Leaf Buds Research Articles

Revealing the dynamic changes of metabolites and molecular mechanisms of chlorogenic acid accumulation during the leaf development of Vaccinium dunalianum based on multi-omic analyses

Vaccinium dunalianum, a medicinal plant, is utilized for Quezui Tea production from its leaf buds and young leaves. Despite prior research on V. dunalianum revealing several medicinal compounds, the comprehensive variations in metabolites during its growth and development, along with the molecular mechanisms underlying high chlorogenic acid (CGA) yield, remain unclear. Through a joint analysis of transcriptomics and proteomics, our study first identified 15 key structural genes and 3 transcription factors influencing CGA biosynthesis in V. dunalianum, offering new evidence to understand its regulatory network. Furthermore, non-targeted metabolomics analysis provides the first extensive report on the metabolic profile of V. dunalianum, furnishing a valuable dataset for deeper exploration of its nutritional and medicinal value, and the development of a quality evaluation system for its product Quezui Tea. This study offers the most comprehensive molecular information on V. dunalianum, marking a significant step toward understanding and enhancing the plant’s potential for medicinal and nutritional applications. Additionally, this study also reveals V. dunalianum holds promise as a natural antioxidant source for functional foods, providing data support for network pharmacology.

First detection of fungal diversity associated with Prunus salicina Lindl malformation syndrome

The Chinese deciduous fruit Prunus salicina Lindl is loved by people because of its distinctive flavor and significant industrial worth. This study presents the first report of abnormal leaf bud in Prunus salicina Lindl. Malformation of Prunus salicina Lindl leaf buds leads to abnormal development and growth, causing deformities and a decrease in fruit yield. Identifying the underlying causes and causative pathogens is essential for effective disease management. In this experiment, we observed the Malformation Syndrome in Prunus salicina Lindl and used the internal transcribed spacer (ITS) to compare fungal diversity between malformed and healthy leaf buds. These results show a higher level of fungal diversity in diseased leaf buds. Alternaria, Curvibasidium, Symmetrospora, Fonsecazyma, and other genera among the identified fungi are suspected to induce the malformations. Potential contributors to these malformations include Endophyte-plant_Pathogen and Plant_pathogen-Undefined_saprotroph. These findings provide valuable insights for further research on the etiology of plum bud diseases, identifying potential pathogens, and formulating control strategies.

Transcriptome Analysis of Multiple Plant Parts in the Woody Oil Tree Camellia drupifera Loureiro

Camellia drupifera is mainly used in forestry for its high-value industrial products; however, limited information is available on its transcriptome. This study aimed to construct a full-length transcriptome sequence based on the PacBio sequencing platform for various plant parts of C. drupifera, including flower buds, leaves, leaf buds, branches, the pericarp, and seed kernels. The transcriptomes were annotated with 23,207 genes, with 58 subgroups in the GO classification. The KEGG database revealed 10,407 genes involved in the metabolic pathway analysis, with 68,192 coding sequences, 3352 TF families, 48,541 SSRs, 1421 IncRNAs, and 2625 variable shears predicted. The transcriptomes of different parts were analyzed and compared. The majority of differentially expressed genes (DEGs) were found between the pericarp and seed kernels, followed by leaves and the pericarp with 5662 DEGs, and flower buds and leaf buds with 1616 DEGs. GO and KEGG enrichment analyses showed that KEGG differential genes were significant in microbial metabolism, carbon metabolism, and other functions. The data annotation and analysis of the full-length transcriptome and the comparative analysis between different plant parts provided a theoretical basis for studying gene function, metabolic pathway regulation, and gene expression analysis in KEGG.

The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis.

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II BBX family member, BBX13/COL15, as a negative regulator of flowering under long-day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers, showing a similar spatial expression pattern to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT and negatively regulates their expression. BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, where CO also binds. Chromatin immunoprecipitation data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation of FT. Together, these findings suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating the binding of CO on the FT promoter.

