Pub Date : 2025-07-24DOI: 10.1016/j.cpb.2025.100525
Sakihito Kitajima , Toshiharu Akino , Hideki Yoshida , Kenji Miura , Toki Taira , Eric Hyrmeya Savadogo , Naoki Tani
This study investigated the anti-insect activity of the caleosin homolog CLO3, which accumulates in the latex of Euphorbia tirucalli (Euphorbiaceae). Nicotiana benthamiana leaves transiently producing EtCLO3 were fed to Spodoptera litura (Lepidoptera) larvae, and their body weights were recorded. The production of EtCLO3 significantly retarded larval growth. Similar effects were observed with other plants’ caleosin homologs that share unique N-terminal motifs located upstream of the Ca2 + -binding EF-hand, including Arabidopsis thaliana CLO3 (AT2G33380) and homologs from lower plants (liverworts Mapoly0027s0099 and Chlamydomonas Cre06.g273650_4532). In contrast, A. thaliana CLO5 (AT5G19530), which belongs to a different class of caleosins, did not exhibit this growth retardation effect. Notably, the anti-insect activity of EtCLO3 persisted even when mutated in its peroxygenase catalytic site or EF-hand. A transcriptome analysis revealed that EtCLO3 up-regulated endogenous defense-related gene expression levels and altered sugar metabolism pathways. These findings suggest that EtCLO3 may, at least in part, exert its anti-insect effects by activating the host plant’s endogenous defense system. This research provides insights into how EtCLO3 and some other homologs influence larval development and suggests potential applications for these proteins in pest management.
{"title":"Caleosin expression enhances plant insect resistance","authors":"Sakihito Kitajima , Toshiharu Akino , Hideki Yoshida , Kenji Miura , Toki Taira , Eric Hyrmeya Savadogo , Naoki Tani","doi":"10.1016/j.cpb.2025.100525","DOIUrl":"10.1016/j.cpb.2025.100525","url":null,"abstract":"<div><div>This study investigated the anti-insect activity of the caleosin homolog CLO3, which accumulates in the latex of <em>Euphorbia tirucalli</em> (Euphorbiaceae). <em>Nicotiana benthamiana</em> leaves transiently producing EtCLO3 were fed to <em>Spodoptera litura</em> (Lepidoptera) larvae, and their body weights were recorded. The production of EtCLO3 significantly retarded larval growth. Similar effects were observed with other plants’ caleosin homologs that share unique N-terminal motifs located upstream of the Ca<sup>2 +</sup> -binding EF-hand, including <em>Arabidopsis thaliana</em> CLO3 (AT2G33380) and homologs from lower plants (liverworts Mapoly0027s0099 and <em>Chlamydomonas</em> Cre06.g273650_4532). In contrast, <em>A. thaliana</em> CLO5 (AT5G19530), which belongs to a different class of caleosins, did not exhibit this growth retardation effect. Notably, the anti-insect activity of EtCLO3 persisted even when mutated in its peroxygenase catalytic site or EF-hand. A transcriptome analysis revealed that EtCLO3 up-regulated endogenous defense-related gene expression levels and altered sugar metabolism pathways. These findings suggest that EtCLO3 may, at least in part, exert its anti-insect effects by activating the host plant’s endogenous defense system. This research provides insights into how EtCLO3 and some other homologs influence larval development and suggests potential applications for these proteins in pest management.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100525"},"PeriodicalIF":4.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144722469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-22DOI: 10.1016/j.cpb.2025.100524
Aline Ballot , Matthieu Gaucher , Marjolaine Rey , Marie-Noelle Brisset , Pierre Joly , Assia Dreux-Zigha , Ahmed Taïbi , Thierry Langin , Claire Prigent-Combaret
The ability of the Bacillus pumilus JM79 strain to induce systemic resistance in wheat against Fusarium graminearum (Fg), a major wheat pathogen, was investigated using the Fusarium crown rot (FCR) pathosystem. The B. pumilus strain JM79 exhibited the ability to colonize both root and leaf surfaces while secreting surfactin-like pumilacidin in the root zone of wheat plantlets. Experiments involving foliar inoculation with JM79 revealed its ability to induce a strong local defense response in wheat, characterized by the selective overexpression of genes associated with phenylpropanoid metabolism and cell wall reinforcement pathways. Moreover, pre-inoculation of the wheat collar, at the soil surface interface, with the JM79 strain prior to Fg inoculation led to the overexpression of wheat genes linked to both jasmonic acid/ethylene (JA/ET) and salicylic acid (SA)-dependent defense pathways. This direct induction occurred during the asymptomatic phase of Fg infection, compensating for the lack or absence of an early immune response triggered by Fg infection. Collectively, these findings reveal for the first time that the B. pumilus strain JM79 produces a higher proportion of long-chain pumilacidins under in planta conditions than under in vitro conditions, and is capable of activating both local and systemic resistance in wheat plants, underscoring its potential as a biocontrol agent against major wheat fungal diseases.
