BMC Plant Biology最新文献

{"title":"Biochemical and gene expression profiling of five pear species under drought stress conditions.","authors":"Lavin Babaei, M Mehdi Sharifani, Reza Darvishzadeh, Naser Abbaspour, Mashhid Henareh","doi":"10.1186/s12870-025-06408-x","DOIUrl":"10.1186/s12870-025-06408-x","url":null,"abstract":"<p><p>Drought is one of the crucial abiotic stresses which affects growth, development, and performance of pear trees. This research was performed to investigate responses of five pear species including Pyrus communis L., Pyrus boissieriana Bushe., Pyrus glabra Boiss., Pyrus syriaca Boiss., and Pyrus salicifolia Pall. to different levels of drought stress. The potted trees were irrigated with water volume of 100%, 60%, or 30% of field capacity (FC) during 90 days. Based on the visual observation, the plant growth was restricted by severe drought in all species. Malondialdehyde (MDA) and glycine betaine (GB) contents, as well as the ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and catalase (CAT) activities were indicated an uprising behavior under drought stress. Principal component analysis (PCA) analysis revealed P. glabra as tolerant and P. communis as sensitive to drought stress. The expression rates of stress-responsive transcription factors (TFs); WRKY29 and DREB6 and their responding genes, including LEA29 and Dehydrin1, were analyzed in the two differentially drought-responding pear species i.e., P. glabra and P. communis. The expression of the studied TFs was induced when both species were exposed to higher drought levels. The species P. glabra exhibited better osmoregulation, antioxidant response, and higher up-regulation of WRKY29, DREB6, LEA29 and Dehydrin1. In conclusion, among the studied pear species, P. glabra could best tolerate drought stress by boosting protective mechanisms.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"397"},"PeriodicalIF":4.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and evaluation of tamarind (Tamarindus indica L.) germplasm: implications for tree improvement strategies.","authors":"A K Singh, Vikas Yadav, V V Appa Rao, Daya Shankar Mishra, Lalu Prasad Yadav, K Gangadhara, Jagadish Rane, A Sahil, Prakashbhai Ravat, P Janani, Prashant Kaushik, Ali Khadivi, Yazgan Tunç","doi":"10.1186/s12870-025-06415-y","DOIUrl":"10.1186/s12870-025-06415-y","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Tamarind (Tamarindus indica L.; Fabaceae) a unique tree is valued not only for its fruits and timber but also for its shade, making it a popular avenue tree. It thrives in diverse climates and soils, particularly in semiarid regions, due to its deep root system, making it valuable in areas prone to water scarcity and high temperatures. It is now extensively grown in subtropical and semi-arid tropical regions of the world particularly common in India, Africa, and Southeast Asia. In this study, the morpho-physico-chemical variations of 30 tamarind genotypes were evaluated using multivariate analysis based on 28 variables which is essential for tree improvement.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;This study characterizes a collection of 30 tamarind genotypes based on a range of qualitative and quantitative traits to assess phenotypic diversity. The analysis revealed wide variation across most of the traits, indicating their potential for distinguishing germplasm diversity. High phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were observed for tree height (24.34 and 21.26), stem girth (26.63 and 23.72), tree spread E-W (23.50 and 21.68), tree spread N-S (27.46 and 24.38), pod yield kg/tree (29.98 and 27.56), pod length (25.29 and 24.51), pod breadth (22.08 and 21.92), pulp weight (30.49 and 28.58), and pod weight 31.03 and 29.74), which indicates these traits display high variation, suggesting significant potential for selection. High heritability coupled with high genetic advance were observed for the most of traits which were influenced by additive or fixable genetic variation. Path coefficient analysis revealed that traits, such as stem girth and tree spread showed direct effects on pod yield, while other characters contributed indirectly. Principal component analysis (PCA) indicated that PC-1 accounted for approximately 27.648% of the total variance, followed by PC-2 (18.250%), and PC-3 (15.835%), and hierarchical clustering uncovered crucial genetic components and distinct clusters, which can be considered for targeted breeding strategies. Cluster II emerged as the most divergent cluster, due to its the highest inter-cluster distances with other clusters and the highest intra-cluster distance.