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Optimizing Soursop leaf disease classification with a lightweight ensemble model and explainable AI 基于轻量级集成模型和可解释人工智能优化刺蒺藜叶病分类
IF 4.5 Q1 PLANT SCIENCES Pub Date : 2025-07-26 DOI: 10.1016/j.cpb.2025.100526
Sumaya Mustofa, Shahrin Khan, Shahriar Ahmed Shovo, Yousuf Rayhan Emon, Md. Sadekur Rahman
Traditional deep-learning methods to detect plant leaf disease can be complex and time-consuming if image numbers and size increase. Moreover, complex deep learning networks take longer and require larger memory to produce results. However, feature extraction methods provide some advantages in such a scenario. Using heavy-weighted models to enhance accuracy without considering the long execution time is a drawback of research. A weighted model increases the time and space complexity of an experiment. Considering the mentioned limitations, this study proposes a lightweight model experimenting with six deep feature extraction models, five feature selection models, and four machine learning classifiers. During the experiment, a soft voting ensemble classifier was developed to remove a single classifier's limitations and the unstable performance of the standalone classifiers. After a rigorous experiment, the (ResNet101 – RFE – Ensemble Classifier) together formed the best performer Soursop Ensemble (S-Ensemble) model that obtained a test accuracy of 99.6 % with an execution time of 648.05 s, outperforming other models. The whole experimental analysis was performed on a primary Soursop leaf disease dataset with six classes containing 3838 images. Finally, the Explainable AI (XAI) model Local Interpretable Model-agnostic Explanations (LIME) is used to interpret the reasons behind the best-performer and lowest-performer models' performance. LIME visually highlights which leaf regions influence each prediction, helping users understand model behaviour and enhancing its practical usability in real-world agricultural settings. This research aims to assist farmers with detecting Soursop leaf disease with less execution time and offer researchers an in-depth preview of deep feature-based detection and classification technology to detect and classify diseases within a short training time.
当图像数量和大小增加时,传统的深度学习方法检测植物叶片病害可能会变得复杂且耗时。此外,复杂的深度学习网络需要更长的时间和更大的内存才能产生结果。然而,特征提取方法在这种情况下提供了一些优势。使用重权重模型来提高准确性而不考虑较长的执行时间是研究的一个缺点。加权模型增加了实验的时间和空间复杂性。考虑到上述局限性,本研究提出了一个轻量级模型,实验了6个深度特征提取模型、5个特征选择模型和4个机器学习分类器。在实验中,开发了一种软投票集成分类器,以消除单个分类器的局限性和独立分类器的不稳定性能。经过严格的实验,(ResNet101 - RFE -Ensemble Classifier)共同形成了性能最好的Soursop Ensemble (s -Ensemble)模型,其测试准确率为99.6 %,执行时间为648.05 s,优于其他模型。整个实验分析是在一个包含6个类3838张图像的刺蒺藜叶病初级数据集上进行的。最后,可解释AI (XAI)模型局部可解释模型不可知解释(LIME)用于解释性能最佳和性能最差模型性能背后的原因。LIME在视觉上突出显示了哪些叶片区域影响每个预测,帮助用户理解模型行为,并增强其在现实农业环境中的实际可用性。本研究旨在帮助农民以更少的执行时间检测番荔枝叶病,并为研究人员提供深度预览基于深度特征的检测分类技术,在较短的培训时间内检测和分类疾病。
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引用次数: 0
Caleosin expression enhances plant insect resistance 钙红蛋白的表达增强了植物的抗虫性
IF 4.5 Q1 PLANT SCIENCES Pub Date : 2025-07-24 DOI: 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.
