Large-scale manual measurements of plant architectural traits in tomato growth are laborious and subjective, hindering deeper understanding of temporal variations in gene expression heterogeneity. This study develops a high-throughput approach for characterizing tomato architectural traits at different growth stages and mapping temporal broad-sense heritability using an unmanned ground vehicle-based plant phenotyping system. The SegFormer with fusion of multispectral and depth imaging modalities was employed to semantically segment plant organs from the registered RGB-D and multispectral images. Organ point clouds were then generated and clustered into instances. Finally, six key architectural traits, including fruit spacing (FS), inflorescence height (IH), stem thickness (ST), leaf spacing (LS), total leaf area (TLA), and leaf inclination angle (LIA) were extracted and the temporal broad-sense heritability folds were plotted. The root mean square errors (RMSEs) of the estimated FS, IH, ST, and LS were 0.014, 0.043, 0.003, and 0.015 m, respectively. The visualizations of the estimated TLA and LIA matched the actual growth trends. The broad-sense heritability of the extracted traits exhibited different trends across the growth stages: (i) ST, IH, and FS had a gradually increased broad-sense heritability over time, (ii) LS and LIA had a decreasing trend, and (iii) TLA showed fluctuations (i.e. an M-shaped pattern) of the broad-sense heritability throughout the growth period. The developed system and analytical approach are promising tools for accurate and rapid characterization of spatiotemporal changes of tomato plant architecture in controlled environments, laying the foundation for efficient crop breeding and precision production management in the future.

Consumers value highly the nutritional content and flavor of fresh fruits, which are influenced by endogenous plant hormones. However, the molecular mechanisms governing the hormonal regulation of essential nutrients such as ascorbic acid (AsA) in fruit are still unclear. This study investigates the regulation of AsA synthesis in kiwifruit by the transcription factor AcABI5a, which is involved in mediating the abscisic acid (ABA) signal. A negative correlation between AcABI5a expression and AsA levels across different developmental stages of kiwifruit was observed. Furthermore, AcABI5a was found to bind both the AcMYBS1 promoter, repressing its transcriptional activity, and its own promoter, fostering expression and maintaining active repression of AcMYBS1. AcMYBS1 activates the expression of AcGGP3, which encodes an enzymatic step in AsA biosynthesis that is highly regulated both transcriptionally and translationally. In-depth interaction studies utilizing yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), firefly luciferase complementation (NC-LUC), and pull-down assays unveiled that AcABI5a also physically interacts with AcMYBS1, further impeding its activation of AcGGP3. Results from knockout by gene editing and overexpression of AcABI5a support the role of AcABI5a in mediating the ABA inhibitory effect on AsA synthesis by repressing the expression of AcMYBS1 and thus AcGGP3. Overall, our findings highlight AcABI5a’s negative regulatory role in AsA synthesis by integrating ABA signaling during fruit development, providing new insights into the regulation of AsA synthesis by phytohormones.

Nodes are a distinct feature of bamboo plants, categorized into three main types: culm, shoot, and rhizome nodes. However, the latter two are often overlooked due to their underground growth, resulting in a limited understanding of their structure and function. In this study, we examined the structure and mineral elements deposition in the nodes of Moso bamboo (Phyllostachys edulis). Our findings indicate that all three node types possess a complex yet well-organized vascular bundle system, with notable differences. Culm nodes feature enlarged vascular bundles with distinct xylem and phloem regions, whereas shoot and rhizome nodes have less developed phloem regions. The rhizome node contains a vascular structure of crown root and coronary shoot bud, which is absent in culm and shoot nodes. In the culm node, iron accumulation decreases gradually from the bottom to the top, primarily localizing in cells near the enlarged and small vascular bundles. Zinc is deposited in both the enlarged and small vascular bundles in the lower part of the node. In contrast, calcium accumulates predominantly in the upper part, particularly in cells adjacent to enlarged and small vascular bundles including diffuse and parenchyma cells. Potassium is distributed throughout most cells but is less abundant in the pith cavity and xylem transfer cells. In shoot and rhizome nodes, iron, zinc, calcium, and potassium exhibit specific regional and cellular deposition patterns. Overall, the vascular structure and mineral element deposition patterns suggest that bamboo nodes function not only as tissue junctions but also as critical hubs for mineral element deposition and distribution.