{"title":"Strong elicitation of plant defense pathways by foliar and collar inoculations of wheat with the Bacillus pumilus strain JM79","authors":"Aline Ballot , Matthieu Gaucher , Marjolaine Rey , Marie-Noelle Brisset , Pierre Joly , Assia Dreux-Zigha , Ahmed Taïbi , Thierry Langin , Claire Prigent-Combaret","doi":"10.1016/j.cpb.2025.100524","DOIUrl":"10.1016/j.cpb.2025.100524","url":null,"abstract":"<div><div>The ability of the <em>Bacillus pumilus</em> JM79 strain to induce systemic resistance in wheat against <em>Fusarium graminearum</em> (<em>Fg</em>), a major wheat pathogen, was investigated using the Fusarium crown rot (FCR) pathosystem. The <em>B. pumilus</em> strain JM79 exhibited the ability to colonize both root and leaf surfaces while secreting surfactin-like pumilacidin in the root zone of wheat plantlets. Experiments involving foliar inoculation with JM79 revealed its ability to induce a strong local defense response in wheat, characterized by the selective overexpression of genes associated with phenylpropanoid metabolism and cell wall reinforcement pathways. Moreover, pre-inoculation of the wheat collar, at the soil surface interface, with the JM79 strain prior to <em>Fg</em> inoculation led to the overexpression of wheat genes linked to both jasmonic acid/ethylene (JA/ET) and salicylic acid (SA)-dependent defense pathways. This direct induction occurred during the asymptomatic phase of <em>Fg</em> infection, compensating for the lack or absence of an early immune response triggered by <em>Fg</em> infection. Collectively, these findings reveal for the first time that the <em>B. pumilus</em> strain JM79 produces a higher proportion of long-chain pumilacidins under <em>in planta</em> conditions than under <em>in vitro</em> conditions<em>,</em> and is capable of activating both local and systemic resistance in wheat plants, underscoring its potential as a biocontrol agent against major wheat fungal diseases.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100524"},"PeriodicalIF":4.5,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144721699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNA sequencing (RNA-Seq) has transformed plant genomics by enabling high-resolution profiling of gene expression across various conditions. However, integrating RNA-Seq data from different studies is challenging due to variability in experimental designs, sequencing platforms, and data processing workflows, which limits the comparability and applicability of transcriptomic datasets. This review provides an overview of current meta-analysis approaches that address these challenges and enhance the consistency, accuracy, and interpretability of RNA-Seq data integration. We discuss methodologies such as data normalization techniques, statistical frameworks for aggregating results, and computational tools that reduce inter-study variability. We also highlight preprocessing strategies, including batch effect correction and standardized gene annotation pipelines, which facilitate reliable cross-study comparisons. We emphasize the practical significance of RNA-Seq meta-analysis in plant genomics. Meta-analysis improves the identification of consistent differentially expressed genes (DEGs), enhances functional annotation, and uncovers conserved regulatory mechanisms across plant species. These insights have applications in precision breeding, stress-response studies, and trait improvement programs. For researchers implementing meta-analysis, this review outlines key considerations, recommended practices, and available resources. We conclude by highlighting the need for standardized protocols and promoting multi-omics integration to unlock deeper insights. As transcriptomic datasets expand, meta-analysis will play a crucial role in advancing our understanding of plant biology and its application in agriculture.
{"title":"Unifying RNA-seq data using meta-analysis: Bioinformatics frameworks and application for plant genomics","authors":"Bahman Panahi , Rasmieh Hamid , Feba Jacob , Hossein Mohammadzadeh Jalaly","doi":"10.1016/j.cpb.2025.100523","DOIUrl":"10.1016/j.cpb.2025.100523","url":null,"abstract":"<div><div>RNA sequencing (RNA-Seq) has transformed plant genomics by enabling high-resolution profiling of gene expression across various conditions. However, integrating RNA-Seq data from different studies is challenging due to variability in experimental designs, sequencing platforms, and data processing workflows, which limits the comparability and applicability of transcriptomic datasets. This review provides an overview of current meta-analysis approaches that address these challenges and enhance the consistency, accuracy, and interpretability of RNA-Seq data integration. We discuss methodologies such as data normalization techniques, statistical frameworks for aggregating results, and computational tools that reduce inter-study variability. We also highlight preprocessing strategies, including batch effect correction and standardized gene annotation pipelines, which facilitate reliable cross-study comparisons. We emphasize the practical significance of RNA-Seq meta-analysis in plant genomics. Meta-analysis improves the identification of consistent differentially expressed genes (DEGs), enhances functional annotation, and uncovers conserved regulatory mechanisms across plant species. These insights have applications in precision breeding, stress-response studies, and trait improvement programs. For researchers implementing meta-analysis, this review outlines key considerations, recommended practices, and available resources. We conclude by highlighting the need for standardized protocols and promoting multi-omics integration to unlock deeper insights. As transcriptomic datasets expand, meta-analysis will play a crucial role in advancing our understanding of plant biology and its application in agriculture.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100523"},"PeriodicalIF":5.4,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144694673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-17DOI: 10.1016/j.cpb.2025.100519
Zhe Lin , Wenxuan Guo , Nathan S. Gill , Glen Ritchie , Brendan Kelly , Xiao-Peng Song
Background
Accurate quantification of open bolls and their distribution is crucial for understanding cotton growth, development, and yield in optimized crop management and enhanced plant breeding. Manual boll counting methods are time-consuming, labor-intensive, and subjective. Leveraging the potential of high-resolution images for high-throughput phenotyping offers a promising avenue for efficient trait quantification. The objectives of this study were to develop methods to detect and count open cotton bolls using LiDAR point cloud and RGB images and to compare the effectiveness of these two data sources.
