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Search Results (592)

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Keywords = crop protection methods

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18 pages, 4237 KiB  
Article
Characterization of the Giant Foxtail’s (Setaria faberi) ALS Gene and Its Enhanced Metabolism-Based Cross-Resistance to Nicosulfuron and Rimsulfuron
by Aristeidis P. Papapanagiotou, Maria V. Alvanou, Ioannis A. Giantsis, Ioannis Vasilakoglou and Ilias G. Eleftherohorinos
Genes 2025, 16(5), 505; https://doi.org/10.3390/genes16050505 - 27 Apr 2025
Viewed by 70
Abstract
Background: Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields. Methods: Five putative resistant giant [...] Read more.
Background: Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields. Methods: Five putative resistant giant foxtail populations, originating from corn monoculture fields in northeastern Greece, were evaluated for possible evolution of ALS-inhibitor resistance (nicosulfuron, rimsulfuron). The resistance ratio, the underlying resistance mechanism, and its impact on competitive ability against corn were studied. Results: The whole-plant rate-response assays showed that these populations were resistant (R) to the sulfonylureas nicosulfuron and rimsulfuron, but susceptible (S) to imidazolinone imazamox, triketone 4-hydroxyphenylpyruvate dioxygenase inhibitor tembotrione, and acetyl-CoA carboxylase inhibitor cycloxydim. The sequencing of the ALS gene did not reveal the presence of resistance-associated point mutations, indicating that the resistance was probably not target-site mediated. This was confirmed by the application of piperonyl butoxide two hours before nicosulfuron application, which reversed the resistance in all R giant foxtail populations, supporting the evidence of enhanced metabolism-mediated resistance. The competition study between corn and R or S giant foxtail populations indicated no stable trend reduction in corn traits, suggesting that the resistance mechanism was not associated with the competitive ability of the R populations. The novel ALS genotype in S. faberi, characterized for the first time and submitted to the GenBank database with accession number PV016837, indicated a closer genetic relationship with the S. viridis ALS gene than with S. italica. Conclusions: Five giant foxtail populations have evolved metabolism-based resistance to the ALS-inhibiting herbicides nicosulfuron and rimsulfuron. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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12 pages, 1916 KiB  
Article
Correlational Analysis with Regards to the Causes of Chemical Intoxication Due to Pesticides Among Farmers in Bogotá, Colombia: A Cross-Sectional Observational Study
by Mayra Daniela Maldonado, Katherine Montaña-Oviedo, Diana M. Ballén, Juan de Dios Villegas and Alejandro Botero Carvajal
Safety 2025, 11(2), 38; https://doi.org/10.3390/safety11020038 - 24 Apr 2025
Viewed by 255
Abstract
Background: Farmers are continuously exposed to pesticides during crop production, which can lead to both acute and chronic poisoning. This exposure poses a significant global public health concern. In response, this study aims to achieve two primary objectives: (1) to identify the correlation [...] Read more.
Background: Farmers are continuously exposed to pesticides during crop production, which can lead to both acute and chronic poisoning. This exposure poses a significant global public health concern. In response, this study aims to achieve two primary objectives: (1) to identify the correlation between pesticide intoxication cases among farmers and their potential causes and (2) to assess the relationship between risk–control measures, hygiene practices, and resulting health effects. Methods: This study employed a cross-sectional mixed-methods observational design, sampling 112 farmers from Bogotá’s rural areas. Data were analyzed using logistic regression in R (version 4.2.1), examining eight associated variables. Results: The use of personal protective equipment (PPE) ranged from approximately 62% to 92%. Additionally, 82% of participants reported changing their workwear and 76% practiced bodily hygiene after exposure. Nevertheless, health complaints persisted—particularly affecting vision (46%), the respiratory system (38%), and the skin (32%). Notably, two out of every three farmers reported experiencing some form of systemic illness associated with pesticide exposure. Conclusion: A strong association was observed between the use of facemasks and changing workwear and the prevention of pesticide-related intoxication. These practices appear to be key in reducing chemical exposure during fumigation activities. Full article
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17 pages, 5105 KiB  
Article
Influence of Drying Methods on the Post-Harvest Quality of Coffee: Effects on Physicochemical, Sensory, and Microbiological Composition
by Danilo José Machado de Abreu, Mário Sérgio Lorenço, Gilson Gustavo Lucinda Machado, Joana Moratto Silva, Estela Corrêa de Azevedo and Elisângela Elena Nunes Carvalho
Foods 2025, 14(9), 1463; https://doi.org/10.3390/foods14091463 - 23 Apr 2025
Viewed by 159
Abstract
This study evaluated the impact of different drying methods on the physicochemical, microbiological, and sensory qualities of coffees produced in the Campos das Vertentes (CV) and Alta Mogiana (AM) regions of Brazil. The sun-drying (S), sun-drying combined with rotary mechanical dryer (SM), and [...] Read more.