The transition of plants from aquatic to terrestrial environments required effective barriers against water loss and UV damage. The plant cuticle, a hydrophobic barrier covering aerial surfaces, emerged as a critical innovation, yet how its biosynthesis is regulated in specialized structures remains poorly understood. This study identifies two long-chain acyl-CoA synthetases, SlLACS1 and SlLACS2, that exhibit both distinct and overlapping functions in cuticle formation across tomato tissues. These genes show striking specificity in different trichome types: SlLACS1 functions in type I/IV trichomes, while SlLACS2 is required for type VI trichome cuticle integrity. However, they act redundantly in leaf epidermal and fruit cuticle formation, as revealed by analysis of single and double mutants. Unexpectedly, simultaneous disruption of both genes severely compromises pollen viability through defective pollen coat formation. Biochemical characterization demonstrates that SlLACS1 and SlLACS2 maintain their ancestral enzymatic function of activating long-chain fatty acids, an activity conserved from algal LACS homologs. These findings reveal how gene duplication and diversification facilitated the development of specialized hydrophobic barrier functions in distinct tissues while maintaining redundancy in fundamental protective structures, representing a sophisticated adaptation to terrestrial life.

Rapeseed is the second largest oilseed crop in the world with short domestication and breeding history. This study developed a batch of genomic prediction models for flowering time (FT), oil content, and yield components in rapeseed. Using worldwide 404 breeding lines, the optimal prediction model for FT and five quality and yield traits was established by comparison with efficient traditional models and machine learning (ML) models. The results indicate that quantitative trait loci (QTLs) and significant variations identified by genome-wide association study (GWAS) can significantly improve the prediction accuracy of complex traits, achieving over 90% accuracy in predicting FT and thousand grain weight. The Genomic Best Linear Unbiased Prediction (GBLUP) and Bayes-Lasso models provided the most accurate prediction overall, while ML models such as GBDT (Gradient-Boosting Decision Trees) exhibited strong predictive performance. Our study provides genome selection solution for the high prediction accuracy and selection of complex traits in rapeseed breeding. The use of a diverse panel of 404 worldwide lines ensures that the findings are broadly applicable across different rapeseed breeding programs.

Lindera megaphylla, a Lauraceae species, is valued for timber, horticulture, landscape architecture, and traditional medicine. Here, a high-quality genome of L. megaphylla was obtained at the chromosome level. A total of 96.77% of genomic sequences were mapped onto 12 chromosomes, with a total length of 1309.2 megabase (Mb) and an N50 scaffold of 107.75 Mb. Approximately, 75.91% of genome consists of repetitive sequences and 7004 ncRNAs were predicted. We identified 29 482 genes, and 28 657 genes were annotated. Gene family analysis showed expanded gene families were mainly involved in energy metabolism and cellular growth, while contracted ones were associated with carbohydrate metabolism and signal transduction. Our analysis revealed that L. megaphylla has undergone two rounds of whole-genome duplication (WGD). Our results revealed that volatile compounds in L. megaphylla leaves inhibited the growth of several fungi and bacteria. Fifty-two terpene synthase (TPS) genes were identified and classified into six subfamilies, with significant expansion observed in the TPS-b, TPS-f, and TPS-g subfamilies in L. megaphylla. Transcriptomic and metabolomic co-analysis revealed that 43 DEGs were correlated with 117 terpenoids. Further analysis revealed that LmTPS1 was significantly correlated with caryophyllene oxide content. The overexpression of LmTPS1 in transgenic tomato lines significantly increased the contents of β-caryophyllene and humulene, which further improved the resistance of transgenic tomato plants to common fungal and bacterial diseases. The integrated analysis of genome, metabolome, and transcriptome provides comprehensive insights into the evolution of L. megaphylla and clarifies the molecular mechanisms underlying the protective effects of caryophyllene against biotic stress.

Unlike animals, plants are sessile organisms that cannot move freely in response to fluctuating and complex environments. As a result, plant development follows post-embryonic processes, enabling flexible developmental strategies to adapt to changing environment. The WUSCHEL-related homeobox (WOX) gene family plays a crucial role in regulating these post-embryonic processes in plants. In this study, we performed an evolutionary analysis of the WOX gene family across 29 plant species, isolating a total of 330 WOX family genes. Our study identified a fern protein with similar length and conserved motifs to WUS gene of spermatophyte, suggesting that the modern clade of the WOX family may have already diverged in ferns. Furthermore, we conducted a pan-genome analysis of the WOX family in Malus, examining the number and gene characteristics of WOX family members across eight varieties. The promoter elements of WUS-1, WUS-2, WOX5-1, and WOX5-2 in different Malus varieties were analyzed further. Additionally, we examined the expression patterns of modern clade WOX family members in developing tissues and during leaf-borne shoot regeneration of Malus. We developed the transgenic lines with inducible overexpression of MdWUS-1 or MdWOX5-1, which revealed that mild upregulation of MdWUS-1 significantly promoted leaf-borne shoot formation, while strong upregulation of MdWUS-1 led to browning and death of explants, likely due to oxidative stress. These findings provide new insights into the evolution of the WOX gene family from ferns into seed plants and lay the foundation for further studies on the spatiotemporal regulation of gene expression during shoot regeneration.