Methods
A DJI Phantom 4 RTK Unmanned Aerial System (UAS) equipped with a 4 K RGB camera was used to acquire high-resolution RGB images, and a DJI Matrice 300 RTK with a Zenmuse L1 sensor was used to acquire LiDAR point cloud data. The RGB images were converted to point cloud using photogrammetry by measuring multiple points of overlapping images. The boll detection workflow involved data filtering and clustering using the density-based spatial clustering of applications with noise (DBSCAN) method. Evaluation of the methods involved 48 plots representing small, medium, and large plant sizes using metrics including mean absolute percentage error (MAPE), root mean square error (RMSE), and coefficient of determination (r²).
Results
The methods using both data sources performed well in estimating open bolls, with LiDAR point cloud data slightly outperforming those derived from RGB images. Generally, the performance of the DBSCAN method in boll detection improved with decreasing plant sizes. Specifically, LiDAR data yielded MAPE values of 5.03 %, 8.05 %, and 13.46 %, RMSE values of 7.26, 14.33, and 23.40 bolls per m², and r2 values of 0.93, 0.84, and 0.84 for small, medium, and large plant sizes, respectively. RGB image-based data exhibited MAPE values of 7.21 %, 6.49 %, and 16.41 %, RMSE values of 11.05, 13.66, and 26.49 bolls per m², and r2 values of 0.82, 0.74, and 0.83 for small, medium, and large plant sizes, respectively.
Conclusions
The method demonstrates the potential of RGB imagery and LiDAR data for estimating boll counts, offering valuable tools for enhanced plant phenotyping in plant breeding and site-specific crop management. Both data sources underestimated boll counts, with smaller plants showing less undercounting, likely due to improved light penetration and separation of bolls. These findings highlight the influence of plant structure on boll detection accuracy and the need to address challenges posed by dense canopies to enhance detection reliability.
{"title":"Open cotton boll detection using LiDAR point clouds and RGB images from unmanned aerial systems","authors":"Zhe Lin , Wenxuan Guo , Nathan S. Gill , Glen Ritchie , Brendan Kelly , Xiao-Peng Song","doi":"10.1016/j.cpb.2025.100519","DOIUrl":"10.1016/j.cpb.2025.100519","url":null,"abstract":"<div><h3>Background</h3><div>Accurate quantification of open bolls and their distribution is crucial for understanding cotton growth, development, and yield in optimized crop management and enhanced plant breeding. Manual boll counting methods are time-consuming, labor-intensive, and subjective. Leveraging the potential of high-resolution images for high-throughput phenotyping offers a promising avenue for efficient trait quantification. The objectives of this study were to develop methods to detect and count open cotton bolls using LiDAR point cloud and RGB images and to compare the effectiveness of these two data sources.</div></div><div><h3>Methods</h3><div>A DJI Phantom 4 RTK Unmanned Aerial System (UAS) equipped with a 4 K RGB camera was used to acquire high-resolution RGB images, and a DJI Matrice 300 RTK with a Zenmuse L1 sensor was used to acquire LiDAR point cloud data. The RGB images were converted to point cloud using photogrammetry by measuring multiple points of overlapping images. The boll detection workflow involved data filtering and clustering using the density-based spatial clustering of applications with noise (DBSCAN) method. Evaluation of the methods involved 48 plots representing small, medium, and large plant sizes using metrics including mean absolute percentage error (MAPE), root mean square error (RMSE), and coefficient of determination (r²).</div></div><div><h3>Results</h3><div>The methods using both data sources performed well in estimating open bolls, with LiDAR point cloud data slightly outperforming those derived from RGB images. Generally, the performance of the DBSCAN method in boll detection improved with decreasing plant sizes. Specifically, LiDAR data yielded MAPE values of 5.03 %, 8.05 %, and 13.46 %, RMSE values of 7.26, 14.33, and 23.40 bolls per m², and r<sup>2</sup> values of 0.93, 0.84, and 0.84 for small, medium, and large plant sizes, respectively. RGB image-based data exhibited MAPE values of 7.21 %, 6.49 %, and 16.41 %, RMSE values of 11.05, 13.66, and 26.49 bolls per m², and r<sup>2</sup> values of 0.82, 0.74, and 0.83 for small, medium, and large plant sizes, respectively.</div></div><div><h3>Conclusions</h3><div>The method demonstrates the potential of RGB imagery and LiDAR data for estimating boll counts, offering valuable tools for enhanced plant phenotyping in plant breeding and site-specific crop management. Both data sources underestimated boll counts, with smaller plants showing less undercounting, likely due to improved light penetration and separation of bolls. These findings highlight the influence of plant structure on boll detection accuracy and the need to address challenges posed by dense canopies to enhance detection reliability.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100519"},"PeriodicalIF":5.4,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-16DOI: 10.1016/j.cpb.2025.100520