Expression profiling of BSD domain-containing genes in apricot during different developmental stages

Plant transcription factors are evolutionarily conserved proteins that play an important role in the transcriptional regulation of gene expression by binding to their specific DNA sequences. BSD (mammalian BTF2-like transcription factors, synapse-associated proteins, and DOS2-like proteins) transcription factors are conserved in various species, from protozoa to humans, and are characterized by a typical BSD domain. However, little information is available about their possible roles in plant growth and development, and to date, members of this transcription factor family have not been systematically identified and analyzed in apricot. In this study, two BSD domain-encoding genes were identified in the apricot genome. Expression profile analysis by RT-qPCR revealed that both genes participate in different developmental stages of three different organs in apricot. PaBSD1 was expressed higher than PaBSD2 only in the stamen. Moreover, PaBSD2 was higher expressed than PaBSD1 in four different fruit stages, young leaf, leaf bud, sepal and petal. This study reveals the critical roles of BSD transcription factors in apricot development, with PaBSD1 showing higher expression in stamen and PaBSD2 in various fruit stages and leaf tissues. These findings provide a foundation for future functional studies and apricot breeding programs.

The effect of mycorrhiza on the growth of Ylang-Ylang seedlings

Abstract Ylang-ylang (Cananga odorata forma genuina Steenis) is a plant with high economic value and many benefits. Mycorrhizal application is necessary to obtain a quality mother plant. Therefore, a study on the mycorrhiza effect on ylang-ylang growth was needed, especially in the seedling stage. This study aimed to analyse the impact of mycorrhiza infection on the development of ylang-ylang seedlings. The method used in this study was the isolation of Claroideoglomus etunicatum spores. Ten of each spore was inoculated onto the sterilised roots (using 5% Natrium hypochlorite) of the three-month-old ylang-ylang seedlings and then planted on zeolite media and soil in a 6 x 10 cm pottery, which was then transferred to each pot 13 cm in diameter and 16 cm in height. For comparison, zeolite and soil media were used without the addition of mycorrhiza. The result of this study showed that the application of mycorrhizae using soil media had the highest increase in height (4.19 cm), diameter (0.72 mm), number of leaves (2.6 strands), and number of buds (0.8 leaf buds) compared to other treatments.

Molecular Characterization and Pathogenicity of Groundnut Bud Necrosis Virus (Orthotospovirus arachinecrosis) Inducing Necrosis in Black Gram

Orthotospovirus arachinecrosis commonly known as Groundnut bud necrosis virus (GBNV), is the causal agent for necrosis disease in black gram. GBNV is the second most important challenge to black gram production in major growing areas following yellow mosaic disease. Symptoms of necrosis disease of black gram include severe downward curling and twisting of leaf lamina, veinal necrosis, petiole necrosis, bud necrosis, and necrotic streaks on the stem. Infection at early growth stages of black gram leads to plant death, while surviving plants exhibited stunted growth with a significant reduction in pod yield. The GBNV-BG isolate was maintained in pure form on cowpea cv. C-152, resulted in chlorotic and necrotic local lesions on primary leaves at seven days post-inoculation. The pathogenicity of GBNV on black gram (LBG-645) was further confirmed by artificial sap inoculation. Amplification of the coat protein gene of GBNV was confirmed through RT-PCR using gene-specific primers, producing an amplicon of 800 bp. Sequence analysis of the coat protein gene revealed that the present study isolates OQ683310 and OR295403 shared sequence identity of 98.0 % and 99.3 % respectively at the nucleotide level, with other isolates in the NCBI database. The phylogenetic analysis of the coat protein gene revealed that the isolates under this study were closely linked with the GBNV tomato isolate from Tamil Nadu (MN718651 and MZ505083).

Probabilistic Bayesian Neural Networks for olive phenology prediction in precision agriculture

Plant phenology is the study of cyclical events in a plant life cycle such as leaf bud burst, flowering, and fruiting. In this article the problem of olive phenology prediction is addressed through the use of Deep Learning. Although Neural Networks have already been used in this area, to the best of our knowledge, this is the first implementation of Probabilistic Bayesian Neural Networks for olive phenology prediction. This architecture gives particular emphasis to estimating the model uncertainty, both aleatoric and epistemic. The Bayesian Inference method, more precisely the Variational Inference one, is compared with the Monte Carlo Dropout technique, which is known to be a less computationally intensive approximation of Variational Inference. For validation purposes, models performance is compared to the state-of-the-art results.