Carnation (Dianthus caryophyllus L.) is an important global flower crop, with great ornamental and economic value. It has more than 2000 years of cultivation history and profound cultural heritage known as mother flower. Now, although carnation is deeply loved by the majority of consumers because of its rich color and various varieties, the original carnation unique clove flavor has disappeared. Furthermore, our understanding of carnation traits such as flower shape, flower color, flower fragrance, disease resistance, and vase life remains limited. Previous reviews have primarily concentrated on individual aspects of carnation, failing to present a comprehensive overview. In this review, we summarize the recent progress of carnation in these aspects, so as to provide a reference for the future research direction in carnation.

Water deficit during flowering can lead to petal wilting, necrosis, and sterility, severely limiting crop fertilization and yield. Therefore, rapid recovery of floral organs after dehydration is essential for angiosperms to achieve their full reproductive potential. Aquaporins (AQPs) are bidirectional membrane channels mediating water transmembrane transport. Plasma membrane intrinsic proteins (PIPs), one of AQP subfamily, play a key role in flower opening and dehydration responses. However, it still needs to be elucidated how PIPs are involved in flower recovery after stress. Cut rose (Rosa hybrida), a globally important ornamental flower, undergoes dehydration and rehydration during the postharvest process. Here, we show that the scaffold protein-encoding gene CASP-LIKE PROTEIN 1D1 (RhCASPL1D1), expressed during flower opening and dehydration, promotes flower recovery after dehydration. Silencing RhCASPL1D1 in rose petals and calli hindered cell recovery following dehydration and reduced the rate of water uptake, whereas RhCASPL1D1 overexpression had the opposite effect. Ethylene upregulated RhCASPL1D1 expression, and RhCASPL1D1 physically interacted with RhPIP2s at the plasma membrane. This interaction facilitated RhPIP2s retention to delay its degradation at the plasma membrane and enhanced proteins abundance under dehydration stress. Taken together, our findings reveal a potential mechanism involved in RhCASPL1D1 scaffold regulating flower recovery after dehydration stress.

Leaf senescence, an essential component of the plant life cycle, seriously affects the productivity of numerous commercial crops, with cytokinins serving as crucial regulators in delaying this process. Here, we observed that apple (Malus domestica) leaves exhibiting deficiencies in sorbitol synthesis due to antisense inhibition of ALOSE-6PHOSPHATE REDUCTASE (A6PR) presented an increase in cytokinin content and exhibited a delay in leaf senescence, in contrast to wild-type (WT) leaves. Transcriptome analysis indicated that the expression of cytokinin oxidase 7 (MdCKX7), encoding a key enzyme in the cytokinin degradation pathway, was significantly downregulated in the A6PR antisense lines. Functional verification confirmed that MdCKX7 facilitated the degradation of cytokinin and accelerated leaf senescence. Moreover, this leaf senescence phenotype was exacerbated by the co-expression of two DNA-binding One Zinc Finger (DOF) transcription factors, cycling DOF factor 3 (MdCDOF3) and MdDOF3.6, along with MdCKX7. Further biochemical and phenotypic analyses demonstrated that MdCDOF3 and MdDOF3.6 bind directly to the promoter region of MdCKX7, thereby transcriptionally activating its expression. Intriguingly, the expression of MdCDOF3, MdDOF3.6, and MdCKX7 is cooperatively induced by sorbitol. These findings demonstrate that the MdCDOF3/MdDOF3.6-MdCKX7 regulatory module orchestrates leaf senescence by facilitating cytokinin degradation in response to sorbitol signaling, revealing a mechanism by which sorbitol signaling modulates leaf senescence specifically through MdCKX7-mediated cytokinin degradation in apple plants.