Huajin Sheng , Peng Gao , Li Liu , Sheng Wang , Achala Bakshi , Zhigang Liu , Hanh Nguyen , Li Xi , Tongfei Qin , Daoquan Xiang , Vivijan Babic , Rui Wen , Teagen D. Quilichini , Maozhi Ren , Raju Datla , Leon Kochian
Drought is an important abiotic stress limiting wheat production worldwide. Hence there is a critical need to develop wheat varieties with improved performance under drought. Target of Rapamycin (TOR) kinase is a central regulator that integrates diverse nutrient, energy, hormone, and environmental stress response signals to coordinate plant growth and development. Recent studies have demonstrated that TOR is also involved in plant responses to abiotic stress. In this current study, in order to address TOR functions in response to wheat drought stress, we generated transgenic wheat lines expressing TaTOR under the control of constitutive and drought-inducible promoters. Inhibition of plant growth in response to drought was discovered to be closely associated with the expression and activity of the wheat TOR protein. Enhancing TaTOR expression driven by a constitutive promoter (UBQ) or drought-inducible promoters (DREB/DEH), significantly improved drought resistance and greatly reduced yield losses caused by drought stress in wheat. Examination of plant water relations, other related physiological parameters, and genome-wide transcriptomic comparisons demonstrated that enhancing TaTOR expression under drought helps wheat minimize transpirational water loss without compromising photosynthetic performance, thus improving water-use efficiency. This is achieved through efficient regulation of stomatal closure, along with enhanced photosynthetic efficiency, upregulation of ABA-mediated stress signaling, increased antioxidant capacity, and more robust recovery from drought. Our findings highlight the functional roles of TaTOR in wheat drought resistance, providing a valuable new molecular tool for developing wheat cultivars with improved drought resistance needed to address the drought and climate change challenges threatening wheat productivity worldwide.
干旱是限制小麦生产的重要非生物胁迫。因此，迫切需要开发干旱条件下性能更好的小麦品种。雷帕霉素靶蛋白（Target of Rapamycin， TOR）激酶是整合多种营养、能量、激素和环境胁迫响应信号，协调植物生长发育的中枢调控因子。最近的研究表明，TOR也参与了植物对非生物胁迫的反应。在本研究中，为了解决TOR在小麦干旱胁迫下的功能，我们在组成启动子和干旱诱导启动子的控制下，产生了表达TOR的转基因小麦品系。研究发现，干旱对植物生长的抑制与小麦TOR蛋白的表达和活性密切相关。在组成启动子（UBQ）或干旱诱导启动子（DREB/DEH）的驱动下，增强TaTOR的表达，可显著提高小麦抗旱性，减少干旱胁迫造成的产量损失。对植物水分关系、其他相关生理参数和全基因组转录组比较的研究表明，干旱条件下增强TaTOR表达有助于小麦在不影响光合性能的情况下减少蒸腾水分损失，从而提高水分利用效率。这是通过气孔关闭的有效调节、光合效率的提高、aba介导的应激信号的上调、抗氧化能力的增强以及更强劲的干旱恢复来实现的。我们的研究结果突出了TaTOR在小麦抗旱性中的功能作用，为开发抗旱性更好的小麦品种提供了一个有价值的新分子工具，以应对威胁全球小麦生产力的干旱和气候变化挑战。
{"title":"Target of Rapamycin (TOR) signaling coordinates a balance between wheat photosynthetic performance and transpirational water conservation for improved water use efficiency and performance under drought","authors":"Huajin Sheng , Peng Gao , Li Liu , Sheng Wang , Achala Bakshi , Zhigang Liu , Hanh Nguyen , Li Xi , Tongfei Qin , Daoquan Xiang , Vivijan Babic , Rui Wen , Teagen D. Quilichini , Maozhi Ren , Raju Datla , Leon Kochian","doi":"10.1016/j.cpb.2025.100520","DOIUrl":"10.1016/j.cpb.2025.100520","url":null,"abstract":"<div><div>Drought is an important abiotic stress limiting wheat production worldwide. Hence there is a critical need to develop wheat varieties with improved performance under drought. Target of Rapamycin (TOR) kinase is a central regulator that integrates diverse nutrient, energy, hormone, and environmental stress response signals to coordinate plant growth and development. Recent studies have demonstrated that TOR is also involved in plant responses to abiotic stress. In this current study, in order to address TOR functions in response to wheat drought stress, we generated transgenic wheat lines expressing <em>TaTOR</em> under the control of constitutive and drought-inducible promoters. Inhibition of plant growth in response to drought was discovered to be closely associated with the expression and activity of the wheat TOR protein. Enhancing <em>TaTOR</em> expression driven by a constitutive promoter (<em>UBQ</em>) or drought-inducible promoters (<em>DREB/DEH</em>), significantly improved drought resistance and greatly reduced yield losses caused by drought stress in wheat. Examination of plant water relations, other related physiological parameters, and genome-wide transcriptomic comparisons demonstrated that enhancing <em>TaTOR</em> expression under drought helps wheat minimize transpirational water loss without compromising photosynthetic performance, thus improving water-use efficiency. This is achieved through efficient regulation of stomatal closure, along with enhanced photosynthetic efficiency, upregulation of ABA-mediated stress signaling, increased antioxidant capacity, and more robust recovery from drought. Our findings highlight the functional roles of TaTOR in wheat drought resistance, providing a valuable new molecular tool for developing wheat cultivars with improved drought resistance needed to address the drought and climate change challenges threatening wheat productivity worldwide.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100520"},"PeriodicalIF":5.4,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144670502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-09DOI: 10.1016/j.cpb.2025.100518
Mahender Anumalla , Margaret Catolos , Joie Ramos , Ma Tersesa Sta. Cruz , Xiaoli Zhang , Ando Radanielson , Sankalp Bhosale , Benildo G. de los Reyes , Waseem Hussain
Methane (CH₄) emissions pose a significant environmental challenge worldwide. Rice cultivation, reliant on flooded fields, accounts for over 45 % of these emissions. Projections indicate that by 2030, CH₄ emissions from rice are expected to increase by 35–60 %. Effective emission reduction strategies include direct seeded rice (DSR) and alternative wetting and drying (AWD) techniques. This review examines CH₄ emissions in saline rice ecosystems, highlighting substantial evidence that emissions are lower in these environments. We explore the distinctive microbial processes within saline environments that modify molecular and physiological pathways, ultimately inhibiting methanogenic microorganisms and reducing CH₄ emissions. Furthermore, we underscore the remarkable potential of saline ecosystems to enhance food security while curbing CH₄ emissions. We also discuss the urgent need to develop next-generation, salinity-resistant rice varieties using modern tools and technologies that address high-salinity conditions. Conclusively, salinity-tolerant rice offers the dual benefits of increased food security and reduced environmental impact, thereby fostering sustainable agricultural practices in saline ecosystem regions.
{"title":"Salinity-tolerant rice: A sustainable solution for food security and greenhouse gas mitigation","authors":"Mahender Anumalla , Margaret Catolos , Joie Ramos , Ma Tersesa Sta. Cruz , Xiaoli Zhang , Ando Radanielson , Sankalp Bhosale , Benildo G. de los Reyes , Waseem Hussain","doi":"10.1016/j.cpb.2025.100518","DOIUrl":"10.1016/j.cpb.2025.100518","url":null,"abstract":"<div><div>Methane (CH₄) emissions pose a significant environmental challenge worldwide. Rice cultivation, reliant on flooded fields, accounts for over 45 % of these emissions. Projections indicate that by 2030, CH₄ emissions from rice are expected to increase by 35–60 %. Effective emission reduction strategies include direct seeded rice (DSR) and alternative wetting and drying (AWD) techniques. This review examines CH₄ emissions in saline rice ecosystems, highlighting substantial evidence that emissions are lower in these environments. We explore the distinctive microbial processes within saline environments that modify molecular and physiological pathways, ultimately inhibiting methanogenic microorganisms and reducing CH₄ emissions. Furthermore, we underscore the remarkable potential of saline ecosystems to enhance food security while curbing CH₄ emissions. We also discuss the urgent need to develop next-generation, salinity-resistant rice varieties using modern tools and technologies that address high-salinity conditions. Conclusively, salinity-tolerant rice offers the dual benefits of increased food security and reduced environmental impact, thereby fostering sustainable agricultural practices in saline ecosystem regions.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100518"},"PeriodicalIF":5.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144596618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-08DOI: 10.1016/j.cpb.2025.100515
Egli C. Georgiadou , Carlos J. García , Anna Maria Taliadorou , Stella Gedeon , Nicolas Valanides , Alice Varaldo , Gholamreza Gohari , Marta Balsells-Llauradó , Ruben Alcázar , Maarten L.A.T.M. Hertog , Francisco A. Tomás-Barberán , George A. Manganaris , Vasileios Fotopoulos
The application of priming agents is a promising strategy to enhance the nutritional content of fruits and overall fruit quality. The current study aimed to assess the effect of the pre-harvest application of various priming agents [melatonin (Mel), sodium alginate (NaA), sodium alginate/melatonin conjugate (Mel-NaA), and putrescine dihydrochloride (Put)] on fruit quality attributes and secondary metabolite profile of a strawberry cultivar (Fragaria x ananassa Duchesne cv. ‘Felicity Q3’). The priming agents were directly applied on fruit at three successive developmental stages, namely large green (LG), small white (SW) and large white (LW). The use of Mel-NaA and Put showed promising results in improving fruit quality indicators (i.e. firmness, color), while Mel-NaA and putrescine-treated fruit were characterized by increased total flavonoid content. HPLC-DAD-ESI-MS/MS data showed variable regulation of flavan-3-ols, hydroxycinnamic acids, and conjugates contents by the different treatments, while ellagitannins and ellagic acid derivatives were significantly enhanced following Mel-NaA pre-treatment. Priming treatments did not result in the differential regulation of volatile organic compounds (VOCs) in comparison with controls, suggesting that primed fruit retain their aroma quality with no aroma profile ‘penalty’. In addition, molecular analysis revealed that fruit pre-treatment with the priming agents resulted in variable transcriptional regulation of known strawberry allergenic proteins, with the Mel-NaA treatment showing no significant effect. This ‘green’ approach holds promise for advancing our understanding of the effects of NaA as a smart delivery mechanism of chemical priming agents and its potential impact on the sustainable improvement of the physicochemical attributes of strawberries during the pre-harvest stage.