研究了大戟科植物(Euphorbia tirucalli)乳胶中积累的角绿蛋白同源物CLO3的抗虫活性。用瞬时产EtCLO3的烟叶饲喂斜纹夜蛾(Spodoptera litura)幼虫,记录其体重。EtCLO3的产生显著延缓了幼虫的生长。其他植物的钙红蛋白同源物也有类似的效果,这些同源物共享位于Ca2 +结合EF-hand上游的独特n端基序,包括拟南芥CLO3 (AT2G33380)和低等植物的同源物(苔类植物Mapoly0027s0099和衣藻Cre06.g273650_4532)。相比之下,a . thaliana CLO5 (AT5G19530)属于另一类红蛋白,没有表现出这种生长迟缓作用。值得注意的是,即使其过氧酶催化位点或EF-hand发生突变,EtCLO3的抗虫活性仍然存在。转录组分析显示,EtCLO3上调了内源性防御相关基因的表达水平,改变了糖代谢途径。这些发现表明,EtCLO3可能至少部分地通过激活寄主植物的内源性防御系统来发挥其抗虫作用。这项研究揭示了EtCLO3和其他一些同源蛋白如何影响幼虫的发育,并提出了这些蛋白在害虫管理中的潜在应用。
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引用次数: 0
Strong elicitation of plant defense pathways by foliar and collar inoculations of wheat with the Bacillus pumilus strain JM79 短柄芽孢杆菌JM79在小麦叶面和穗部接种后对植物防御途径的激活作用
IF 4.5 Q1 PLANT SCIENCES Pub Date : 2025-07-22 DOI: 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.
采用镰孢冠腐病(Fusarium crown rot, FCR)病原菌系统,研究了矮秆芽孢杆菌JM79菌株诱导小麦对主要小麦病原菌镰刀菌(Fusarium graminearum, Fg)产生全身抗性的能力。短柄双歧杆菌JM79在小麦植株根区分泌类似于表面素的短柄双歧杆菌素,同时具有在根和叶表面定殖的能力。叶面接种JM79的实验表明,JM79能够诱导小麦产生强烈的局部防御反应,其特征是与苯丙素代谢和细胞壁强化途径相关的基因选择性过表达。此外,在接种Fg之前,在土壤表面界面处预先接种了JM79菌株,导致与茉莉酸/乙烯(JA/ET)和水杨酸(SA)依赖性防御通路相关的小麦基因过表达。这种直接诱导发生在Fg感染的无症状阶段,弥补了Fg感染引发的早期免疫反应的缺乏或缺失。综上所述,这些研究结果首次揭示了矮螺旋体菌株JM79在植物体内比在体外条件下产生更高比例的长链矮螺旋体酸素,并且能够激活小麦植株的局部和全身抗性,强调了其作为主要小麦真菌病害生物防治剂的潜力。
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引用次数: 0
Unifying RNA-seq data using meta-analysis: Bioinformatics frameworks and application for plant genomics 使用元分析统一RNA-seq数据:生物信息学框架及其在植物基因组学中的应用
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-21 DOI: 10.1016/j.cpb.2025.100523
Bahman Panahi , Rasmieh Hamid , Feba Jacob , Hossein Mohammadzadeh Jalaly
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.
RNA测序(RNA- seq)通过实现不同条件下基因表达的高分辨率分析,改变了植物基因组学。然而,由于实验设计、测序平台和数据处理工作流程的差异,整合来自不同研究的RNA-Seq数据具有挑战性,这限制了转录组数据集的可比性和适用性。这篇综述概述了当前的元分析方法,这些方法解决了这些挑战,并提高了RNA-Seq数据整合的一致性、准确性和可解释性。我们讨论了数据规范化技术、汇总结果的统计框架和减少研究间可变性的计算工具等方法。我们还强调了预处理策略,包括批效应校正和标准化基因注释管道,这有助于可靠的交叉研究比较。我们强调RNA-Seq meta分析在植物基因组学中的实际意义。荟萃分析提高了一致性差异表达基因(DEGs)的鉴定,增强了功能注释,揭示了植物物种间保守的调控机制。这些见解在精确育种、应激反应研究和性状改良项目中都有应用。对于实施元分析的研究人员,本综述概述了关键考虑因素、推荐做法和可用资源。最后,我们强调了标准化协议和促进多组学集成的必要性,以解锁更深入的见解。随着转录组学数据集的扩展,元分析将在促进我们对植物生物学的理解及其在农业中的应用方面发挥至关重要的作用。
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引用次数: 0
Open cotton boll detection using LiDAR point clouds and RGB images from unmanned aerial systems 利用激光雷达点云和无人机系统的RGB图像进行开棉铃检测
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-17 DOI: 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.