This study evaluated the impact of different drying methods on the physicochemical, microbiological, and sensory qualities of coffees produced in the Campos das Vertentes (CV) and Alta Mogiana (AM) regions of Brazil. The sun-drying (S), sun-drying combined with rotary mechanical dryer (SM), and CoffeeDryer® mechanical dryer (C) methods were compared at different harvest times for the same crop (2024). The results indicated that CoffeeDryer® preserved relatively high levels of phenolic compounds and antioxidant activity, reaching 3.24 g of gallic acid equivalents per 100 g (g EAG·100 g−1) and 47.96% antioxidant protection in the coffees produced in Alta Mogiana, whereas the sun-dried coffees presented relatively low values (2.20 g EAG·100 g−1 and 28.96% protection). In the Campos das Vertentes region, C maintained 2.78 g EAG·100 g−1 phenolic compounds and 50.29% antioxidant protection, outperforming combined drying (2.48 g EAG·100 g−1 and 41.17%). Regardless of the region and time of harvest, the coffees dried by C had a water activity of less than 0.6 and more stable moisture content (7.73–10.42%), reducing the possibility of proliferation of filamentous fungi and, consequently, mycotoxins. In the sensory evaluation, CoffeeDryer® guaranteed higher scores for fragrance/aroma and flavor, allowing the coffees to reach 80 to 81 points on the SCA scale, which is classified as special. Thus, the use of CoffeeDryer® proved to be an efficient alternative for optimizing coffee drying, preserving its chemical and microbiological qualities, and enhancing its commercial and sensory value. Full article
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15 pages, 1608 KiB  
Article
Dissipation Kinetics and Dietary Risk Assessment of Boscalid Residues in Two Table-Grape Varieties Under Field Conditions
by Paraskevas Parlakidis, George S. Adamidis, Theodoros Doulaveris, Dimitrios Makaridis, Christos Alexoudis, Zisis Vryzas and Georgios D. Gikas
Environments 2025, 12(5), 133; https://doi.org/10.3390/environments12050133 - 22 Apr 2025
Viewed by 191
Abstract
Grape cultivation is crucial due to its significant dietary benefits and the production of various byproducts. Fungicides, like boscalid, are frequently applied to protect grape crops from several disease, ensuring both yield and quality. However, the excessive or inappropriate application of boscalid may [...] Read more.
Grape cultivation is crucial due to its significant dietary benefits and the production of various byproducts. Fungicides, like boscalid, are frequently applied to protect grape crops from several disease, ensuring both yield and quality. However, the excessive or inappropriate application of boscalid may pose health risks to humans. Therefore, the objectives of this field study were (a) to assess the pre-harvest interval (PHI) and dissipation of boscalid in two table-grape varieties (Soultanina and Crimson) under field conditions and (b) evaluate the potential health risks associated with grape consumption for both adults and children. The residue of boscalid in the grapes was determined using a modified QuEChERS method coupled with a high-performance liquid chromatography diode array detector (HPLC–DAD). The dissipation of boscalid followed first- and second-order kinetics, with half-lives ranging from 3.32 to 6.42 days and PHIs from 8.11 to 10.90 days. The dietary risk assessment indicated that the early to mid-post application period could pose risks for both age groups, with children facing three times the risk of adults. Full article
(This article belongs to the Special Issue Environmental Pollutant Exposure and Human Health)
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19 pages, 1786 KiB  
Article
Contamination of Wheat Flour and Processed Foodstuffs with Soybean and Mustard Allergenic Proteins
by Mariachiara Bianco, Domenico De Palma, Antonio Pagano, Ilario Losito, Tommaso R. I. Cataldi and Cosima D. Calvano
Int. J. Mol. Sci. 2025, 26(8), 3891; https://doi.org/10.3390/ijms26083891 - 20 Apr 2025
Viewed by 101
Abstract
In recent years, sustainable agricultural practices in wheat cultivation have garnered significant attention, particularly those focused on minimizing pesticide and herbicide usage to safeguard the environment. One effective approach is green manuring, which entails rotating wheat with crops such as soybean and mustard [...] Read more.