Although extensively studied in various plants, the roles of aquaporin proteins in litchi remain unclear. In this study, low moisture content was observed in the dormant terminal buds of litchi. Transcriptome analysis revealed that two aquaporin genes, PLASMA MEMBRANE INTRINSIC PROTEIN 1;4 (LcPIP1;4) and LcPIP1;5, could be remarkably inhibited by exogenous ethylene (ETH), which also reduced the moisture content of litchi buds. Quantitative real-time polymerase chain reaction assays indicated that LcPIP1;4 expression was relatively elevated in the dormancy stage of litchi terminal buds. Inhibition of LcPIP1;4 in the buds of litchi during the growth stage delayed the onset of dormancy, resulting in a significantly reduced dormancy rate and increased moisture content. Further study indicated that LcPIP1;4 interacts with LcPIP1;4a, and they are capable of self-interaction. Silencing of LcPIP1;4a in litchi buds resulted in a phenotype consistent with silencing of LcPIP1;4. Additionally, simultaneous silencing of both LcPIP1;4 and LcPIP1;4a resulted in a more severe bud dormancy phenotype. Moreover, LcPIP1;4 was directly upregulated by LcRAP2.4. Silencing of LcRAP2.4 also delayed the onset of dormancy in litchi terminal buds, which is regulated by LcSVP2. ETH treatment at 1000 mg/l significantly downregulated the expression of LcPIP1;4 and LcRAP2.4, but had no significant effect on LcPIP1;4a. In contrast, abscisic acid (ABA) treatment at 200 mg/l significantly upregulated the expression of LcPIP1;4, LcPIP1;4a, and LcRAP2.4. Combined treatment with ETH and ABA exerted a stronger inhibitory effect on the bud break and upregulated LcPIP1;4 and LcRAP2.4 to lower degrees than ABA alone, suggesting that ABA reversed the inhibitory effect of ETH on the expression of LcPIP1;4 and LcRAP2.4. ABA treatment and combined treatment with ETH and ABA effectively reduced the moisture content of the terminal buds. These results demonstrate that LcRAP2.4, LcPIP1;4, and LcPIP1;4a play a vital role in dormancy onset of litchi terminal buds by regulating moisture levels.

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This study aimed to predict dry matter partitioning in cucumber fruit (Cucumis sativus L.) by developing a simulation model that integrates photosynthetic characteristics based on leaf age and cropping type. Leaf gas exchange, growth, and environmental data from semi-forcing and forcing cropping types were used to calibrate models including the Farquhar-von Caemmerer-Berry (FvCB) model and other growth-related models. The FvCB model revealed reduced Vcmax and Jmax values in older leaves across all cropping types, with semi-forcing crops showing higher photosynthetic capacities than forcing crops. Simulation results showed that, in predicting dry matter partitioning to fruit, the leaf-position-specific simulation model exhibited higher average R² and lower RMSE (g m⁻²) compared to the leaf position-independent model, which applied the middle leaf FvCB model across all leaf ranks. Additionally, bias comparisons indicated greater consistency in the leaf-position-specific model. This approach allows growers to optimize environmental strategies by utilizing photosynthetic data form each leaf position. However, to further improve canopy-level predictions, future models should incorporate the temperature dependence of mesophyll conductance and the effects of photoperiodicity. This study underscores the value of integrating physiological and environmental complexities into crop simulation models, providing a foundation for enhanced predictions and the development of improved crop management strategies across various cultivation scenarios.

Investigating the regulatory mechanisms that govern plant growth is crucial for developing high-yield wood varieties. In this context, the KNOX gene family has been identified as a significant regulator of plant growth. Our study focuses on PagKNAT5a, a class II member of the KNOX gene family, which has been found to promote the growth of poplar. Transgenic plants overexpressing PagKNAT5a exhibited significant increases in both plant height and stem diameter compared to wild-type controls. Histochemical analyses revealed that these overexpression lines had elongated xylem vessels and fiber cells, which correlated with elevated auxin levels. Additionally, we observed thickened secondary cell walls (SCWs) and increased lignin content in the fiber cells of these transgenic lines. Further protein interaction assays indicated that PagKNAT5a physically interacts with MYB46, a crucial regulator of SCW biosynthesis. This interaction activates downstream secondary wall MYB-responsive elements (SMREs), leading to the upregulation of lignin biosynthesis genes driven by these cis-acting elements. Moreover, the increased photosynthetic rate observed in the overexpression lines is likely to significantly support overall plant development. Our findings suggest that PagKNAT5a facilitates the longitudinal elongation of vascular cells by modulating auxin levels while simultaneously promoting the radial growth of xylem tissue through the activation of the MYB46-mediated lignin biosynthesis pathway. The functional analysis of PagKNAT5a highlights its potential for improving wood yield in forestry applications.