准确量化开铃及其分布对了解棉花的生长发育和产量、优化作物管理和提高育种水平具有重要意义。人工计数法耗时、费力、主观。利用高分辨率图像的潜力进行高通量表型分析,为有效的性状量化提供了一条有前途的途径。本研究的目的是开发利用激光雷达点云和RGB图像检测和计数开放棉铃的方法,并比较这两种数据源的有效性。方法采用搭载4 K RGB相机的大疆Phantom 4 RTK无人机系统(UAS)获取高分辨率RGB图像,采用搭载Zenmuse L1传感器的大疆matrix 300 RTK获取LiDAR点云数据。采用摄影测量法,通过测量重叠图像的多个点,将RGB图像转换为点云。棉铃检测工作流程包括使用基于密度的空间聚类(DBSCAN)方法对数据进行过滤和聚类。采用平均绝对百分比误差(MAPE)、均方根误差(RMSE)和决定系数(r²)等指标对48个代表小型、中型和大型植物规模的地块进行了方法评估。结果使用两种数据源的方法在估计开铃方面表现良好,激光雷达点云数据略优于RGB图像。一般来说,DBSCAN方法在棉铃检测中的性能随着株型的减小而提高。具体来说,激光雷达数据得出的MAPE值分别为5.03 %、8.05 %和13.46 %,RMSE值分别为7.26、14.33和23.40铃/ m²,r2值分别为0.93、0.84和0.84。基于RGB图像的数据显示,小、中、大株型的MAPE值分别为7.21 %、6.49 %和16.41 %,RMSE值分别为11.05、13.66和26.49铃/ m²,r2值分别为0.82、0.74和0.83。结论该方法显示了RGB图像和激光雷达数据在估计铃数方面的潜力,为植物育种和特定地点作物管理提供了有价值的工具。这两个数据来源都低估了铃数,较小的植株显示较少的铃数,可能是由于改善了光穿透和铃的分离。这些发现强调了植物结构对棉铃检测精度的影响,以及解决密集冠层带来的挑战以提高检测可靠性的必要性。
{"title":"Open cotton boll detection using LiDAR point clouds and RGB images from unmanned aerial systems","authors":"Zhe Lin ,&nbsp;Wenxuan Guo ,&nbsp;Nathan S. Gill ,&nbsp;Glen Ritchie ,&nbsp;Brendan Kelly ,&nbsp;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}
引用次数: 0
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 雷帕霉素(Rapamycin, TOR)信号靶协调小麦光合性能和蒸腾水分保持之间的平衡,以提高干旱条件下的水分利用效率和性能
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-16 DOI: 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。
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引用次数: 0
Salinity-tolerant rice: A sustainable solution for food security and greenhouse gas mitigation 耐盐碱水稻:粮食安全和温室气体减排的可持续解决方案
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-09 DOI: 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.
甲烷(CH₄)的排放对全球环境构成了重大挑战。依赖水田的水稻种植占这些排放量的45% %以上。预测表明,到2030年,大米的氯化碳排放量预计将增加35 - 60% %。有效的减排策略包括直接播种水稻(DSR)和替代干湿(AWD)技术。这篇综述研究了盐碱稻生态系统中4氯化甲烷的排放,强调了这些环境中排放量较低的大量证据。我们探索了盐水环境中独特的微生物过程,这些过程可以改变分子和生理途径,最终抑制产甲烷微生物并减少CH₄排放。此外,我们还强调了盐碱化生态系统在加强粮食安全的同时遏制氯化甲烷排放方面的巨大潜力。我们还讨论了利用现代工具和技术开发下一代耐盐水稻品种的迫切需要,以应对高盐条件。最后,耐盐碱水稻提供了增加粮食安全和减少环境影响的双重好处,从而促进了盐碱地生态系统区域的可持续农业做法。
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引用次数: 0
Pre-harvest application of sodium alginate functionalized with melatonin enhances secondary metabolism in strawberry fruit 采前施用褪黑素功能化海藻酸钠促进草莓果实次生代谢
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-08 DOI: 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。
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引用次数: 0
CRISPR/Cas9 mutagenesis generated elite alleles of a novel yield gene An-1 leading to increased grain number in rice (Oryza sativa L.) CRISPR/Cas9诱变产生水稻产量新基因An-1的精英等位基因,导致水稻粒数增加
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-07 DOI: 10.1016/j.cpb.2025.100511
Shobica Priya Ramasamy , Sakthi Ambothi Rathnasamy , Sudha Manickam , Veeraranjani Rajagopalan , Rakshana Palaniswamy , Vignesh Mohanavel , Rohit Kambale , Manonmani Swaminathan , Kalaimagal Thiyagarajan , Raja Ragupathy , Raveendran Muthurajan
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.