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The results demonstrate how varied germplasm might be used to improve tamarind cultivars. To overcome heterogeneity in desired features, a complete collection of 28 morphological descriptors is provided to characterize, evaluate, and identify tamarind genotypes. The results underscore the importance of phenotypic diversity for developing core collections with enhanced variability and for designing targeted tamarind tree breeding strategies. This study provides valuable insights for the improvement and conservation of tamarind germplasm, a valuable species with considerable potential for fruit production and other economic uses.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Clinical tri","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"396"},"PeriodicalIF":4.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seed treatment with macroalgal-derived fucoidan and nanohydroxyapatite mitigates Fusarium falciforme ASU26 infection in faba bean: insights from morphological, physiological, anatomical, and FT-IR analyses.","authors":"Mohamed Gomaa, Eman S E Aldaby, Ghada Abd-Elmonsef Mahmoud","doi":"10.1186/s12870-025-06347-7","DOIUrl":"10.1186/s12870-025-06347-7","url":null,"abstract":"<p><strong>Background: </strong>Soil-borne diseases are becoming more prevalent due to climate change, while the use of pesticides is being discouraged due to their harmful environmental impacts. This study explored the potential of natural compounds, specifically fucoidan from brown seaweed and nanohydroxyapatite from calcareous red seaweed, as eco-friendly alternatives for mitigating Fusarium infections. The treatments aimed to enhance the plant's defense mechanisms and improve seedling growth.</p><p><strong>Results: </strong>The treatments using fucoidan, nanohydroxyapatite, or their combination at concentrations of 250-500 µg mL⁻¹ for 6 h, significantly enhanced seedling growth, including increased height, root area, and both fresh and dry weights. Photosynthetic pigment levels and total flavonoid contents increased by more than 30% in treated seedlings compared to the infected control. Malondialdehyde levels, an indicator of oxidative stress, were notably reduced, comparable to or lower than those in the non-infected control. Enzymatic activities associated with plant defense, such as chitinase and polyphenol oxidase, were also higher in treated seedlings. Anatomical improvements were observed, including enhanced vascular cylinder and metaxylem areas. FT-IR analyses highlighted several biochemical changes, such as an increased CH₂/CH₃ ratio indicating lipid structural variation, reduced amide I and II bands, an increase in the C = C band (linked to lignin), and a higher degree of esterification compared to infected controls.</p><p><strong>Conclusions: </strong>The study demonstrates that fucoidan and nanohydroxyapatite are promising sustainable, cost-effective, and environmentally friendly treatments that effectively boost the defense responses and growth of faba bean seedlings against Fusarium falciforme ASU26 infection. These natural compounds could serve as alternatives to conventional pesticides, offering enhanced plant resistance to pathogens and supporting healthier plant growth.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"394"},"PeriodicalIF":4.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Amino acid metabolism pathways as key regulators of nitrogen distribution in tobacco: insights from transcriptome and WGCNA analyses.","authors":"Shichen Li, Waqar Ahmed, Tao Jiang, Dehai Yang, Linyuan Yang, Xiaodong Hu, Meiwei Zhao, Xiaoci Peng, Yingfen Yang, Wei Zhang, Mingmin Li, Zhengxiong Zhao","doi":"10.1186/s12870-025-06390-4","DOIUrl":"10.1186/s12870-025-06390-4","url":null,"abstract":"<p><strong>Background and aim: </strong>Nitrogen (N) is crucial for plant growth and is distributed across various N morphologies within plant organs. However, the mechanisms controlling the distribution of these N morphologies are not fully understood. This study investigated key amino acid (AA) biosynthesis pathways regulating N distribution and their impact on plant physiology and growth.</p><p><strong>Methods: </strong>We examined N distribution in the leaves, stems, and roots of two tobacco cultivars (Hongda and K326) under different N treatments at 75, and 100 days after transplanting (DAT). Transcriptome analysis was performed at 75 and 100 DAT to explore N distribution and AA metabolism pathways. Weighted gene co-expression network analysis (WGCNA) identified pathways regulating N distribution, and the Mantel test assessed the impact of N treatments, growth stages, and cultivars on N distribution.