Blueberry (Vaccinium spp. section Cyanococcus) ripening is a complex process involving physiological and molecular changes that affect harvest timing, fruit quality, and market value. This review examines scientific literature on blueberry ripening, aiming to establish a unified phenological framework for lowbush (Vaccinium angustifolium), highbush (Vaccinium corymbosum, including northern and southern types), and rabbiteye (Vaccinium virgatum Ait; syn. Vaccinium ashei Reade) blueberries. Blueberries follow a double-sigmoid growth pattern, with epidermis color changes marking the onset of ripening. Traditionally, fruits are classified as climacteric or nonclimacteric based on respiration rates and ethylene production. However, blueberry genotypes exhibit significant variability in these traits. Some genotypes exhibit high respiration rates during fruit color transition, but ethylene production maxima vary or may be absent. The diversity among blueberry genotypes and differences in research methodologies contribute to inconsistencies in reported data. Thus, a unified classification of blueberry ripening remains premature. Nevertheless, agronomic practices and ripening-related gene networks are available to enable future studies. This review also explores the implications of these findings for farmers and consumers.

One of China’s most important resources is flax (Linum usitatissimum L.), an ancient crop with significant nutritional and therapeutic benefits. Despite its importance, existing flax reference genomes remain incomplete, with many unassembled sequences. Here, we report a gapless 482.51 Mb telomere-to-telomere (T2T) flax genome assembly, predicting 46 634 genes, of which 42 805 were functionally annotated. Repetitive sequences constitute 60.05% of the genome, and we identified 30 telomeres and 15 centromeres across the chromosomes. Whole-genome duplication (WGD) events were detected at approximately 11.5, 53.5, and 114 million years ago (MYA) based on synonymous substitution rates (Ks). The T2T assembly enabled the reconstruction of the fatty acid metabolic pathway, identifying 49 related genes, including six newly annotated ones. Furthermore, genomic colocalization was observed between fatty acid metabolism pathway-related genes and transposable elements, suggesting that functional differentiation of these genes in flax evolution may have occurred through transposon-mediated duplication events. Phylogenetic analysis of SAD and FAD gene families revealed that FAD genes segregate into FAD2 and FAD3/7/8 subfamilies. Gene structure and motif analyses demonstrated conserved exon-intron architectures and motif organization within each phylogenetic clade of SAD and FAD genes. Promoter region characterization identified numerous cis-acting elements responsive to phytohormones (MeJA and abscisic acid) and abiotic stresses (low temperature and anaerobic induction) in both SAD and FAD genes. Our knowledge of the evolution of the flax genome is improved by this excellent genome assembly, which also offers a strong basis for enhancing agricultural attributes and speeding up molecular breeding.

Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study integrates deep learning (DL)/machine learning (ML) algorithms, plant phenomics, quantitative genetics, and transcriptomics to conduct genomic selection (GS) of pest resistance in grapevine. Building deep convolutional neural networks (DCNNs), we accurately assess pest damage on grape leaves, achieving 95.3% classification accuracy (VGG16) and a 0.94 correlation in regression analysis (DCNN-PDS). The pest damage was phenotyped as binary and continuous traits, and genome resequencing data from 231 grapevine accessions were combined in a Genome-Wide Association Studies, which maps 69 quantitative trait locus (QTLs) and 139 candidate genes involved in pest resistance pathways, including jasmonic acid, salicylic acid, and ethylene. Combining this with transcriptome data, we pinpoint specific pest-resistant genes such as ACA12 and CRK3, which are crucial in herbivore responses. ML-based GS demonstrates a high accuracy (95.7%) and a strong correlation (0.90) in predicting pest resistance as binary and continuous traits in grapevine, respectively. In general, our study highlights the power of DL/ML in plant phenomics and GS, facilitating genomic breeding of pest-resistant grapevine.

