BMC Plant Biology最新文献

{"title":"Genetic diversity and genome-wide associations for frost survival in sorghum.","authors":"Natalja Kravcov, Luisa Neitzert, Rod Snowdon, Steffen Windpassinger","doi":"10.1186/s12870-025-07014-7","DOIUrl":"https://doi.org/10.1186/s12870-025-07014-7","url":null,"abstract":"<p><strong>Background: </strong>The ability to withstand periods of light frost during juvenile development is an important adaptive trait for sorghum (Sorghum bicolor L. Moench) production in high-latitude temperate areas. Frost tolerance would allow for earlier sowing and prolongation of growing season and maturity, thereby increasing yield potential. Using a broad diversity set (n = 285), a field cold emergence trial and two semi-controlled frost survival experiments were conducted to investigate the phenotypic diversity and genetic architecture of frost survival traits.</p><p><strong>Results: </strong>The results show high phenotypic diversity for frost survival, including superior genotypes combining high frost tolerance and cold emergence levels via quantitative trait inheritance. Tolerance to temperatures above and below 0 °C was not correlated, suggesting separate genetic control. The found QTL do not overlap for the traits of frost survival and plant emergence under cold sowing conditions. Genome-wide association studies revealed four significant associations for frost survival, where the QTLs are located on chromosomes Sb02, Sb07, and Sb08. For the trait of emergence under cold sowing conditions, a total of 12 QTLs were found on chromosomes Sb01, Sb03, Sb04, Sb05, and Sb06.</p><p><strong>Conclusion: </strong>A good overview regarding the suitability of the tested genotypes for early sowing was obtained due to the large diversity investigated in this study, with surprisingly high survival rates of numerous genotypes after frost stress. These results will contribute to the breeding of cultivars with improved cold and frost tolerance, facilitating better adaptation for production in high-latitude temperate areas, as well as earlier sowing to avoid summer drought.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"966"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the role of brassinosteroid signaling genes and their promoters in Arabidopsis revealed regulatory mechanisms in plant development and responses to different abiotic stresses.","authors":"Sunny Ahmar, Muhammad Sohaib Shafique, Marcin Rapacz, Ewa Pociecha","doi":"10.1186/s12870-025-06960-6","DOIUrl":"https://doi.org/10.1186/s12870-025-06960-6","url":null,"abstract":"<p><p>Brassinosteroids (BRs) are essential plant steroid phytohormones that regulate a wide range of developmental processes and mediate plant responses to various biotic and abiotic stresses. BR signaling regulators have significant potential to optimize plant architecture and enhance resilience to environmental stress. Although the BR signaling pathway is well-characterized in the dicot model species Arabidopsis (Arabidopsis thaliana), our knowledge of this pathway at the transcriptional level remains limited and requires further investigation. Moreover, the functional roles of several other conserved genes involved in the BR signaling pathway in Arabidopsis are not yet fully understood. Therefore, the present study was designed to conduct detailed and comprehensive analysis of BR signaling genes, promoter regions, and their encoded proteins in Arabidopsis. A bibliometric approach was used to compile a list of potential BR-signalling genes. A total of 41 BR signaling genes and their promoter sequences were selected for comprehensive silico analyses, including gene structure visualization, characterization, phylogenetic evolution, identification of cis-regulatory elements, and prediction of different transcription factor binding sites (TFbs) within 1.5 kb upstream of the promoter sequences in Arabidopsis. The expression patterns of these 41 BR signaling genes were examined in various plant organs and under different abiotic and hormonal stress conditions. Quantitative PCR (qPCR) was performed to validate the expression profiles of several BR signaling genes under osmotic stress (polyethylene glycol (PEG)-induced) and salt stress. In addition, protein-protein interactions (PPI) encoded by BR signaling genes were predicted in Arabidopsis. These analyses identified different types and frequencies of cis-elements and TFbs associated with plant growth and stress responses. Overall, this study provides valuable insights into the regulatory mechanisms underlying the coordinated expression of BR signaling genes in Arabidopsis, with potential implications for both monocots and dicots.