Design and Experiment of Ordinary Tea Profiling Harvesting Device Based on Light Detection and Ranging Perception

Due to the complex shape of the tea tree canopy and the large undulation of a tea garden terrain, the quality of fresh tea leaves harvested by existing tea harvesting machines is poor. This study proposed a tea canopy surface profiling method based on 2D LiDAR perception and investigated the extraction and fitting methods of canopy point clouds. Meanwhile, a tea profiling harvester prototype was developed and field tests were conducted. The tea profiling harvesting device adopted a scheme of sectional arrangement of multiple groups of profiling tea harvesting units, and each unit sensed the height information of its own bottom canopy area through 2D LiDAR. A cross-platform communication network was established, enabling point cloud fitting of tea plant surfaces and accurate estimation of cutter profiling height through the RANSAC algorithm. Additionally, a sensing control system with multiple execution units was developed using rapid control prototype technology. The results of field tests showed that the bud leaf integrity rate was 84.64%, the impurity rate was 5.94%, the missing collection rate was 0.30%, and the missing harvesting rate was 0.68%. Furthermore, 89.57% of the harvested tea could be processed into commercial tea, with 88.34% consisting of young tea shoots with one bud and three leaves or fewer. All of these results demonstrated that the proposed device effectively meets the technical standards for machine-harvested tea and the requirements of standard tea processing techniques. Moreover, compared to other commercial tea harvesters, the proposed tea profiling harvesting device demonstrated improved performance in harvesting fresh tea leaves.

Trinexapac-Ethyl Dose–Response Curve for Eucalyptus Growth and Hormonal Crosstalk Between Leaf and Shoot Apical Bud

Trinexapac-Ethyl Dose–Response Curve for Eucalyptus Growth and Hormonal Crosstalk Between Leaf and Shoot Apical Bud

Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface

The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.

Geographic conditions impact the relationship between plant phenology and phylogeny

Plant phenology is influenced by a combined effect of phylogeny and climate, although it is yet unclear how these two variables work together to change phenology. We synthesized 107 previously published studies to examine whether phenological changes were impacted by both phylogeny and climate changes in various geographical settings globally. Phenological observation data from 52,463 plant species at 71 sites worldwide revealed that 90 % of phenological records showed phylogenetic conservation. i.e., closely related species exhibited similar phenology. To explore the significant and non-significant phylogenetic conservation between plant phenophases, our dataset comprises 5,47,000 observation records from the four main phenophases (leaf bud, leaf, flower, and fruit). Three-dimensional geographical distribution (altitude, latitude, and longitude) data analysis revealed that plant phenology may exhibit phylogenetic signals at finer special scales (optimal environmental conditions) that vanish in high altitude and latitude regions. Additionally, climatic sensitivity analysis suggested that phylogenetic signals were associated with plant phenophases and were stronger in the regions of ideal temperature (7–18 °C) and photoperiod (10–14 h) and weaker in harsh climatic conditions. These results show that phylogenetic conservation in plant phenological traits is frequently influenced by the interaction of harsh climatic conditions and geographical ranges. This meta-analysis enhances our knowledge of predicting species responses over geographic gradients under varied climatic conditions.

Transcriptomic profiling and gene network analysis revealed regulatory mechanisms of bract development in Bougainvillea glabra

BackgroundBracts are important for ornamental plants, and their developmental regulation process is complex; however, relatively little research has been conducted on bracts. In this study, physiological, biochemical and morphological changes in Bougainvillea glabra leaves, leaf buds and bracts during seven developmental periods were systematically investigated. Moreover, transcriptomic data of B. glabra bracts were obtained using PacBio and Illumina sequencing technologies, and key genes regulating their development were screened.ResultsScanning electron microscopy revealed that the bracts develop via a process involving regression of hairs and a color change from green to white. Transcriptome sequencing revealed 79,130,973 bp of transcript sequences and 45,788 transcripts. Differential gene expression analysis revealed 50 expression patterns across seven developmental periods, with significant variability in transcription factors such as BgAP1, BgFULL, BgCMB1, BgSPL16, BgSPL8, BgDEFA, BgEIL1, and BgBH305. KEGG and GO analyses of growth and development showed the involvement of chlorophyll metabolism and hormone-related metabolic pathways. The chlorophyll metabolism genes included BgPORA, BgSGR, BgPPH, BgPAO and BgRCCR. The growth hormone and abscisic acid signaling pathways involved 44 and 23 homologous genes, and coexpression network analyses revealed that the screened genes BgAPRR5 and BgEXLA1 are involved in the regulation of bract development.ConclusionsThese findings improve the understanding of the molecular mechanism of plant bract development and provide important guidance for the molecular regulation and genetic improvement of the growth and development of ornamental plants, mainly ornamental bracts.