The prostrate growth habit is an important ornamental trait in ground-cover chrysanthemum, offering high aesthetic value, strong lodging resistance, and excellent landscape greening capability. However, the genetic basis underlying this trait in chrysanthemum remains largely unclear. In this study, we utilized the prostrate-type Chrysanthemum yantaiense (tetraploid), the erect-type C. indicum (tetraploid), and their 199 F₁ hybrid progenies to construct a high-density genetic linkage map through genotyping-by-sequencing. The biparental linkage maps included 4614 and 5180 SNP markers, with an average marker distance of 0.84 and 0.73 cM, respectively. After four years of phenotypic evaluation and one year of dynamic trait measurement in progenies for traits related to prostrate growth habit, we confirmed a stable quantitative trait locus (QTL) located on LG1-1 among co-localized QTLs using KASP markers. This QTL explained up to 20.13% of the phenotypic variation. As a result, a total of 44 genes were identified as candidate due to their tightly linkage with the peak QTL marker, Tag16173. Further phytohormone measurement, gene expression analysis, and transgenic studies confirmed that one of these candidates, the D type cyclin-encoding gene CyCYCD3;1, played a key role in the formation of prostrate growth habit in C. yantaiense. Our results not only enhance the understanding of the molecular mechanisms behind prostrate growth habit but also provide valuable molecular markers for improving plant architecture-related traits in chrysanthemum breeding.

Anthocyanins and terpenoids are secondary metabolites with well-documented health benefits. Isopentenyl transferases (IPTs) are key enzymes in cytokinin (CK) biosynthesis. While ADP/ATP-type IPTs and their associated trans-zeatin (tZ)-CKs and iP-CKs are considered to play regulatory roles in growth and development, as well as stress acclimation in plants, tRNA-type IPTs and cis-zeatin CKs (cZ-CKs), which may serve housekeeping functions, remain less studied. In this study, the tRNA-type IPT gene FveIPT2 was overexpressed in woodland strawberries (Fragaria vesca). Overexpression had minimal impact on plant growth and CK levels but resulted in transgenic fruits exhibiting a significant increase in total phenolic, flavonoid, and anthocyanin contents, indicating enhanced fruit quality. Metabolite profiling revealed substantial increases in nine specific anthocyanins and 24 out of 47 detected terpenoids in the transgenic fruits. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis confirmed the upregulation of genes involved in anthocyanin and terpenoid biosynthesis and transport. These findings demonstrate that while tRNA-type IPTs may primarily play housekeeping roles, FveIPT2 overexpression can significantly enhance fruit quality by boosting terpenoid and anthocyanin accumulation, highlighting the unexpected potential of these genes to improve the nutritional value of edible fruits.

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Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in cases where known diploid ancestors are absent. In this study, we introduce a novel approach that leverages long terminal repeat retrotransposons (LTR-RTs) coupled with the serial similarity matrix (SSM) method to assign genome assemblies to subgenomes, particularly beneficial for those without known diploid progenitor genomes. The SSM method helps identify subgenome-specific LTRs and facilitates the inference of the timing of allopolyploidization events. We validated the efficacy of the SSM approach using well-studied allopolyploid genomes, Eragrostis tef and Gossypium hirsutum, alongside artificially created allotetraploid genomes, GarGra and GmaGso. Our results demonstrated the robustness of the method and its effectiveness in assigning chromosomes to subgenomes. We then applied the SSM method to the octoploid strawberry genome. Our analysis revealed three allopolyploidization events in the evolutionary trajectory of the octoploid strawberry genome, shedding light on the evolutionary process of the origin of the octoploid strawberry genome and enhancing our understanding of allopolyploidization in this complex species.

Oleanane-type triterpenoid saponins are the primary medicinal components of Eleutherococcus senticosus. During saponin biosynthesis in E. senticosus, various members of the 2,3-oxidosqualene cyclase (OSC) gene family can direct 2,3-oxidosqualene into triterpene saponin and sterol synthesis pathways. However, the precise molecular mechanism underlying this phenomenon remains unclear. We initially screened for β-amyrin synthase 1 (bAS1) and cycloartenol synthase 1 (CAS1) among 10 EsOSC genes using genome-wide identification and correlation analysis. Subcellular localization, catalytic experiments, and in vivo transient overexpression demonstrated that EsbAS1 and EsCAS1 catalyze the formation of the triterpene skeleton β-amyrin and sterol precursor cycloartenol exclusively in the cytoplasm, enhancing and inhibiting the in vivo biosynthesis of oleanane-type saponins, respectively. Results from site-directed mutagenesis and molecular docking indicated that W-WY and Y-WH triplets characterized the active sites of EsbAS1 and EsCAS1, respectively. GUS (β-glucuronidase) staining and electrophoretic mobility shift assay (EMSA) experiments on the promoter region revealed that various colored light quality, DNA methylation, and five transcription factors (EsNAC047, EsNAC098, EsWRKY40, EsMYB4, and EsERF66) regulated the expression of EsbAS1 and EsCAS1. This study provides preliminary insights into the molecular mechanisms by which EsbAS1 and EsCAS1 regulate saponin synthesis in E. senticosus.