应用引物剂是提高果实营养成分和整体品质的一种很有前途的策略。本研究旨在评估采前施用各种引物剂[褪黑素（Mel）、海藻酸钠（NaA）、海藻酸钠/褪黑素共轭物（Mel-NaA）和盐酸腐胺（Put）]对草莓（Fragaria x ananassa Duchesne cv）果实品质属性和次生代谢物谱的影响。“费利西蒂Q3”)。在大绿、小白、大白三个连续发育阶段直接施用引物剂。Mel-NaA和Put处理在改善果实硬度、色泽等品质指标方面效果显著，而Mel-NaA处理和腐胺处理的果实中总黄酮含量均有所增加。HPLC-DAD-ESI-MS/MS数据显示，不同处理对黄烷-3-醇、羟基肉桂酸和偶联物的含量有不同的调节，而Mel-NaA预处理显著增强了鞣花单宁和鞣花酸衍生物的含量。与对照相比，启动处理没有导致挥发性有机化合物（VOCs）的差异调节，这表明启动的水果在没有香气特征“惩罚”的情况下保持了其香气品质。此外，分子分析显示，用引物预处理的果实对已知草莓致敏蛋白的转录有不同的调节作用，Mel-NaA处理的效果不显著。这种“绿色”方法有望促进我们对NaA作为化学引发剂的智能递送机制的作用的理解，以及它对收获前阶段草莓物理化学属性可持续改善的潜在影响。
{"title":"Pre-harvest application of sodium alginate functionalized with melatonin enhances secondary metabolism in strawberry fruit","authors":"Egli C. Georgiadou , Carlos J. García , Anna Maria Taliadorou , Stella Gedeon , Nicolas Valanides , Alice Varaldo , Gholamreza Gohari , Marta Balsells-Llauradó , Ruben Alcázar , Maarten L.A.T.M. Hertog , Francisco A. Tomás-Barberán , George A. Manganaris , Vasileios Fotopoulos","doi":"10.1016/j.cpb.2025.100515","DOIUrl":"10.1016/j.cpb.2025.100515","url":null,"abstract":"<div><div>The application of priming agents is a promising strategy to enhance the nutritional content of fruits and overall fruit quality. The current study aimed to assess the effect of the pre-harvest application of various priming agents [melatonin (Mel), sodium alginate (NaA), sodium alginate/melatonin conjugate (Mel-NaA), and putrescine dihydrochloride (Put)] on fruit quality attributes and secondary metabolite profile of a strawberry cultivar (<em>Fragaria</em> x <em>ananassa Duchesne</em> cv. ‘Felicity Q3’). The priming agents were directly applied on fruit at three successive developmental stages, namely large green (LG), small white (SW) and large white (LW). The use of Mel-NaA and Put showed promising results in improving fruit quality indicators (i.e. firmness, color), while Mel-NaA and putrescine-treated fruit were characterized by increased total flavonoid content. HPLC-DAD-ESI-MS/MS data showed variable regulation of flavan-3-ols, hydroxycinnamic acids, and conjugates contents by the different treatments, while ellagitannins and ellagic acid derivatives were significantly enhanced following Mel-NaA pre-treatment. Priming treatments did not result in the differential regulation of volatile organic compounds (VOCs) in comparison with controls, suggesting that primed fruit retain their aroma quality with no aroma profile ‘penalty’. In addition, molecular analysis revealed that fruit pre-treatment with the priming agents resulted in variable transcriptional regulation of known strawberry allergenic proteins, with the Mel-NaA treatment showing no significant effect. This ‘green’ approach holds promise for advancing our understanding of the effects of NaA as a smart delivery mechanism of chemical priming agents and its potential impact on the sustainable improvement of the physicochemical attributes of strawberries during the pre-harvest stage.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100515"},"PeriodicalIF":5.4,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144662253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Domestication of rice (Oryza sativa L.) dates back to 8000 years ago when selection for yield traits began through artificial selection. Projected demand in rice production, yield plateau and changing climate gives us a clue that enhancing yield potential is vital for food security. Identifying genes controlling yield traits and mechanisms like C4 photosynthesis is warranted to achieve sustained increase in rice production. In this study, efforts were made to exploit a novel domestication gene An-1 for enhancing yield potential in rice through creation of targeted mutations using CRISPR/Cas9 mutagenesis. Evaluation of 312 T0 progenies of a rice cultivar ASD 16 identified 17 multi-allelic, seven bi-allelic and four mono-allelic mutations. Evaluation of T2 and T3 progenies identified homozygous and transgene free mutants possessing increased number of grains per panicle. Evaluation of T4 progenies revealed that the mutant progenies were found to possess increased secondary branches in the panicle (22.8 %), increased number of spikelets per panicle (34.8 %) and increased single plant yield (35.25 %) when compared to the wild type ASD 16. This study has identified An-1 as a novel candidate gene for yield enhancement in rice.