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"970"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DBA-ViNet: an effective deep learning framework for fruit disease detection and classification using explainable AI.","authors":"Saravanan Srinivasan, Lalitha Somasundharam, Sukumar Rajendran, Virendra Pal Singh, Sandeep Kumar Mathivanan, Usha Moorthy","doi":"10.1186/s12870-025-07015-6","DOIUrl":"https://doi.org/10.1186/s12870-025-07015-6","url":null,"abstract":"<p><strong>Objective: </strong>The primary aim of this research is to develop an effective and robust model for identifying and classifying diseases in general fruits, particularly apples, guavas, mangoes, pomegranates, and oranges, utilizing computer vision techniques.</p><p><strong>Material: </strong>An open-source collection of fruit disease images, comprising both diseased and healthy samples from the first five fruit types, was used in this study. The data was split into 70% training, 15% validation, and 15% testing. A 5-fold cross-validation was used to maintain the generalizability and stability of the model's performance.</p><p><strong>Models: </strong>For performance comparisons of these models on the dataset, we benchmarked state-of-the-art pre-trained convolutional neural network (ConvNet) models, including Swin Transformer (ST), EfficientNetV2, ConvNeXt, YOLOv8, and MobileNetV3. A new model, the Dual-Branch Attention-Guided Vision Network (DBA-ViNet), was introduced. A hybrid with two branches of DBA-ViNet can efficiently integrate global and local features for improved disease identification accuracy. Grad-CAM was used to visualize the regions that contributed to each prediction, helping to interpret the model. These heatmaps verified that DBA-ViNet can correctly direct its attention to disease-specific symptoms, thereby increasing trust and transparency in the classification results.</p><p><strong>Results: </strong>The proposed DBA-ViNet achieved a high testing classification accuracy of 99.51%, specificity of 99.42%, recall of 99.61%, precision of 99.30% and F1 score of 99.45% outperforming baseline models in all evaluation metrics. While the improvements were consistent, statistical significance testing was not performed and will be explored in future work.</p><p><strong>Conclusion: </strong>These results confirm the effectiveness of the proposed DBA-ViNet architecture in fruit disease detection, suggesting that incorporating both global and local feature extraction into the design of the double-branch attention mechanism for classification can achieve high accuracy and reliability. It is potentially practical in smart agriculture and the automated crop health monitoring system.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"965"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prohexadione calcium and KH₂PO₄ synergy optimizes pod pepper plant architecture for mechanized harvesting and boosts yield and fruit quality.","authors":"Yongqi Geng, Ke Xia, Xiangda Song, Pu Yan, Xueying He, Guoxiu Wu, Yang Li, Yanman Li, Fan Wang, Wenyue Li, Dandan Cui, Shengli Li","doi":"10.1186/s12870-025-06979-9","DOIUrl":"https://doi.org/10.1186/s12870-025-06979-9","url":null,"abstract":"<p><p>Labor shortages and rising high labor costs are primary drivers of increased production costs in pod pepper cultivation. While mechanization represents a viable solution, current incompatibility between agronomic practices and agricultural machinery constrains its efficiency. This underscores the critical need for plant architecture regulation technologies to enable effective mechanized production. This study evaluated the effects of foliar spraying of plant growth regulator prohexadione calcium (ProCa) combined with different substances on the plant architecture, yield and quality of pod peppers. Five treatments were set up in the experiment: (1) ProCa, (2) ProCa + KH₂PO₄ (ProCa + KDP), (3) ProCa + boron (ProCa + B), (4) ProCa + mepiquat chloride (ProCa + MC), (5) water (CK). The results demonstrated that all treatments significantly altered pod pepper plant architecture indices relative to CK. Specifically, treatments reduced plant height and width, while increasing branch number and decreasing branch angles, with ProCa + KDP treatment exhibiting the most pronounced effects. These effects led to a compact and multiple-branched architecture conductive to mechanical harvesting. Meanwhile, ProCa + KDP treatment enhanced root activity and leaf pigment content of pod pepper during initial and full fruit stages. All treatments except ProCa + B increased fruit dry matter accumulation. ProCa and ProCa + KDP evaluated fruit yield primarily through increased fruit number per plant and individual fruit dry weight. Furthermore, ProCa + KDP treatment significantly improved fruit quality parameters versus control, elevating soluble protein, vitamin C and capsaicin contents. These findings demonstrate that foliar application of ProCa + KDP represents a promising strategy for optimizing plant architecture to enhance mechanized production suitability while simultaneously boosting pod pepper yield and quality.