Cell expansion in petals plays a crucial role in flower opening and final size in rose (Rosa hybrida), which largely determines its market value. While cell expansion is known to be closely associated with gibberellins (GAs), the underlying molecular mechanism remains elusive. Here, we measured the levels of GAs during flower opening and demonstrated that GA₃ treatment significantly increases petal size. Moreover, we identified RhMYB70, an R2R3 MYB transcription factor, whose expression was inhibited by GA₃ treatment. RhMYB70 silencing resulted in larger petals and petal cell size than those of TRV control. Through transcriptome analysis and biochemical identification, RhMYB70 could directly bind to the promoter of the cellulose synthase gene RhCESA8 and repress its transcription, thereby resulting in decreased cellulose content of petals and final size. In addition, we also identified the GA biosynthesis gene RhGA3ox3 as an RhMYB70 target and demonstrated that RhMYB70 directly binds to and inhibits the promoter activity of RhGA3ox3, leading to decreased cellulose content of petals and petal size. Besides, knocking down RhMYB70 expression not only resulted in increasing GA₁ and GA₃ levels in petals compared to TRV but also elevated cellulose content. Together, our findings reveal that the feedback regulation of GAs and RhMYB70 signaling fine-tunes cell expansion and petal size by modulating cellulose content of rose petals, providing genetic targets for improving rose flower quality.

Cultivated strawberry (Fragaria × ananassa) is a kind of Rosaceae fruit crops grown worldwide. It is popularly consumed for its attractive color, juicy flesh, and nutrient content. The rich anthocyanin in strawberry fruits is responsible for its coloration. Anthocyanins are polyphenolic compounds, belonging to the four types of natural plant pigments. As important antioxidant secondary metabolites, anthocyanins substantially affect the internal quality and nutritional value of strawberry fruits. Here, we summarize the molecular mechanism underlying anthocyanin accumulation in strawberry fruits and discuss the ways to increase the content of anthocyanins in order to provide theoretical support for improving the color of strawberry fruits and enhance its commercial value by molecular biology methods.

Downy mildew is a major disease that significantly impacts the yield and quality of Brassica rapa. While histone deacetylase (HDAC) family members are implicated in stress responses, their role in regulating downy mildew resistance in B. rapa remains unclear. Herein, we treated the susceptible B. rapa line R32 with Trichostatin A (TSA), a potent HDAC inhibitor. Notably, TSA application significantly enhanced the susceptibility of B. rapa seedlings to downy mildew infection, demonstrating that HDAC plays a crucial role in mediating resistance against this pathogen. Subsequently, we conducted phylogenetic analysis of HDAC family members and performed high-throughput sequencing to assess HDAC gene expression patterns in the resistant (R31) and susceptible (R32) lines following downy mildew inoculation. Notably, the expression of BrHDA6 was significantly higher in the resistant line R31 compared to the susceptible line R32, suggesting its potential role in disease resistance. Using a genetic transformation system, we generated stable transgenic B. rapa plants overexpressing or silenced for BrHDA6. Inoculation with the downy mildew pathogen revealed that BrHDA6 positively regulates disease resistance. Modification omics and parallel reaction monitoring analysis demonstrated that BrHDA6 directly reduces the acetylation level of sulphotransferase 12 (BrSOT12), which likely enhances sulfotransferase activity, consequently boosting salicylic acid production during downy mildew infection. Interaction between BrHDA6 and BrSOT12 was further validated through yeast two-hybrid and dual-luciferase assays. Our study reveals that BrHDA6 confers downy mildew resistance in B. rapa through nonhistone protein deacetylation of BrSOT12, uncovering a novel regulatory mechanism in plant-pathogen interactions.