In recent years, sustainable agricultural practices in wheat cultivation have garnered significant attention, particularly those focused on minimizing pesticide and herbicide usage to safeguard the environment. One effective approach is green manuring, which entails rotating wheat with crops such as soybean and mustard to harness their natural pesticidal and herbicidal properties. While this method presents clear environmental advantages, it also poses a risk of cross-contamination, as these globally recognized allergens may unintentionally pass through wheat-based products. To protect consumers with allergies, there is an urgent need for a reliable analytical method to detect and quantify these allergenic proteins in wheat-derived foodstuffs. In this study, we assessed various protein extraction protocols to optimize the recovery of soybean and mustard allergens from wheat flour. The extracted proteins were analyzed using a bottom-up proteomics approach involving trypsin digestion, coupled with reversed-phase liquid chromatography and mass spectrometry in multiple reaction monitoring (MRM) mode. Two key allergenic proteins, Glycinin G1 and 11S Globulin, were selected as representative for soybean and mustard, respectively. The identified quantifier marker of Glycinin G1 was VLIVPQNFVVAAR (m/z 713.4312+), while FYLAGNQEQEFLK (m/z 793.8962+) and VFDGELQEGR (m/z 575.2802+) were designated as qualifier markers. The selection of specific marker peptides for mustard proved challenging due to the high structural similarity among proteins from Sinapis alba and other members of the Brassicaceae family. For 11S Globulin, FNTLETTLTR (m/z 598.3192+) was recognized as the quantifier marker, with VTSVNSYTLPILQYIR (m/z 934.0192+) serving as the qualifier marker. The developed method underwent thorough validation for linearity, limit of detection (LOD), limit of quantification (LOQ), recovery, repeatability, and reproducibility, as well as potential matrix and processing effects. This strategy successfully facilitated the identification and quantification of soybean and mustard allergenic proteins in complex, processed food matrices, including naturally contaminated flour and cookies. These findings enhance food safety monitoring and regulatory compliance, thereby helping to mitigate allergen-related risks in wheat-based products. Full article
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26 pages, 3678 KiB  
Article
Digital Image Copyright Protection and Management Approach—Based on Artificial Intelligence and Blockchain Technology
by Jikuan Xu, Jiamin Zhang and Junhan Wang
J. Theor. Appl. Electron. Commer. Res. 2025, 20(2), 76; https://doi.org/10.3390/jtaer20020076 - 18 Apr 2025
Viewed by 309
Abstract
The issue of image copyright infringement is prevalent in current e-commerce activities. Users employ methods such as image cropping, compression, and noise addition, making it difficult for traditional copyright detection technologies to identify and track infringements. This study proposes an image copyright registration, [...] Read more.
The issue of image copyright infringement is prevalent in current e-commerce activities. Users employ methods such as image cropping, compression, and noise addition, making it difficult for traditional copyright detection technologies to identify and track infringements. This study proposes an image copyright registration, protection, and management method based on artificial intelligence and blockchain technology, aiming to address the current challenges of low accuracy in digital copyright infringement judgment, the vulnerability of image fingerprints stored on the chain to tampering, the complexity of encryption algorithms and key acquisition methods through contract calls, and the secure storage of image information during data circulation. The research combines artificial intelligence technology with traditional blockchain technology to overcome the inherent technical barriers of blockchain. It introduces an originality detection model based on deep learning technology after conducting both off-chain and on-chain detection of unidentified images, providing triple protection for digital image copyright infringement detection and enabling efficient active defense and passive evidence storage. Additionally, the study improves upon the traditional image perceptual hashing in blockchain, which has poor robustness, by adding chaotic encryption sequences to protect the image data on the chain, and its effectiveness has been verified through experiments. Ultimately, the research hopes to provide e-commerce entities with an effective and feasible digital copyright protection and management solution, safeguarding their intellectual property rights and fostering a legal and reasonable competitive environment in e-commerce. Full article
(This article belongs to the Special Issue Blockchain Business Applications and the Metaverse)
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13 pages, 1396 KiB  
Article
Occurrence and Ecological Risks of Neonicotinoids in Wheat, Corn and Rice Field Soils in China
by Junxue Wu, Pingzhong Yu, Ziyu Zou, Ercheng Zhao, Junjie Jing, Jinwei Zhang, Yan Tao, Lirui Ren, Min He, