenomic conflicts through multilayered regulatory coordination. In conclusion, coordinated genomic and epigenomic convergence provides critical insights into the stability and adaptive evolution of allopolyploids.

Ethylene response factors (ERFs) are pivotal regulators in mediating plant stress adaptation; however, the roles of osmotic stress-responsive ERFs in tomato remain poorly characterized. Here, we comprehensively investigate the function of SlERF.D2, a member of the ERF transcription factor family, in modulating osmotic stress adaptation. Expression profiling indicated that SlERF.D2 responded to diverse abiotic stimuli, such as drought and salt, as well as ethylene and abscisic acid (ABA). Combined physiological and metabolomic analyses of SlERF.D2 overexpression and knockout lines revealed a negative regulatory role of SlERF.D2 in tomato's osmotic stress adaptation. Biochemical and molecular assays further revealed that SlERF.D2 directly targets the promoter of SlPP2C1, an ABA signaling suppressor, to activate its expression, thereby impairing ABA-dependent stomatal closure and accelerating water loss. Notably, ethylene-induced SlERF.D2 expression required the direct binding of SlEIL1/2/3/4 to the SlERF.D2 promoter. Furthermore, ethylene activated SlPP2C1 transcription in an SlERF.D2-dependent manner through direct transcriptional regulation by SlERF.D2. Thus, the ethylene-SlEIL1/2/3/4-SlERF.D2-SlPP2C1 transcriptional cascade module is involved in the antagonism of ABA-induced stomatal closure. Concurrently, transcriptomic profiling and metabolic analyses further demonstrated that SlERF.D2 repressed the anthocyanin biosynthetic pathway, leading to a reduced anthocyanin content and increased reactive oxygen species (ROS) levels. Our findings delineate a novel regulatory module wherein SlERF.D2 coordinates stomatal closure and ROS homeostasis to modulate the sensitivity of tomato plant to osmotic stresses, providing an applicable target for improving osmotic stress adaptation in tomato.

Aphids are demonstrated to be voracious phloem feeders, among the most damaging insect pests, due to their capacity to decrease crop production and vector plant viruses. Plant secondary metabolites (PSMs) comprise an essential element of plant protection, which in most cases deters and affects aphid performance. Nonetheless, aphids have developed various resistance mechanisms to counteract these chemicals. This review provides an extensive overview of the biological and molecular adaptations that aphids employ to counteract PSMs, including enzymatic detoxification, antioxidant defense, sequestration, behavioral response shifts, suppression of plant defense mechanisms by symbionts, and manipulation of host signaling pathways by effector proteins. We also described the suppression of the defense pathways by aphid-associated viruses, which further complicates plant-aphid interactions. Although significant insights have been gained about each of the individual mechanisms, research gaps remain, particularly in the functional confirmation of detox genes, the communication interactions of the symbionts, and whether sequestration could play an ecological role across species. Intensive efforts involving molecular-based breeding of horticultural crops, as well as traditional breeding with wild relatives highly endowed with aphid-resistant PSM traits, should be employed in the future to provide sustainable crop protection. New technologies in crop genomics, the identification of effectors, and microbiome research promise the development of resistant cultivars that are not only resistant to aphids but also prevent the spread of disease by their vectors. Together, all this knowledge has the potential to produce high-yielding crops that are resistant to aphids and to implement sustainable farming practices.

The development of blue flower coloration involves the biosynthesis, transport, and accumulation of flavonoids in petal epidermal cells. Although the mechanisms of flavonoid biosynthesis and regulation are well understood, much less is known about the molecular basis of vacuolar anthocyanin/flavonoid sequestration. Here, we identified two tonoplast-localized MATE transporters, MaMATE11 and MaMATE14, that participate in flavonoid transport and influence the blue color of grape hyacinth petals. In vitro transport experiments revealed that both proteins transported a range of flavonoid substrates, with a preference for malonylated anthocyanins, but differed in their substrate specificity and kinetic parameters. Both MaMATE11 and MaMATE14 could complement the anthocyanin-deficient phenotype of the Arabidopsis AtDTX35 mutant, and silencing of either gene by RNA interference significantly reduced anthocyanin accumulation in petals of grape hyacinth. Expression of MaMATE11 and MaMATE14 was directly activated by the anthocyanin-biosynthesis-related transcription factors MaMybA and MaAN2, respectively, establishing a coordinated anthocyanin synthesis-transport module. These findings provide insight into mechanisms of floral coloration and flavonoid translocation in blue-pigmented species and identify valuable target genes for molecular breeding of ornamental flower colors.