{"title":"CRISPR/Cas9 mutagenesis generated elite alleles of a novel yield gene An-1 leading to increased grain number in rice (Oryza sativa L.)","authors":"Shobica Priya Ramasamy , Sakthi Ambothi Rathnasamy , Sudha Manickam , Veeraranjani Rajagopalan , Rakshana Palaniswamy , Vignesh Mohanavel , Rohit Kambale , Manonmani Swaminathan , Kalaimagal Thiyagarajan , Raja Ragupathy , Raveendran Muthurajan","doi":"10.1016/j.cpb.2025.100511","DOIUrl":"10.1016/j.cpb.2025.100511","url":null,"abstract":"<div><div>Domestication of rice (<em>Oryza sativa</em> L.) dates back to 8000 years ago when selection for yield traits began through artificial selection. Projected demand in rice production, yield plateau and changing climate gives us a clue that enhancing yield potential is vital for food security. Identifying genes controlling yield traits and mechanisms like C<sub>4</sub> photosynthesis is warranted to achieve sustained increase in rice production. In this study, efforts were made to exploit a novel domestication gene <em>An-1</em> for enhancing yield potential in rice through creation of targeted mutations using CRISPR/Cas9 mutagenesis. Evaluation of 312 T<sub>0</sub> progenies of a rice cultivar ASD 16 identified 17 multi-allelic, seven bi-allelic and four mono-allelic mutations. Evaluation of T<sub>2</sub> and T<sub>3</sub> progenies identified homozygous and transgene free mutants possessing increased number of grains per panicle. Evaluation of T<sub>4</sub> progenies revealed that the mutant progenies were found to possess increased secondary branches in the panicle (22.8 %), increased number of spikelets per panicle (34.8 %) and increased single plant yield (35.25 %) when compared to the wild type ASD 16. This study has identified <em>An-1</em> as a novel candidate gene for yield enhancement in rice.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100511"},"PeriodicalIF":5.4,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144605744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bitter gourd is an important cucurbitaceous vegetable widely grown in India and other tropical and subtropical regions and appreciated for its nutritional, medicinal, and economic values. Traditional way of detecting diseases and nutrient deficiencies in bitter gourd leaves requires significant effort and expertise whereas, precision farming and automated disease detection methods can greatly support farmers by facilitating sustainable agriculture To address this challenge a novel web based application AgriCure was developed which incorporated a multilevel approach to detect the plant disease and nutrient deficiency with high level. It uses a hybrid augmentation-based YOLOv8 DL model for image analysis. The study focuses on detecting diseases like Downy Mildew, Leaf Spot, and Jassid, as well as nutrient deficiencies such as Potassium, Magnesium, and Nitrogen Deficiency and their combinations. The initial dataset of 785 images was increased to 2430 images using advanced data augmentation. The results on the augmented dataset after 100 epochs demonstrated high effectiveness with the augmented dataset. The model achieved an impressive mean Average Precision (mAP50) of 92.9 % at an Intersection over Union (IoU) threshold of 0.50 and a mAP50–95 of 91.5 % across IoU thresholds from 0.50 to 0.95. Nearly all predicted positive instances were true positives, with a precision rate of 89.6 % and a recall of 86.6 %, which showed the capacity of the model in identifying true positives. The F1 score of 91.66 % highlighted balanced performance of the model between precision and recall, emphasising its reliability and accuracy. The model shows low losses, with a Box loss of 0.2435, a Class loss of 0.1689, and a Distribution Focal Loss (dfl loss) of 0.9024. This approach offered a valuable tool for early and accurate detection of disease and nutrient deficiency. Detection results indicate that, compared to previous methods, the proposed approach significantly improves overall performance and addresses challenges tied to limited dataset sizes.
