BMC Plant Biology最新文献

{"title":"New species and new records of genus Melampsora (Melampsoraceae) from Pakistan using electron microscopy and DNA barcoding techniques.","authors":"Najam-Ul-Sehar Afshan, Muhammad Aijaz Ahmad, Muhammada Jabeen, Sadia Binyameen, Abdul Nasir Khalid","doi":"10.1186/s12870-025-06593-9","DOIUrl":"10.1186/s12870-025-06593-9","url":null,"abstract":"<p><p>The genus Melampsora, known for its significant role as a plant pathogen, exhibits a rich species diversity. Current study reports Melampsora himalayensis sp. nov. as new species with M. ferrinii and M. populnea as new records from different regions (Fairy Meadows, Gilgit Baltistan; Khanspur, Khyber Pakhtunkhwa) of Pakistan, contributing to the knowledge of rust fungi diversity and distribution. Their placement within genus Melampsora was validated by comparative morpho-anatomical investigation. Detailed morphological characterization was employed using Scanning electron microscopy which provided features of spore morphology including their surface ornamentation. Additionally, molecular analysis was performed for species delimitation and to resolve phylogenetic relationships within genus Melampsora. Combined morpho-anatomical and phylogenetic data led to the discovery of previously unrecorded species, Melampsora ferrinii and M. populnea from Pakistan, including a novel taxon, Melampsora himalayensis sp. nov. This study provides information about taxonomy, host range and distribution of Melampsora in Pakistan.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1310"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225166","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 chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus.","authors":"Na Duan, Dafu Ru, Bingbing Liu","doi":"10.1186/s12870-025-07398-6","DOIUrl":"10.1186/s12870-025-07398-6","url":null,"abstract":"<p><strong>Backgroud: </strong>Sophora L. is a medicinally significant genus within Papilionoideae (Fabaceae), renowned for its medicinal, ecological, and economic importance. However, taxonomic and phylogenetic uncertainties persist within this genus, especially in China, due to limited genetic data and the lack of effective molecular markers. This study aimed to address these limitations by sequencing and analyzing chloroplast (cp.) genomes from six Sophora species endemic to China, thereby enriching genetic resources for future research.</p><p><strong>Result: </strong>Here, we reported and characterized six chloroplast (cp.) genomes of Sophora species (Sophora xanthantha, Sophora davidii, Sophora moocroftiana, Sophora tonkinensis, Sophora velutina, and Sophora velutina var. cavaleriei) from China, sequenced using the Illumina HiSeq platform. Comparative analyses of these newly generated cp. genomes, alongside previously published Sophora cp. genomes, revealed that the Sophora cp. genomes exhibited a size range of 151,270 - 154,378 bp (excluding S. japonica and S. xanthantha). We observed expansions of the inverted repeat (IR) regions in Sophora, leading to the translocation of rpl2 into the large single-copy (LSC) region, pseudogenization of ycf1, and absence of trnH in some species. Comparative genome analysis revealed a ~ 24-kb inversion between trnC-GCA and trnF-GAA within the genus, a phenomenon first observed to involve at least three rearrangements. Furthermore, we identified three valuable molecular markers (trnT-UGU - trnL-UAA, psbE - petL, and rps11 - rpl36) that are suitable for phylogenetic inference within Sophora.</p><p><strong>Conclusions: </strong>Phylogenetic analyses based on the chloroplast genomes robustly supported the monophyly of sect. Pseudosophora. Importantly, our phylogenetic results suggested that S. japonica and S. xanthantha should not be classified within the genus Sophora. These findings contribute significantly to the chloroplast genomic data of Sophora and provide valuable genetic resources and molecular markers for resolving taxonomic ambiguities and advancing future phylogenetic, evolutionary, and taxonomic investigations of Sophora.