The genetic control of phenological traits in Japanese plum (Prunus salicina Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F₁ populations: ‘Black Splendor’ × ‘Pioneer’ (BS×PIO), ‘Red Beaut’ × ‘Black Splendor’ (RB×BS), and ‘Red Beaut’ × ‘Santa Rosa Precoz’ (RB×SRP), comprising 121, 103, and 103 seedlings, respectively. Whole-genome sequencing (~80×) was conducted for the four parents, and progenies were genotyped using a cost-efficient reduced-representation sequencing strategy. SNPs heterozygous in one parent and homozygous in the other were used to build six parental linkage maps. Phenological traits, including beginning, full, and end of flowering (BF, FF, EF), flowering intensity (FI), ripening date (RD), fruit development period (FDP), and productivity (P), were evaluated over three years. A total of 53 QTLs were identified for flowering stages, 16 for RD, 18 for FDP, 10 for FI, and 16 for P. Many QTLs were stable across years. Major QTLs for flowering traits were mapped to LG1, LG2, LG4, and LG6, with a strong QTL for FF on LG6 of ‘Black Splendor’. In BS×PIO, BF was uncorrelated with FF and EF, indicating distinct genetic control likely inherited from ‘PIO’, a low-chill cultivar. RD and FDP were consistently associated with LG4, while productivity QTLs were detected on LG1, LG2, and LG4, often overlapping, suggesting pleiotropic or tightly linked loci. In addition, candidate genes within stable QTLs were detected, providing immediate targets for functional studies. This study provides one of the first genome-wide QTL analyses of phenology in Japanese plum using low-coverage whole genome sequencing and offers valuable tools for marker-assisted breeding in this species.

Fruit color is a key quality trait in strawberry breeding and cultivar development, as it directly influences consumer preference and marketability. Anthocyanins are the pigments responsible for the red coloration in strawberries, and the transcription factor MYB10 gene plays a crucial role in regulating the anthocyanin biosynthetic pathway. Our previous study identified a homoeolog-specific copy, MYB10-1B, located on chromosome 1B, as a key regulator of fruit color. The natural mutation in MYB10-1B, such as in the variety ‘Florida Pearl’ leads to the development of white fruit. Building on this discovery, we applied CRISPR/Cas9-mediated homoeolog-specific editing to target the functional dominant allele, MYB10-1B, in the cultivated octoploid strawberry ‘Florida Brilliance’, successfully altering the fruit color from red to white. Gene expression analysis in the edited lines revealed downregulation of MYB10-1B and key anthocyanin biosynthesis genes (CHS, DFR, and ANS). Furthermore, whole-genome resequencing results showed precise on-target mutations in MYB10-1B with minimal off-target effects. This study highlights the successful application of homoeolog-specific CRISPR/Cas9-mediated gene editing in polyploid species and provides a foundation for functional genomics and advanced breeding strategies in strawberries. Importantly, our findings demonstrate that specific targeting of the dominantly expressed homoeologous copy is essential for inducing phenotypic changes in polyploids. This underscores the importance of precise gene editing in octoploid strawberry to drive trait improvement.

Hydrogen sulfide (H₂S) has garnered significant attention as a novel gaseous signaling molecule. While its physiological roles in animals are well documented, research over the past two decades has increasingly uncovered its vital functions in plants, establishing it as a crucial component in plant signaling processes. In plants, endogenous H₂S is produced across various subcellular compartments and plays indispensable roles in stress responses, growth, and development. Research has progressed from model plants to horticultural crops, underscoring the prospective agricultural benefits of H₂S. Nevertheless, several challenges persist, including unclear signaling targets and limited real-world applications. This comprehensive review explores the discovery, biosynthesis, physiological roles, mechanisms, and molecular targets of H₂S in plants, offering valuable insights in future research.

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.

The MYB protein family comprises numerous transcription factors with important functions in various biological processes in plants; however, their role in modulating banana fruit ripening has been rarely investigated. In this study, we identified an R2R3-type MYB gene, MaMYB69, which promotes fruit ripening by directly modulating cell wall degradation. The expression of MaMYB69, which encodes a nucleus-localized transcription activator, was induced by ethylene and upregulated during banana ripening. MaMYB69 activated the expression of MaPE, MaPL1, MaGAL, and MaPG3 by directly targeting their promoters. MaMYB69 overexpression in tomato and banana accelerated fruit ripening and stimulated cell wall-modifying gene expression. Moreover, MaMYB69 interacted with MaERF55 and strengthened its transactivation activity through downstream target genes. MabZIP5, an aroma biosynthesis regulator, acted directly upstream of MaMYB69, enhancing its transcription. MaMYB69 also formed a homodimer with itself and activated its expression. Collectively, our results show that MaMYB69 is pivotal in controlling banana ripening and softening and improve our understanding of the regulatory cascades involved in fruit ripening. MaMYB69 may serve as a potential target for improving fruit quality and extending the shelf life.