{"title":"AgriCure: A web application based layered augmentation-enhanced YOLOv8 for disease and nutrient deficiency detection in bitter gourd leaves","authors":"Kamaldeep Joshi , Sumit Kumar , Varun Kumar , Rainu Nandal , Yogesh Kumar , Narendra Tuteja , Ritu Gill , Sarvajeet Singh Gill","doi":"10.1016/j.cpb.2025.100517","DOIUrl":"10.1016/j.cpb.2025.100517","url":null,"abstract":"<div><div>Bitter gourd is an important cucurbitaceous vegetable widely grown in India and other tropical and subtropical regions and appreciated for its nutritional, medicinal, and economic values. Traditional way of detecting diseases and nutrient deficiencies in bitter gourd leaves requires significant effort and expertise whereas, precision farming and automated disease detection methods can greatly support farmers by facilitating sustainable agriculture To address this challenge a novel web based application AgriCure was developed which incorporated a multilevel approach to detect the plant disease and nutrient deficiency with high level. It uses a hybrid augmentation-based YOLOv8 DL model for image analysis. The study focuses on detecting diseases like Downy Mildew, Leaf Spot, and Jassid, as well as nutrient deficiencies such as Potassium, Magnesium, and Nitrogen Deficiency and their combinations. The initial dataset of 785 images was increased to 2430 images using advanced data augmentation. The results on the augmented dataset after 100 epochs demonstrated high effectiveness with the augmented dataset. The model achieved an impressive mean Average Precision (mAP50) of 92.9 % at an Intersection over Union (IoU) threshold of 0.50 and a mAP50–95 of 91.5 % across IoU thresholds from 0.50 to 0.95. Nearly all predicted positive instances were true positives, with a precision rate of 89.6 % and a recall of 86.6 %, which showed the capacity of the model in identifying true positives. The F1 score of 91.66 % highlighted balanced performance of the model between precision and recall, emphasising its reliability and accuracy. The model shows low losses, with a Box loss of 0.2435, a Class loss of 0.1689, and a Distribution Focal Loss (dfl loss) of 0.9024. This approach offered a valuable tool for early and accurate detection of disease and nutrient deficiency. Detection results indicate that, compared to previous methods, the proposed approach significantly improves overall performance and addresses challenges tied to limited dataset sizes.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100517"},"PeriodicalIF":5.4,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144587713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-05DOI: 10.1016/j.cpb.2025.100516
Enikő Mészáros , Márton Szabó , Kamilla Kovács , Etelka Kovács , Klaudia Hoffmann , Katalin Perei , Attila Bodor , Gábor Feigl
During the COVID-19 pandemic, the widespread use of single-use personal protective equipment (PPE), such as masks and gloves, led to their increasing appearance in natural environments. These items continue to be detected in plastic pollution surveys, raising concerns about their ecological impacts, as PPE waste can release smaller plastic fragments and hazardous compounds during degradation. This study examines the effects of polypropylene mask, latex, and nitrile glove leachates on early root development in 12 species of crops, including legumes, crucifers, monocots, and other dicots. Leachates were chemically characterized using humification indices and plastic aging was assessed via Fourier transform infrared spectroscopy. The results revealed species-specific phytotoxic responses. Crimson clover showed strong sensitivity to all leachates, with reduced germination, germination index, and root elongation. Among the crucifers, radish was inhibited, while white mustard and cress exhibited root stimulation under certain treatments. Buckwheat showed high sensitivity to latex leachates, while flax showed variable responses. Monocots generally tolerated PPE leachates, rice showed minimal response, and sorghum showed growth stimulation. These differences probably reflect species-specific physiological traits and the composition of the leachates. The use of multiple plant species also highlights contrasting sensitivity profiles that are not apparent in single-species tests. This preliminary screening demonstrates that PPE-derived leachates can alter early plant development in a species-dependent manner. The findings underscore the ecological risks posed by PPE waste and support the need for further studies on the environmental impact of pandemic-related plastic pollution.
{"title":"Preliminary phytotoxicological screening of personal protective equipment leachates: Species-specific root growth responses in early plant stages","authors":"Enikő Mészáros , Márton Szabó , Kamilla Kovács , Etelka Kovács , Klaudia Hoffmann , Katalin Perei , Attila Bodor , Gábor Feigl","doi":"10.1016/j.cpb.2025.100516","DOIUrl":"10.1016/j.cpb.2025.100516","url":null,"abstract":"<div><div>During the COVID-19 pandemic, the widespread use of single-use personal protective equipment (PPE), such as masks and gloves, led to their increasing appearance in natural environments. These items continue to be detected in plastic pollution surveys, raising concerns about their ecological impacts, as PPE waste can release smaller plastic fragments and hazardous compounds during degradation. This study examines the effects of polypropylene mask, latex, and nitrile glove leachates on early root development in 12 species of crops, including legumes, crucifers, monocots, and other dicots. Leachates were chemically characterized using humification indices and plastic aging was assessed via Fourier transform infrared spectroscopy. The results revealed species-specific phytotoxic responses. Crimson clover showed strong sensitivity to all leachates, with reduced germination, germination index, and root elongation. Among the crucifers, radish was inhibited, while white mustard and cress exhibited root stimulation under certain treatments. Buckwheat showed high sensitivity to latex leachates, while flax showed variable responses. Monocots generally tolerated PPE leachates, rice showed minimal response, and sorghum showed growth stimulation. These differences probably reflect species-specific physiological traits and the composition of the leachates. The use of multiple plant species also highlights contrasting sensitivity profiles that are not apparent in single-species tests. This preliminary screening demonstrates that PPE-derived leachates can alter early plant development in a species-dependent manner. The findings underscore the ecological risks posed by PPE waste and support the need for further studies on the environmental impact of pandemic-related plastic pollution.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100516"},"PeriodicalIF":5.4,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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