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1308"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225062","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":"Screening for resistance to Pyrenophora graminea in hulless barley germplasm and subsequent morphological and transcriptomic analyses.","authors":"You Long, Lu Hou, Erjing Si","doi":"10.1186/s12870-025-06976-y","DOIUrl":"10.1186/s12870-025-06976-y","url":null,"abstract":"","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1298"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225179","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":"Multi-omics analyses reveal the defense mechanisms behind the tolerance of the 'Parson Brown' sweet orange to Huanglongbing.","authors":"Lamiaa M Mahmoud, Shelley E Jones, Pedro Gonzalez-Blanco, Yu Fahong, Manjul Dutt, Nabil Killiny","doi":"10.1186/s12870-025-07372-2","DOIUrl":"10.1186/s12870-025-07372-2","url":null,"abstract":"<p><strong>Background: </strong>'Parson Brown' sweet orange is an early-maturing variety and is considered a resilient tree in the face of Huanglongbing (Citrus Greening) disease. Its ability to maintain productivity under endemic HLB conditions has demonstrated its value for growers battling this devastating disease. This study compared the metabolomic profile, transcriptomic analysis, and physiological responses of three early-maturing sweet oranges: 'Hamlin', 'Roble', and 'Parson Brown'.</p><p><strong>Results: </strong>Healthy greenhouse-grown trees were propagated and exposed to 'Candidatus Liberibacter asiaticus' via psyllid infestation. We recorded a decrease of landed psyllids on 'Parson Brown' (20.58%) compared to 'Hamlin' (34.38%) and 'Roble' (45.04%), in addition to a lower 'Ca. L. asiaticus' titer in 'Parson Brown'. Transcriptomic profiling indicated cultivar-specific expression patterns, with 'Parson Brown' showing strong upregulation of genes involved in terpenoid and flavonoid biosynthesis. Infected 'Parson Brown' trees exhibited significantly higher total phenolic and flavonoid contents, lower ROS and H₂O₂ levels, and enhanced expression of antioxidant-related genes. Volatile analysis revealed distinct profiles in 'Parson Brown', including elevated levels of certain monoterpenes, which may contribute to reduced vector attraction.</p><p><strong>Conclusion: </strong>The tolerance of 'Parson Brown' is driven by a multifaceted defense response, emphasizing the value of traditional breeding in combining diverse resistance traits from parental lines.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1303"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225192","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":"Sequential RGB light optimization across developmental stages enhances lettuce growth through carry-over effects.","authors":"Eunjeong Lim, Myung-Min Oh","doi":"10.1186/s12870-025-07295-y","DOIUrl":"10.1186/s12870-025-07295-y","url":null,"abstract":"<p><p>Light is a critical factor regulating plant development and productivity under controlled environment conditions. However, the light conditions are often kept static throughout the cultivation period, potentially overlooking plants' dynamic responses to changing environmental stimuli over time. This study proposes a stage-specific optimization strategy to maximize lettuce growth, based primarily on shoot fresh weight by adjusting red:green:blue (R:G:B) light ratio at different growth stages. After transplanting 2-week-old seedlings, their growth period was divided into an early stage (ES, the first 2 weeks) and a late stage (LS, after 2 weeks). To account for potential carry-over effects, the ES optimization was designed to evaluate how early-stage light conditions influence final growth performance. Response surface methodology was then employed to identify the optimal spectral combinations for each stage. The optimal R:G:B light ratios were determined to be 44.2:55.8:0 for ES and 25.2:57.8:16.9 for LS. These results suggest that excluding B light during ES promotes morphological traits favorable for light interception, presumably at the expense of immediate photosynthetic efficiency, and ultimately supporting enhanced biomass accumulation during LS. A sequential-optimized lighting strategy combining these two stage-specific light ratios was then evaluated against other lighting strategies, including a static-optimized, a reference, two white LED treatments with different color temperatures of 2700 and 5000 K. While the static-optimized treatment with an R:G:B ratio of 77:23:0 produced the highest shoot fresh weight during ES, the sequential-optimized ultimately delivered the greatest biomass by the end of the growth stage. These findings highlight the importance of stage-specific light requirements and demonstrate that dynamic light management aligned with developmental physiology can significantly enhance crop productivity. This study provides a practical framework for implementing adaptive light strategies in controlled environment systems.