Flower color is a key trait influencing insect pollination and ornamental value, yet the molecular mechanisms underlying heterozygous flower color remain unclear. In this study, we identified the creation of a yellow-white chimeric flower (cf) mutation in Brassica napus, characterized as the coexistence of yellow and white colors on petals of the same flower. Genetic analysis revealed that chimeric flower formation is controlled by a completely dominant gene. Map-based cloning, transgenic complementation, and CRISPR/Cas9 experiments consistently confirmed that BnaC05G0385300ZS on chromosome C05 is the causal gene of CF, which encodes a plastid DNA polymerase IB (BnaC05.POLIB). A G-to-A mutation in the seventh exon results in a D742N substitution, which disrupts Mg²⁺ binding and impairs polymerase activity. This leads to a reduced plastid genome copy number, decreased chromoplast formation, and aberrant carotenoid accumulation, ultimately resulting in the chimeric phenotype in a dosage-dependent manner. These findings reveal a novel role for BnaC05.POLIB in petal color patterning and provide a strategy for breeding ornamental plants with heterozygous flowers.

Fruit growth and development are generally initiated following successful pollination and fertilization. Seedless chestnut rose (Rosa sterilis), an elite promising fruit tree for both edible and medicinal purposes due to the extremely high vitamin C and superior quality, exhibits a naturally parthenocarpic character, however the underlying mechanism has been still unclear so far. Currently, gibberellins (GAs) were justified as the key hormone for parthenocarpy induction in seedless chestnut rose by endogenous hormone analysis and exogenous plant growth regulator (PGR) application. In total, 43 members of the GA oxidase gene family (RsGAoxs) were systematically identified and characterized based on genome-wide analysis of seedless chestnut rose. On the basis of transcriptomic analysis, overexpression experiments in tomato, as well as virus-induced gene silencing (VIGS) assay in seedless chestnut rose, RsGA3ox9 was substantially justified to be involved in the parthenocarpic fruitsetting of this species. Transcription factors RsMYB3, RsMYB8, and RsMYB73 were proven to positively regulate the expression of RsGA3ox9. Further, yeast two-hybrid (Y2H) and luciferase complementation assay illuminated that RsMYB8 and RsMYB73 may interact, leading to upregulating RsGA3ox9. Thereby, RsGA3ox9 substantially regulates parthenocarpy of seedless chestnut rose, and RsMYB8-RsMYB73 complex promotes parthenocarpic fruitsetting by upregulating RsGA3ox9, which may facilitate the seedless fruit breeding in chestnut rose (Rosa roxburghii Tratt.), as well as provide novel insights for better understanding the mechanism underlying the parthenocarpic fruitsetting in fruit species.

Plants continuously integrate metabolic and hormonal signals to coordinate growth, development, and responses to environmental stimuli. Among these signals, sugars and strigolactones (SLs) have emerged as central regulators. Beyond serving as metabolic fuels, sugars act as signaling molecules that govern key developmental transitions and stress responses. SLs, a relatively recent addition to the phytohormone family, play pivotal roles in shaping plant architecture, modulating resource allocation, and facilitating environmental adaptation. While the individual signaling functions of sugars and SLs are well documented, their crosstalk remains an emerging and largely underexplored area of plant biology. This review synthesizes current knowledge on both the independent and interactive roles of sugar and SL signaling across critical developmental processes, including seed germination, hypocotyl elongation, root and shoot architecture, flowering, senescence, and plant responses to abiotic and biotic stress. By analyzing antagonistic and synergistic interactions, we point out several potential integrative hubs where metabolic and hormonal signals converge to fine-tune the final decision. Notably, the nodal roles of BRC1/TB1 (BRANCHED1/TEOSINTE BRANCHED1), FT (FLOWERING LOCUS T), in mediating sugar-SL crosstalk in shoot branching, flowering, respectively, are highlighted. We also explore how sugar-SL interplay influences seed germination and plant adaptation to environmental stresses through shared regulators such as TOR (Target of Rapamycin) kinase, SnRK1 (Sucrose non-fermenting-1 Related Kinase 1), and SMXLs (Suppressor of MAX2-Like proteins). Understanding these interactions not only deepens our knowledge of fundamental plant biology but also offers new insights for improving the performance and resilience of crop and horticultural species.