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"967"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The response of Panax ginseng root microbial communities and metabolites to nitrogen addition.","authors":"Kexin Li, Mingming Wan, Mei Han, Limin Yang","doi":"10.1186/s12870-025-07031-6","DOIUrl":"https://doi.org/10.1186/s12870-025-07031-6","url":null,"abstract":"<p><strong>Background: </strong>Nitrogen availability plays a pivotal role in shaping the composition of root-associated microbial consortia in plants. Nevertheless, elucidating the mechanisms by which nitrogen availability regulates microbial populations and their metabolic activities across different root-associated ecological niches requires further investigation. This research employed an integrative approach combining microbiological approaches with non-targeted metabolomic analyses to examine nitrogen-mediated variations in microbial communities and metabolic processes within ginseng root systems. High-throughput sequencing alongside UPLC-MS/MS analytical platforms was utilized to conduct this multidimensional investigation.</p><p><strong>Results: </strong>Our findings reveal that ginseng treated with N1 exhibited significantly increased yield by 29.90% compared to N0 and by 38.05% compared to N2 (p < 0.05). Additionally, nitrogen application markedly reduced the diversity of microbial communities within various segments of the root system, including rhizosphere soil (RS), rhizoplane soil (TS), fibrous roots (F), and phloem (P). Concurrently, there was a shift in bacterial communities from oligotrophic to eutrophic groups, with specific enrichment of groups such as Rhodanobacter and Burkholderia-Caballeronia-Paraburkholderia, which play crucial roles in the nitrogen cycling process. Metabolomic profiling revealed substantial modifications in soil metabolite profiles under nitrogen treatment, with marked alterations detected across 11 critical biochemical pathways encompassing plant-derived secondary metabolite biosynthesis and environmental microbial metabolic processes. Correlation analysis further indicated that the yield of ginseng and total ginsenoside content in F consistently varied in conjunction with soil nitrate nitrogen (NO₃⁻-N) content in the RS. Additionally, m-cresol was found to play a pivotal role in inhibiting the pathogenic fungus Alternaria, actively responding to pH fluctuations and promoting the synthesis of total ginsenosides in ginseng.</p><p><strong>Conclusion: </strong>These insights elucidate the complex interplay between nitrogen levels and both microbial and metabolomic dynamics, providing a foundational understanding for the strategic manipulation of microbial communities to enhance the sustainability of ginseng agriculture.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"969"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytochemical profile and antioxidant activity of Dracocephalum kotschyi boiss. affected by environmental conditions of cultivation regions.","authors":"Sahar Zamani, Davood Bakhshi, Mohammad-Taghi Ebadi, Amir Sahraroo","doi":"10.1186/s12870-025-06949-1","DOIUrl":"https://doi.org/10.1186/s12870-025-06949-1","url":null,"abstract":"","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"968"},"PeriodicalIF":4.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multivariate assessment of morpho-biochemical and bioactive diversity in Syzygium cumini (L.) Skeels for the selection of superior genotype and breeding applications.","authors":"Ajay Kumar, Kanhaiya Singh, Jai Prakash, Amit Kumar Goswami, Vishaw Bandhu Patel, Aditya Dnyaneshwar Ingole, Bhupendra Sagore, Gyan Prakash Mishra, Virendra Singh Rana, Rakesh Bhardwaj, Amit Kumar Singh","doi":"10.1186/s12870-025-06977-x","DOIUrl":"https://doi.org/10.1186/s12870-025-06977-x","url":null,"abstract":"<p><p>BACKGROUND JAMUN: [Syzygium cumini (L.) Skeels] is an underutilized fruit crop in India, despite having numerous medicinal and nutritional benefits. Although the Indian subcontinent harbours a vast natural population of Jamun, limited knowledge exists regarding superior genotypes. This study evaluates the diversity among Jamun genotypes using morpho-biochemical and bioactive traits to facilitate superior genotype selection and commercial breeding applications. RESULTS: Twenty-seven characteristics were studied to identify superior genotypes from a seedling-origin Jamun population. Significant variation