</p><p><strong>Results: </strong>Statistically significant differences in N distribution were observed across environmental conditions, growth stages, cultivars, and plant organs (p < 0.05). WGCNA identified phenylalanine metabolism (ko00360), alanine, aspartate, and glutamate metabolism (ko00250), and glycine, serine, and threonine metabolism (ko00260) pathways regulating the distribution of N_in-SDS (sodium dodecyl sulfate insoluble N), N_W (water soluble N), and N_S (sodium dodecyl sulfate soluble N), respectively. Increased N application promoted N_in-SDS accumulation, while earlier growth stages and cultivar Hongda favored N_W distribution. N_S distribution was inhibited under high N conditions. Gene expression in these pathways correlated with N distribution, biomass, and N accumulation.</p><p><strong>Conclusion: </strong>This study elucidates the mechanisms regulating N distribution in tobacco, emphasizing the role of AA metabolism pathways. These findings are essential for improving N utilization and optimizing N management practices, ultimately enhancing crop productivity and supporting sustainable agricultural practices.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"393"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring drought tolerance for germination traits of diverse wheat genotypes at seedling stage: a multivariate analysis approach.","authors":"Kashif Ahmed, Ghulam Shabbir, Mukhtar Ahmed","doi":"10.1186/s12870-025-06345-9","DOIUrl":"10.1186/s12870-025-06345-9","url":null,"abstract":"<p><p>Wheat holds crucial global importance as a staple food in many regions. Drought stress significantly impedes seed germination of wheat. The lack of drought-tolerant wheat varieties hampers wheat production, especially in arid regions of the world. This study investigated seed germination and seedling growth in eighty wheat genotypes under moisture stress stimulated by polyethylene glycol (PEG⁶⁰⁰⁰). The study included two osmotic potentials induced by PEG-20% (ψ: -0.491 MPa) and PEG-25% (ψ: -0.735 MPa), as well as a control set without PEG. The data showed that dehydration caused by polyethylene glycol generally had an adverse effect on the morphological characteristics of wheat seedlings by causing substantial losses during the early germination stage. The results acquired from analysis of variance explained highly significant variances (p < 0.01) across genotypes (G), PEG-Treatments (T^PEG), and interactions between genotypes and PEG-Treatments (G x T^PEG) for all observed variables. Moisture deficit radically affected all studied seedling traits of bread wheat under rising osmotic stress, with germination percentage (GP), shoot length (SL), root length (RL), coleoptile length (CL), seedling length (SDL), root fresh weight (FRW), root dry weight (DRW), shoot fresh weight (FSW), shoot dry weight (DSW), seedling biomass (SBM) and seedling vigor index (SVI) reduced by about 30-95% compared to control (PEG-0%) to the maximum induced osmotic stress at -0.735 MPa. The coefficient of relative inhibition (CRI) rose in response to osmotic stress, demonstrating growth inhibition. Boxplots demonstrated a considerable decline under stress, although scatter plots and correlation matrices revealed significant positive associations for most seedling traits, except CRI. The histograms for most variables showed a wider value range and more diversified distribution patterns. Principal component analysis (PCA) and genotype by trait biplot emphasized that PC1 represented 94.29% of the cumulative variation, with an eigenvalue of 11.31 out of 12 components. The heatmap displayed diverse genotype and trait characteristics, indicating higher values for drought resistance and lower values for susceptibility in genotype performance. As indicated by a range of multivariate analyses, the wheat lines NR-499, NARC-2009 and Pakistan-2013 stood out as the most drought-tolerant among the genotypes; whereas Borlaug-2016, NR-514 and NR-516 were found to be highly susceptible, whereas SBM, SDL, SVI and CRI have been found key indicators for subsequent screening. These tolerant wheat lines offer promising potential for developing drought-tolerant varieties that could thrive in arid regions, thereby strengthening wheat production in water-stressed environments. Integrating these findings into breeding programs is crucial for realizing the potential of drought-tolerant wheat varieties in transforming global wheat production.