水稻(Oryza sativa L.)的驯化可以追溯到8000年前,当时通过人工选择开始了产量性状的选择。水稻生产的预计需求、产量平台和气候变化给我们提供了一个线索,即提高产量潜力对粮食安全至关重要。确定控制产量性状的基因和C4光合作用等机制是实现水稻持续增产的必要条件。在这项研究中,我们利用CRISPR/Cas9诱变技术,利用一种新的驯化基因An-1来提高水稻的产量潜力。对水稻品种ASD 16的312个 T0后代进行评价,鉴定出17个多等位基因突变、7个双等位基因突变和4个单等位基因突变。对T2和T3后代的评价发现了每穗粒数增加的纯合子和无转基因突变体。结果表明,与野生型ASD 16相比,T4突变体的穗次分枝增加(22.8 %),穗粒数增加(34.8 %),单株产量增加(35.25 %)。本研究发现An-1是水稻增产的一个新的候选基因。
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引用次数: 0
AgriCure: A web application based layered augmentation-enhanced YOLOv8 for disease and nutrient deficiency detection in bitter gourd leaves 农业:基于web应用程序的分层增强YOLOv8,用于苦瓜叶片的疾病和营养缺乏检测
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-07-07 DOI: 10.1016/j.cpb.2025.100517
Kamaldeep Joshi , Sumit Kumar , Varun Kumar , Rainu Nandal , Yogesh Kumar , Narendra Tuteja , Ritu Gill , Sarvajeet Singh Gill
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.
苦瓜是一种重要的葫芦科蔬菜,广泛种植在印度和其他热带和亚热带地区,具有营养、药用和经济价值。传统的检测苦瓜叶片疾病和营养缺乏的方法需要大量的努力和专业知识,而精准农业和自动化疾病检测方法可以通过促进可持续农业极大地支持农民。为了解决这一挑战,开发了一种新的基于web的应用程序农业,该应用程序结合了多层次的方法来检测植物疾病和营养缺乏。它使用基于混合增强的YOLOv8 DL模型进行图像分析。该研究的重点是检测霜霉病、叶斑病和茉莉病等疾病,以及钾、镁、氮缺乏及其组合等营养缺乏症。使用高级数据增强技术,将初始数据集785张图像增加到2430张图像。在增强数据集上进行100次epoch后的结果表明,增强数据集具有较高的有效性。该模型实现了令人印象深刻的平均精度(mAP50),在交叉口交叉口(IoU)阈值为0.50时,平均精度(mAP50)为92.9 %,在IoU阈值为0.50至0.95时,平均精度(mAP50 - 95)为91.5 %。几乎所有预测的阳性实例都是真阳性,准确率为89.6 %,召回率为86.6 %,表明该模型具有识别真阳性的能力。F1得分为91.66 %,突出了模型在查准率和查全率之间的平衡表现,强调了模型的可靠性和准确性。该模型具有较低的损耗,盒损耗为0.2435,类损耗为0.1689,分布焦损耗(dfl损耗)为0.9024。这种方法为早期准确检测疾病和营养缺乏提供了有价值的工具。检测结果表明,与以前的方法相比,所提出的方法显着提高了整体性能,并解决了与有限数据集大小相关的挑战。
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引用次数: 0
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Current Plant Biology
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