was recorded in fruit and seed-related traits. The pulp-to-seed ratio exhibited the highest variation. Predominant fruit shape was oblong, with variation in fruit stalk end, fruit color and pulp color. Biochemical traits, such as TSS, TSS: acid ratio, total sugar and non-reducing sugars, showed significant variability. Similarly, substantial variation was observed in bioactive traits, including ascorbic acid, total phenolic content, total flavonoid content and antioxidant activity. Genotypes PCJ-9 and PCJ-17 exhibited higher fruit weight, pulp weight, pulp content, pulp-to-seed ratio, TSS, vitamin-C, with lower phenolic content and medium values of total flavonoid and antioxidant activity. Six genotypes (PCJ-15, PCJ-30, PCJ-22, PCJ-3, PCJ-1 and PCJ-16) showed high TPC, TFC, antioxidant and seed content, making them suitable for breeding bioactive-rich cultivars and functional food development. Pearson correlation analysis evaluated a significant positive correlation between fruit weight and pulp weight, fruit size and fruit width. PCA analysis identified PC1 and PC2 as the most important components. Heatmap clustering analysis emphasized the relationship between fruit morph-biochemical and bioactive characteristics. CONCLUSIONS: The presented study offers a novel and comprehensive assessment of diversity among seedling-origin Jamun genotypes based on morpho-biochemical and bioactive traits. The identified superior genotypes present promising candidates for cultivar development and direct cultivation, contributing to improved Jamun productivity and functional food value.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"962"},"PeriodicalIF":4.3,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ceramides play a significant role in the response of Pogostemon cablin to bacterial wilt by regulating the ABA pathway.","authors":"Jian Li, Dan-Xia Wu, He-Nan Bao, Ke-Yu Li, Ming-Yong Zhang, Yun-Hao Sun, Kuai-Fei Xia","doi":"10.1186/s12870-025-07009-4","DOIUrl":"https://doi.org/10.1186/s12870-025-07009-4","url":null,"abstract":"<p><p>As a strategic resource for both medicine and essential oil, the healthy development of the Pogostemon cablin industry is crucial for the traditional medicine and fragrance sectors. Bacterial wilt represents one of the most significant threats to patchouli cultivation; however, the molecular mechanisms underlying P. cablin's response to bacterial wilt remain unexplored. Here, we conducted transcriptome and metabolome analyses, revealing an increase in the expression of genes associated with lipid pathways and a corresponding rise in the concentration of lipid metabolites in P. cablin following infection by the bacterial wilt pathogen SY1. Further lipidomics analysis demonstrated a significant upregulation of ceramide levels due to SY1 infection. Additionally, hormone analysis indicated that SY1 significantly induced an increase in abscisic acid (ABA) concentration, accompanied by the upregulation of genes involved in the ABA synthesis pathway and its downstream signaling pathways. Furthermore, we treated P. cablin seedlings with the ceramide synthase inhibitor FB1, which significantly reduced ceramide concentration in P. cablin. FB1 treatment also inhibited the expression of ABA-synthesizing genes, leading to a notable decrease in ABA concentration and downstream pathway genes. These data indicate that ceramides and ABA may participate in P. cablin's response to SY1.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"964"},"PeriodicalIF":4.3,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in morphological characteristics, photosynthetic capacity and Chloroplast genomes reveal molecular markers to distinguish Angelica sinensis, A. acutiloba and A. gigas.","authors":"Xia Li, Weihua Zhao, Yan Zhao, Mengfei Li","doi":"10.1186/s12870-025-06987-9","DOIUrl":"https://doi.org/10.1186/s12870-025-06987-9","url":null,"abstract":"<p><strong>Background: </strong>The dried roots of Angelica sinensis, A. acutiloba, and A. gigas in the Angelica L. have been used as the same traditional medicines for nourishing the blood, regulating female menstrual disorders, relieving pains, and relaxing bowels for thousands of years. Although significant differences in geographical distribution, morphological characteristics, chemical components, and gene sizes have been observed in previous studies, they were limited to distinguishing the three species through an efficient, unique, and accurate approach.