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"390"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of transcriptomic and metabolomic analysis reveals light-regulated anthocyanin accumulation in the peel of 'Yinhongli' plum.","authors":"Bo Xiong, Yisong Li, Junfei Yao, Jialu Wang, Linlyu Han, Qingqing Ma, Taimei Deng, Ling Liao, Lijun Deng, Guochao Sun, Mingfei Zhang, Xun Wan, Siya He, Jiaxian He, Zhihui Wang","doi":"10.1186/s12870-025-06414-z","DOIUrl":"10.1186/s12870-025-06414-z","url":null,"abstract":"<p><strong>Background: </strong>The 'Yinhongli' cultivar of Chinese plum (Prunus salicina Lindl.) is characterized by a distinctive bicolored peel phenotype, in which anthocyanins serve as crucial determinants of both its visual characteristics and nutritional quality. However, the molecular mechanism of underlying light-dependent anthocyanin biosynthesis of plum, especially its regulatory network and pathway, need to be further studied and explored.</p><p><strong>Results: </strong>Comprehensive physiological analyses demonstrated distinct pigmentation patterns, revealing that dark-treated (YD) plum peels retained green coloration, whereas light-exposed (YL) and bag-removed samples (YDL) exhibited red pigmentation. Utilizing an integrated approach combining metabolomic and transcriptomic analyses, we identified 266 differentially accumulated flavonoids (DAFs), among which seven anthocyanin metabolites were established as principal determinants of peel coloration. Transcriptomic profiling revealed 6,900 differentially expressed genes (DEGs) between YD and YL, demonstrating significant correlations between the phenylpropanoid and flavonoid biosynthetic pathways. Through Weighted Gene Co-expression Network Analysis (WGCNA) and correlation heatmap analysis, we identified crucial regulatory networks encompassing five structural genes (PAL, 4CL, F3'H, CHI, and UFGT) and 15 candidate regulatory genes, including six light signal transduction factor genes (UVR8, COP1, PHYBs, PIF3, and HY5) and nine transcription factor genes (MYB1, MYB20, MYB73, MYB111, LHY, DRE2B, ERF5, bHLH35, and NAC87). Subsequent RT-qPCR validation demonstrated significant light-mediated up-regulation of key structural genes (PAL, F3H, CHI, 4CL, and UFGT) involved in anthocyanin biosynthesis along with positive regulatory factors (DRE2B and NAC87). Conversely, a cohort of negative regulators, including HY5, MYB1, MYB20, MYB73, MYB111, LHY, ERF5, and bHLH35, showed marked down-regulation in response to light exposure, suggesting their potential repressive roles in the light-dependent anthocyanin biosynthesis pathway.</p><p><strong>Conclusions: </strong>This investigation provides comprehensive insights into the molecular mechanisms of anthocyanin biosynthesis in light-dependent anthocyanin biosynthesis in 'Yinhongli' plum, identifying critical structural genes and potential regulatory TFs. The findings offer substantial contributions to the understanding of anthocyanin regulation in fruit crops and provide a valuable foundation for molecular breeding initiatives aimed at enhancing quality traits in plum cultivars.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"391"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional analysis of the StERF79 gene in response to drought stress in potato (Solanum tuberosum L.).","authors":"Jingjing Wei, Ning Zhang, Yurong Deng, Shengyan Liu, Liang Yang, Xiaofeng Wang, Ruiting Wen, Huaijun Si","doi":"10.1186/s12870-025-06417-w","DOIUrl":"10.1186/s12870-025-06417-w","url":null,"abstract":"<p><strong>Background: </strong>The AP2/ERF (APETALA 2/ethylene-responsive element binding factors) is a class of superfamily of plant-specific transcription factor that play an important regulatory role in many physiological and biochemical processes in plants.</p><p><strong>Results: </strong>In this study, overexpression of the StERF79 gene increased drought tolerance in potato plants, whereas StERF79 RNA interference expression (RNAi) lines decreased drought tolerance in potato plants. In addition, the superoxide dismutase (SOD), peroxide dismutase (POD), and catalase (CAT) activities, as well as proline (Pro) content of StERF79 transgenic lines, showed significantly higher results than those of the wild type (WT) potato plants under natural drought stress conditions, while the malondialdehyde (MDA) content was lower. The StERF79 transcription factor can respond to drought stress by interacting with a DRE cis-acting element in the promoter region of the downstream target gene (StDHN-2), and activating its expression, the result was validated by using yeast one hybrid (Y1H), Dual-Luciferase and β-glucuronidase (GUS) staining assays both in vivo and in vitro. The StDHN-2 gene is a member of the dehydrin (DHN) subfamily of the potato plant late embryonic developmentally abundant (LEA) protein family. LEA, hydrophilic proteins found in plants, serve as cellular dewatering protectants to prevent desiccation during various stresses.