Orchard management factors affecting rates of bud damage to kiwifruit orchards

Although bird damage to fruit crops is well documented, bird damage to flower and leaf buds is relatively understudied. In Aotearoa/New Zealand, bird damage to kiwifruit (Actinidia deliciosa and Actinidia chinensis) buds has been reported to be widespread. However, the responsible bird species and rates of damage have not been investigated, nor is it known if orchard management such as the presence of shelterbelts, and management of swards (grass) between vines or characteristics of the surrounding landscape affect patterns of bud damage. We aimed to identify the bird species responsible for damage to kiwifruit buds, the extent of damage across orchards, and factors correlated with bud damage. A combination of bird surveys, trail cameras, and bud damage surveys were employed across 18 kiwifruit orchards in the Bay of Plenty, Aotearoa/New Zealand. House sparrows (Passer domesticus), chaffinches (Fringilla coelebs), and silvereyes (Zosterops lateralis) were identified as the most frequent species damaging buds. On average, 10% of buds were damaged, but rates of damage varied widely across orchards. Increasing availability of sward seeds was associated with increasing bird abundance but decreasing bud damage levels, potentially because seeds from sward vegetation offer an alternative food source. Shelterbelt volume, block management type (conventional vs organic), and the proportion of vegetation in the surrounding landscape also influenced bird abundance and damage. Understanding which management and environmental factors influence bird abundance and damage may benefit bird management in orchards, such as leaving swards unmown to increase sward seed availability and to reduce bird damage levels to kiwifruit buds.

Determining the Main Infection Courts in Sweet Cherry Trees of the Canker Pathogens Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata.

The major fungal canker pathogens causing branch dieback of sweet cherry trees in California include Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata. These pathogens have long been known to infect cherry trees mainly through pruning wounds. However, recent field observations revealed numerous shoots and fruiting spurs exhibiting dieback symptoms with no apparent pruning wounds or mechanical injuries. Accordingly, this study was conducted to assess the incidence of the three pathogens in symptomatic terminal shoots and dying fruiting spurs, in addition to the wood below pruning wounds in branches. Surveys were conducted in five sweet cherry orchards across three counties in California. We also investigated the possibility that leaf scars, bud scars, and wounds resulting from fruit picking could serve as infection courts for Cal. pulchella, Cyt. sorbicola, and E. lata by means of artificial inoculations in the field. Orchard surveys revealed that Cal. pulchella had the highest pathogen incidence below pruning wounds in branch samples, followed by Cyt. sorbicola and E. lata. Among terminal shoots with dieback symptoms and dying fruiting spurs, Cyt. sorbicola was the most prevalent, followed by Cal. pulchella. Results from field inoculations indicated that fruit-picking wounds could serve as important infection courts for Cal. pulchella, Cyt. sorbicola, and E. lata, with average pathogen recovery of 41.5, 63, and 36.2%, respectively. Results also indicated that leaf and bud scars could serve as an entry site for Cyt. sorbicola, although recovery was relatively low. The present study is the first to identify harvest-induced wounds on fruiting spurs of sweet cherry as an important infection court of Cal. pulchella, Cyt. sorbicola, and E. lata.

Establishment of an efficient regeneration system of ‘ZiKui’ tea with hypocotyl as explants

Zikui (Camellia sinensis cv. Zikui) is a recently discovered cultivar of local purple tea in Guizhou, China. It is a purple leaf bud mutation material of Meitan Taicha (Camellia sinensis cv. ‘Meitan-taicha’) ‘N61’ strain, which is an important local germplasm resource in Guizhou. It is also a model plant for the study of anthocyanins, but the limited germplasm resources and the limitation of traditional reproduction hinder its application. Here, an efficient regeneration system is established by using hypocotyl as explants for the first time. Different plant growth regulators (PGRs) are evaluated during different regeneration processes including callus and root induction. According to our findings, using the optimal disinfection conditions, the seed embryo contamination rate is 17.58%. Additionally, the mortality rate is 9.69%, while the survival rate is measured as 72.73%. Moreover, the highest germination rate of 93.64% is observed under MS + 2.40 mg/L GA3 medium conditions. The optimal callus induction rate is 95.19%, while the optimal adventitious bud differentiation rate is 20.74%, Medium with 1.6 mg/L IBA achieved 68.6% rooting of the adventitious shoots. The survival rate is more than 65% after 6 days growth in the cultivated matrix. In summary, our research aims to establish a regeneration system for Zikui tea plants and design a transformation system for tea plant tissue seedlings. This will enable transfer of the target gene and ultimately facilitate the cultivation of new tea varieties with unique characteristics.

Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers

Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5–9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.

Optimizing Efficiency of Tea Harvester Leaf-Collection Pipeline: Numerical Simulation and Experimental Validation

To address the challenges of missed and disorderly picking in tea harvesters, this study focused on the leaf-collection pipeline and utilized Fluent simulation 19.0 software. A single-factor test identified key parameters affecting airflow velocity. An orthogonal test evaluated the main pipe taper, number of branch pipes, and branch pipe outlet diameter, with average outlet wind speed and wind speed non-uniformity as indicators. The optimal parameters were a main pipe taper of 25.5 mm, 10 branch pipes, and an inner diameter of 17.10 mm for the outlet, resulting in 10.73 m/s average wind speed and 8.24% non-uniformity. Validation tests showed errors under 1%. Further optimization on the internal structure’s extension length led to 11.02 m/s average wind speed and 8.04% non-uniformity. Field experiments demonstrated a 3.40% stalk leakage rate and 90.36% bud leaf integrity rate; the optimized structure of the leaf-collecting pipeline significantly improved the uniformity of airflow and the picking efficiency. These findings offer valuable insights and practical benefits for enhancing the efficiency of tea harvesters.

Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Cucumber (Cucumis sativus L.): Identification, Evolution, Expression Profiles, and Function under Abiotic Stresses.

Cucumber (Cucumis sativus L.) is a globally prevalent and extensively cultivated vegetable whose yield is significantly influenced by various abiotic stresses, including drought, heat, and salinity. Transcription factors, such as zinc finger-homeodomain proteins (ZHDs), a plant-specific subgroup of Homeobox, play a crucial regulatory role in stress resistance. In this study, we identified 13 CsZHDs distributed across all six cucumber chromosomes except chromosome 7. Phylogenetic analysis classified these genes into five clades (ZHDI-IV and MIF) with different gene structures but similar conserved motifs. Collinearity analysis revealed that members of clades ZHD III, IV, and MIF experienced amplification through segmental duplication events. Additionally, a closer evolutionary relationship was observed between the ZHDs in Cucumis sativus (C. sativus) and Arabidopsis thaliana (A. thaliana) compared to Oryza sativa (O. sativa). Quantitative real-time PCR (qRT-PCR) analysis demonstrated the general expression of CsZHD genes across all tissues, with notable expression in leaf and flower buds. Moreover, most of the CsZHDs, particularly CsZHD9-11, exhibited varying responses to drought, heat, and salt stresses. Virus-induced gene silencing (VIGS) experiments highlighted the potential functions of CsZHD9 and CsZHD10, suggesting their positive regulation of stomatal movement and responsiveness to drought stress. In summary, these findings provide a valuable resource for future analysis of potential mechanisms underlying CsZHD genes in response to stresses.

Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.

Ginkgo (Ginkgo biloba L.) is one of the earliest extant species in seed plant phylogeny. Embryo development patterns can provide fundamental evidence for the origin, evolution, and adaptation of seeds. However, the architectural and morphological dynamics during embryogenesis in G. biloba remain elusive. Herein, we obtained over 2,200 visual slices from 3 stages of embryo development using micro-computed tomography imaging with improved staining methods. Based on 3-dimensional (3D) spatiotemporal pattern analysis, we found that a shoot apical meristem with 7 highly differentiated leaf primordia, including apical and axillary leaf buds, is present in mature Ginkgo embryos. 3D rendering from the front, top, and side views showed 2 separate transport systems of tracheids located in the hypocotyl and cotyledon, representing a unique pattern of embryogenesis. Furthermore, the morphological dynamic analysis of secretory cavities indicated their strong association with cotyledons during development. In addition, we identified genes GbLBD25a (lateral organ boundaries domain 25a), GbCESA2a (cellulose synthase 2a), GbMYB74c (myeloblastosis 74c), GbPIN2 (PIN-FORMED 2) associated with vascular development regulation, and GbWRKY1 (WRKYGOK 1), GbbHLH12a (basic helix-loop-helix 12a), and GbJAZ4 (jasmonate zim-domain 4) potentially involved in the formation of secretory cavities. Moreover, we found that flavonoid accumulation in mature embryos could enhance postgerminative growth and seedling establishment in harsh environments. Our 3D spatial reconstruction technique combined with multiomics analysis opens avenues for investigating developmental architecture and molecular mechanisms during embryogenesis and lays the foundation for evolutionary studies of embryo development and maturation.