</p><p><strong>Results: </strong>In this study, morphological characteristics, photosynthetic capacity, and chloroplast (CP) genomes of the three species were performed. There were obvious differences in morphological characteristics, such as leaf margin irregularly coarse-cuspidate-serrate of A. sinensis, leaf margin irregularly acute-serrate of A. acutiloba, and leaf margin irregularly coarse-toothed apex acute of A. gigas. There was a higher photosynthetic capacity of A. gigas and A. acutiloba than A. sinensis, which was consistent with root biomass. The length of CP genomes of A. sinensis, A. acutiloba and A. gigas were 141,869, 147,057 and 147,050 bp with encoding 124,128 and 128 genes, respectively. There were 3 genes (i.e., psbA, ndhB, and ycf15) affecting the expansion and contraction of inverted repeat (IR), and 7 genes (i.e., matK, psbN, ccsA, rps8, ndhF, ycf1, and ycf2) in the gene regions presenting notably high nucleotide diversity.</p><p><strong>Conclusion: </strong>The distinct phenotypes of leaf shape and stem color can be used for species delimitation of the three species. The 3 genes (i.e., psbA, ndhB, and ycf15) can be used to distinguish A. sinensis from A. acutiloba and A. gigas using the agarose gel electrophoresis and the base sequence. The 7 genes (i.e., matK, psbN, ccsA, rps8, ndhF, ycf1, and ycf2) can accurately distinguish the three species using the base sequence. We establish a rapid and reliable multi-level identification system for the three Angelica species. This approach addresses critical challenges in medicinal plant taxonomy and supports quality control in herbal product industries.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"961"},"PeriodicalIF":4.3,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on the dynamics of fruits color related genes and metabolites during the fruit development of Zanthoxylum bungeanum 'Hanyuan'.","authors":"Yafang Zhai, Kai Wang, Jiaojiao Wu, Wenkai Hui, Shuaijie Lu, Jing Qiu, Han Wu, Wei Gong, Jingyan Wang","doi":"10.1186/s12870-025-06962-4","DOIUrl":"https://doi.org/10.1186/s12870-025-06962-4","url":null,"abstract":"<p><strong>Background: </strong>Anthocyanins play a crucial role in determining the coloration of plant fruits and are essential for enhancing their economic traits. However, studies on anthocyanin biosynthesis in Zanthoxylum bungeanum 'Hanyuan' fruit have yet to be reported.</p><p><strong>Results: </strong>In this study, the patterns of anthocyanin synthesis in fruit through phenotypic analysis and total anthocyanin measurements across 13 development stages were traced. The results indicated that the pericarp of Z. bungeanum 'Hanyuan' exhibited a gradual transition in color from light red to dark red between 64 d AF and 100 d AF, with the highest total anthocyanin content recorded at 64 d AF. Based on this conclusion, five key stages were selected for the transcriptome and anthocyanin-targeted metabolome analysis to further elucidate the molecular mechanisms underlying anthocyanin synthesis. Metabolomic analysis identified eight metabolites that influence the formation of red color in fruit: Cyanidin-3-O-rutinoside, cyanidin-3-O-xyloside, naringenin, peonidin-3-O-rutinoside, cyanidin-3-O-(6-O-malonyl-beta-D-glucoside), petunidin-3-O-sambubioside, petunidin-3-O-(6-O-p-coumaroyl)-glucoside, and delphinidin-3-O-(6-O-malonyl-beta-D-glucoside). These metabolites exhibited the highest concentrations at 64 d AF, 86 d AF, and 100 d AF. Transcriptome analysis, WGCNA analysis, and correlation analysis indicate that ZbFLS11 and ZbCYP98A32 positively regulate the biosynthesis of cyanidin-3-O-xyloside, petunidin-3-O-(6-O-p-coumaroyl) glucoside, and petunidin-3-O-sambubioside. Zb4CL1 exhibits a positive correlation with petunidin-3-O-(6-O-p-coumaroyl)-glucoside and naringenin. Additionally, the upregulation of five genes (ZbCHS1, ZbCHS2, ZbCHS3, ZbCHS4, and ZbCHS5), ZbC4H2, and ZbC4H3 expressions at 64 d AF and 86 d AF was associated with the accumulation of delphinidin-3-O-(6-O-malonyl-beta-D-glucoside) during the development stages of Z. bungeanum 'Hanyuan' fruit. Furthermore, it was found that MYB113 interact with the structural genes Zb4CL1, ZbCYP98A32, and ZbFLS11, thereby regulating the biosynthesis of petunidin-3-O-(6-O-p-coumaroyl)-glucoside. Additionally, bHLH6 exhibits a positive regulatory relationship with the five genes (ZbCHS1, ZbCHS2, ZbCHS3, ZbCHS4, and ZbCHS5), ZbC4H2, and ZbC4H3, which influence the biosynthesis of delphinidin-3-O-(6-O-malonyl-beta-D-glucoside).</p><p><strong>Conclusion: </strong>In summary, the findings of this study elucidate the molecular mechanisms underlying color development in Z. bungeanum 'Hanyuan' fruit across various development stages. This research offers valuable insights for future investigations into the intricate molecular network governing anthocyanin biosynthesis in Z. bungeanum 'Hanyuan' fruit.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"960"},"PeriodicalIF":4.3,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}