The tea plant (Camellia sinensis), native to warm and humid low-latitude regions of southwestern China, has expanded to higher altitudes, including southeastern Xizang, where cultivation above 2500 m poses challenges due to low accumulated temperatures. However, the impact of high-altitude climatic conditions, particularly temperature, on tea growth remains underexplored. To investigate, weather stations were deployed at three altitudes in southeastern Xizang to monitor spring temperature fluctuations: Medog (MD, 1200 m), Zayü (ZY, 1720 m), and Layue in Bayi District (BY, 2600 m). Field observations and meteorological data indicated that the milder spring temperatures in MD and ZY facilitated normal budburst and growth, whereas the lower temperatures in BY delayed budburst and resulted in leaf yellowing and browning. Comparative experiments revealed that seedlings exposed to fluctuating low temperatures (10°C/4°C) experienced the most severe cold injury and exhibited the lowest germination rates compared to seedlings under constant-temperature treatments. Transcriptome analysis uncovered differential expression of genes involved in chlorophyll degradation, lignin biosynthesis, and flavonoid pathways under cold stress. Functional characterization of the cold-induced transcription factor CsABF2 revealed its central role in activating these pathways, as evidenced by antisense oligodeoxynucleotide (AsODN) silencing and promoter activation assays, to activate key downstream genes: CsSGR1 (chlorophyll degradation), CsPALa (phenylpropanoid pathway), and CsMYB6c (flavonoid biosynthesis). These results provide mechanistic insights into how spring temperature variability at high altitudes impairs tea plant development and alters quality-related metabolites, offering a molecular basis for improving cold resilience in tea cultivation.

AP2/ERF transcription factors (TFs) constitute a large, plant-specific family that acts as a central hub integrating developmental and environmental signals to modulate the biosynthesis of secondary metabolites. These compounds, including terpenoids, phenolic compounds, and alkaloids, are vital for plant survival and are of immense value to human health and industry. This review provides a comprehensive synthesis of the molecular mechanisms by which AP2/ERF TFs regulate these crucial metabolic pathways. We systematically classify and dissect their regulatory modes, including direct binding to cis-elements (e.g. GCC-box, CE1, and DRE/CRT), indirect control via upstream signaling cascades, co-regulation through physical interactions with other TF families (e.g. MYB, bHLH, WRKY), and feedback regulation. We present numerous case studies across diverse plant species, highlighting both conserved principles and species-specific adaptations in the control of high-value natural products like artemisinin, tanshinones, anthocyanins, and nicotine. Furthermore, we discuss the emerging roles of AP2/ERF TFs in metabolic engineering and synthetic biology, and outline future research directions, emphasizing the application of multi-omics and CRISPR/Cas9 technologies to unravel and engineer these complex regulatory networks for targeted overproduction of valuable phytochemicals.

The tea plant is an important nonalcoholic beverage crop known for its abundant secondary metabolites, particularly in buds and leaves. However, the coordinated regulation of bud-to-leaf development and metabolism remains poorly understood. Here, we applied single-nucleus RNA sequencing (snRNA-Seq), bulk RNA sequencing (RNA-Seq), and metabolomics to comprehensively profile the developmental trajectory and metabolic characteristics of tea plant buds and leaves. The snRNA-Seq analysis revealed 17 cell clusters and 8 cell types in buds and leaves, respectively. Notably, the proportion of palisade mesophyll (PM) cells increased progressively during development, while proliferating cells (PC) decreased. Interestingly, key enzymes in the flavonoid biosynthetic pathway were specifically localized to PM cells. Metabolomic analyses demonstrated dynamic accumulation patterns of various metabolites, including phytohormones, flavonoids, and amino acids, as the buds transitioned to mature leaves. Using multi-omics profiling, we identified CsmiRNA396b, CsUGT94P1, CsTCP3, and CsTCP14 as critical regulatory components. Enzyme activity assays confirmed that CsUGT94P1 catalyzes the conversion of flavonols into flavonol glycosides in vitro. Furthermore, CsmiRNA396b was found to regulate leaf development by inhibiting CsGRF3 expression, while CsTCP3 and CsTCP14 played antagonistic roles in leaf development and flavonoid biosynthesis. Our findings provide novel insights into the regulatory mechanisms underlying bud-to-leaf development and metabolite production in tea plants.

Anthurium, a highly diverse genus in the family Araceae, is well known for its ornamental spathes and spadices. However, limited genomic resources hinder the study of floral traits and their evolutionary histories. Here, we present high-quality chromosome-level genome assemblies of Anthurium andraeanum and Anthurium scherzerianum. Comparative genomics revealed extensive chromosomal rearrangements and species-specific transposon expansions, which likely contributed to genome divergence. Two lineage-specific whole-genome duplications were identified, associated with gene family expansions linked to stress adaptation. Population structure analysis uncovered strong genetic admixture, reflecting widespread historical hybridization. Integrated transcriptomic and metabolomic analyses revealed dynamic regulatory networks governing spathe coloration through flavonoid-anthocyanin pathways. In addition, CER3, KCS1, and KCS3 were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes SOC1 and AGL6, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding Anthurium evolution, offer molecular targets for breeding programs, and elucidate transposon-driven genome expansion mechanisms that advance our knowledge of speciation in tropical epiphytes with exceptionally large genomes.