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1297"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225209","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":"Light grazing enhances microbial-mediated nitrogen transformation in desert steppe soils.","authors":"Aimin Zhu, Qian Wu, Guodong Han","doi":"10.1186/s12870-025-07356-2","DOIUrl":"10.1186/s12870-025-07356-2","url":null,"abstract":"<p><strong>Aims: </strong>Soil microorganisms play a central role in nitrogen transformation and availability, yet their regulatory functions in mediating nitrogen transfer between soil and plants under long-term grazing remain poorly understood. This study aims to elucidate how grazing intensity influences soil microbial communities and nitrogen-cycling functional genes, and how these microbial shifts affect nitrogen transformation processes and plant nitrogen uptake in desert steppe ecosystems.</p><p><strong>Methods: </strong>Here, we present a comprehensive study on soil microbes and nitrogen cycling functions in a desert grassland subjected to four grazing intensities - no grazing, light (0.91 sheep/ha), moderate (1.82 sheep/ha), and heavy (2.71 sheep/ha) - over 17 years.</p><p><strong>Results: </strong>We found that both the structural composition and the function of soil microbial communities varied across grazing intensities, with more pronounced changes in rhizosphere soil than in bulk soil. The relative abundance of nitrogen-cycling functional genes was generally higher under no grazing or light grazing conditions. Structural equation modeling (SEM) revealed that increases in soil pH under long-term grazing were significantly associated with shifts in microbial communities and with reduced net nitrogen mineralization rates. These changes were further linked to decreased soil nitrogen availability and lower nitrogen content in plant tissues.</p><p><strong>Conclusions: </strong>Light grazing in desert steppe ecosystems partially maintains microbial nitrogen cycling potential by supporting the abundance of nitrogen functional genes and preserving microbial community structure, despite an overall decline in nitrogen mineralization under grazing. These results suggest that low-intensity grazing may help mitigate grazing-induced suppression of nitrogen availability and plant uptake.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1301"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225255","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":"Genome-Wide analysis of the NRAMP gene family in Arabidopsis thaliana: identification, expression and response to multiple heavy metal stresses and phytohormones.","authors":"Muhammad Arif, Hina Abbas, Noman Mahmood, Muhammad Uzair, Muhammad Aamir Manzoor, Shahbaz Atta Tung, Yao Xin, Ruhong Xu, Luhua Li","doi":"10.1186/s12870-025-07396-8","DOIUrl":"10.1186/s12870-025-07396-8","url":null,"abstract":"<p><p>Heavy metal stress is a critical challenge to agricultural productivity, necessitating deeper insights into the molecular mechanisms of metal transport in plants. In this study, we conducted a comprehensive genome-wide characterization of the Natural Resistance-Associated Macrophage Protein (NRAMP) gene family in Arabidopsis thaliana and identified six AtNRAMP genes. Phylogenetic and synteny analyses revealed their distribution into two distinct clades and evolutionary conservation with legumes such as Glycine max and Arachis hypogaea, indicating functional divergence and gene duplication events maintained under purifying selection. Conserved protein motifs and domains, particularly the NRAMP transmembrane domain, highlighted their conserved role in divalent metal ion transport, while cis-regulatory element analysis demonstrated enrichment of stress- and hormone-responsive elements, pointing to tight transcriptional regulation under environmental challenges. Structural modeling further supported the functional conservation of AtNRAMP proteins. Expression profiling showed clear tissue-specific expression under normal conditions and strong, differential regulation in response to cadmium and other heavy metals, as well as to the phytohormone abscisic acid (ABA). Collectively, these results provide foundational insights into the evolutionary relationships, regulatory mechanisms, and stress-responsive expression of the AtNRAMP gene family, offering a framework for future functional studies and potential applications in developing crops with enhanced heavy metal tolerance and improved growth under stress conditions.