</p><p><strong>Conclusion: </strong>The results could provide novel knowledge into the functional analysis of the StERF79 gene in positive regulation of the StDHN-2 gene to drought response and its possible mechanisms in potato plants.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"387"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pollen and anther morphological variation in rye was shaped by domestication.","authors":"Christina Waesch, Yixuan Gao, Natalie Koch, Noah Gaede, Thomas Hornick, Christian Dusny, Jörg Fuchs, Andreas Börner, Axel Himmelbach, Martin Mascher, Klaus Pillen, Susanne Dunker, Steven Dreissig","doi":"10.1186/s12870-025-06416-x","DOIUrl":"10.1186/s12870-025-06416-x","url":null,"abstract":"<p><strong>Background: </strong>In plants and animals, pollen or sperm morphology differ greatly between species. Across plant species, pollen morphological diversity is broadly linked to different pollination systems. However, the extent of within-species diversity is less well understood. To address this question, we explored pollen and anther diversity in rye (Secale cereale L.), a wind-pollinating grass species.</p><p><strong>Results: </strong>We analysed 339 domesticated, feral and wild rye individuals of 64 diverse accessions. Population structure analysis revealed a differentiation gradient from wild to domesticated rye. We found pronounced within-species diversity of pollen and anther morphology. Genome-wide association scans uncovered a polygenic architecture of pollen and anther traits, with medium to high heritability and mostly small-effect loci. A subset of these loci overlapped with previously identified domestication loci, for which the underlying traits were unknown. A P_ST-F_ST analysis suggests that pollen and anther traits were under selection throughout rye domestication. Population genomic analyses revealed signatures of selection at 37% of all identified loci.</p><p><strong>Conclusion: </strong>Our work shows that selection for larger pollen grains and longer anthers occurred throughout rye domestication. The present study extends our knowledge of the genetic architecture underlying within-species pollen and anther morphological diversity, and further unravels domestication traits in rye.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"389"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.","authors":"Muhammad Tahir Ul Qamar, Kinza Fatima, Muhammad Junaid Rao, Qian Tang, Muhammad Sadaqat, Baopeng Ding, Ling-Ling Chen, Xi-Tong Zhu","doi":"10.1186/s12870-025-06397-x","DOIUrl":"10.1186/s12870-025-06397-x","url":null,"abstract":"<p><p>Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"388"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A precise and high-throughput assay for stem structural characteristics deepens understanding of lodging resistance in sorghum.","authors":"Jianguo Li, Liyan Zhao, Hongzeng Fan, Falin Zhao, Dandan He, Bo Li, Jibin Wang, Guosheng Xie, Zhen Hu, Chuchuan Fan, Lingqiang Wang","doi":"10.1186/s12870-025-06396-y","DOIUrl":"10.1186/s12870-025-06396-y","url":null,"abstract":"<p><strong>Background: </strong>Plant stem structural characteristics are crucial factors determining plant lodging resistance, while high throughput methods for rapid surveys of these traits are still lacking in sorghum.</p><p><strong>Results: </strong>Among 103 sorghum accessions, two kinds of stem powders (dry and water-washed) were subject to visible and near-infrared spectra acquisition, and 16 models (combinations) for stem structural characteristics were generated, revealing that the support vector machine regression model has significant positive effects on the prediction of stem structural characteristics while powder type and pretreatment of spectra has minor effects on the prediction of stem structural characteristics. In addition, we found that stem structure characteristics were positively correlated with agronomic traits but negatively correlated with lodging index which is the criterion that negatively accounts for plant lodging resistance.</p><p><strong>Conclusion: </strong>This study for the first time provided a precise and high throughput method for the prediction of sorghum stem structural characteristics based on spectra, which could facilitate the improvement of lodging resistance in crop breeding.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"386"},"PeriodicalIF":4.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}