Interspecific interactions including plant-plant, plant-microbe, and plant-insect are the important elements to drive the positive plant-soil feedback for maintaining ecosystem stability in biodiversity ecosystems. Yet, the role of diversified foliar pathogens in biodiversity system in influencing the plant-soil feedback (PSF) has often been underestimated. Here, we assessed the effects of foliar Alternaria panax pathogenicity diversity from agroforestry system on PSF and rhizosphere microbial community. We show that a moderate intensity of foliar pathogen infection by A. panax could activate jasmonic acid (JA)-mediated defense from shoots to roots. This activation enhanced the synthesis and secretion of 2-aminoethanesulfonic acid into the rhizosphere for a disease-suppressive rhizo-microbiota assembly, contributing to positive PSF. However, excessive foliar pathogen infection allocated JA-mediated defense only in leaf and disrupted this rhizomicrobial enrichment, resulting negative PSF. This study enhances the understanding of the ecological roles of foliar pathogen within agroforestry systems and provides an insight into agricultural sustainability.

Melon (Cucumis melo L.) is a fruit crop in the world; fruit size and fruit shape are major traits for melon quality. Fruit length is a crucial indicator affecting fruit size and shape, but few genes regulating this trait have been identified. Here, we identified the transcription factor CmFUL1 (FRUITFULL) as a candidate for regulating fruit length using genome-wide association analysis (GWAS) and phylogenetic analysis. CmFUL1 is mainly expressed during flower and ovary development by tissue-specific expression. Transcriptional analysis revealed that CmFUL1 expression levels exhibited a negative correlation with fruit length across diverse melon germplasm. Furthermore, functional characterization demonstrated that CmFUL1 acts as a negative regulator of fruit elongation, CR-Cmful1 mutants generated by CRISPR-Cas9 showing enhanced longitudinal fruits. This repressive role was evolutionarily conserved, as heterologous overexpression of CmFUL1 in tomato consistently inhibited fruit elongation. Collectively, the results suggested that CmFUL1 is a candidate gene involved in regulating fruit length in melon, and provided genetic resources for molecular breeding of melon.

Geraniol contributes significantly to the floral scent of herbaceous peony (Paeonia lactiflora) and is abundant in fragrant cultivars. However, the regulatory mechanism of geraniol biosynthesis in herbaceous peony remains unclear. In this study, we identified a transcriptional regulatory complex (PlMYB73-PlMYB70-PlMYB108) that cooperatively regulated geraniol biosynthesis in herbaceous peony. The three MYB members were identified through correlation analysis between geraniol content and gene expression profiles in 17 herbaceous peony cultivars. Transient overexpression and gene silencing experiments revealed that PlMYB73, PlMYB108, and PlMYB70 positively regulated PlTPS1 expression and geraniol accumulation. PlMYB108 and PlMYB70 directly upregulate PlTPS1 by binding to the TAACCA and CAACTG motifs, respectively, as demonstrated by yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays. Although PlMYB73 did not directly bind to the PlTPS1 promoter, yeast two-hybrid, bimolecular fluorescence complementation, luciferase complementation imaging, and dual-luciferase assays revealed its interaction with PlMYB70 in the nucleus, resulting in synergistic activation of PlTPS1. PlMYB108 was also found to interact with PlMYB70. The three MYB transcription factors formed the PlMYB73-PlMYB70-PlMYB108 complex. Gene co-overexpression and co-silencing experiments demonstrated that the complex significantly enhanced geraniol biosynthesis. In conclusion, our research provides novel insights into the molecular mechanism by which transcription factors cooperatively regulate geraniol biosynthesis.

The extensive accumulation of genetic, genomic, expression, and breeding data on Prunus species often results in valuable information being lost or difficult to access for breeding purposes. We report a recent effort to increase curation on Prunus data in the Genome Database for Rosaceae (GDR, rosaceae.org) and a case study that explores 25 years of curated data (from 1998 to 2023) to uncover the genetic architecture of key traits in Prunus species, provide actionable insights for breeding, and encourage the use of shared molecular data across Prunus species. The curated data includes 177 genetic maps, primarily for almond (19), apricot (21), peach (52), and sweet cherry (46). A total of 28 971 trait-associated loci were reported, with 72.4% derived from genome-wide association studies, 18.7% from quantitative trait loci (QTL), and 8.9% from Mendelian trait loci. Notably, 76.4% of these loci are associated with morphological and quality traits, reflecting breeders’ focus on consumer preferences. We identified 16 potential QTL hotspots linked to key traits such as morphology, phenology, fruit quality, and disease resistance. Additionally, we identified 17 high-priority syntenic regions among peach, sweet cherry, and almond. The colocalized markers and genes within the QTL hotspots and syntenic regions offer a valuable resource for tool development for Prunus breeding, especially for complex polyploid genomes and lesser studied species with limited genetic and genomic data.

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