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1305"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225042","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":"Rhizosphere phosphorus fractions controlled through P fertilization influence wheat infection by Heterodera avenae.","authors":"Mengli Zhao, Pengfei Wang, Xiuli Dong, Siyao Huang, Cihong Wang, Jun Yuan, Wei Qiu, Junhui Chen","doi":"10.1186/s12870-025-07399-5","DOIUrl":"10.1186/s12870-025-07399-5","url":null,"abstract":"<p><strong>Background: </strong>Heterodera avenae (cereal cyst nematode, CCN) infects wheat and causes severe yield losses. CCN infestations can be decreased by applying phosphate fertilizer in wheat fields, but the underlying mechanisms are still largely unclear.</p><p><strong>Results: </strong>In this study, the relationships among CCN, wheat root morphological traits, soil P fractions, and soil phosphatase activity in the rhizosphere were investigated with single superphosphate (SSP), monoammonium phosphate (MAP), diammonium phosphate (DAP), and ammonium polyphosphate (APP) application and without phosphate fertilizer (CK) application. APP most effectively inhibited the occurrence of CCN, with the number of cysts decreasing by 48.8%, and was decreased by 31.6%, 33.9%, and 16.4% in SSP, MAP, and DAP treatments, respectively. With APP, the concentrations of Resin-Pi and NaOH-Pi in rhizosphere soil increased significantly, and the proportional lengths of medium (1-3 mm) and coarse roots (> 3 mm) increased, while that of fine roots (0-1 mm diameter) decreased. Moreover, soil phosphatase activity decreased along with highest shoot P accumulation in APP treatment, suggesting that P nutrition provided by APP is more easily absorbed by wheat than the other tested fertilizers. Furthermore, negative relationships were observed between cyst numbers and shoot P accumulation (r = -0.87, p < 0.001), coarse root length proportion (r = -0.59, p < 0.01), Resin-Pi (r = -0.50, p < 0.05), and NaOH-Pi concentrations (r = -0.57, p < 0.01). SEM analysis indicated that the concentrations of Resin-Pi and NaOH-Pi increased by phosphate fertilizer additions, enhancing shoot P accumulation and inhibiting the occurrence of CCN in wheat.</p><p><strong>Conclusions: </strong>As an effective P source that elevates rhizosphere Resin-Pi and NaOH-Pi, APP not only promotes wheat growth by enhancing P uptake, but also increases the resistance of wheat against CCN. These findings provide an in-depth understanding of the control of CCN through phosphate fertilization management, enabling sustainable agricultural development.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1299"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225221","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":"Tissue-specific partitioning of flavonoids and phenolic acids coordinates bioactivities in Ormosia henryi Prain.","authors":"Ruyi Zhang, Lufeng Dan, Li Su, Xiaoli Wei","doi":"10.1186/s12870-025-07390-0","DOIUrl":"10.1186/s12870-025-07390-0","url":null,"abstract":"<p><p>The accumulation patterns of bioactive compounds in Ormosia henryi Prain, a traditional Chinese medicinal herb, remain poorly understood, limiting its potential for development. In this study, LC-MS/MS-based untargeted metabolomics was used to profile metabolic patterns across six tissues: new leaves (NL), old leaves (OL), stem bark (SB), stem xylem (SX), root bark (RB), and root xylem (RX). Multivariate analyses (PCA, OPLS-DA) identified key differentially accumulated metabolites (DAMs), including 34 phenolic compounds: 29 flavonoids and 5 phenolic acids. The total flavonoid content (TFC) was highest in the old leaves, while the total phenolic content (TPC) peaked in the root bark. Tissue extracts demonstrated strong antioxidant and hypoglycemic activities, with the old leaves showing the most significant bioactivity. Integrated correlation analysis further revealed significant relationships between TFC/TPC, core metabolites, and biological activities, highlighting potential biomarkers for functional evaluation. This study reveals the tissue-specific accumulation of bioactive phenolics in O. henryi Prain, providing valuable insights for the development of natural antioxidants, hypoglycemic drugs, and functional foods.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1309"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225224","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":"Relationships between leaf structural and functional traits of urban landscape plant species: implications for sustainable landscape planning.","authors":"Funda Ankaya","doi":"10.1186/s12870-025-07363-3","DOIUrl":"10.1186/s12870-025-07363-3","url":null,"abstract":"","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1300"},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225253","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}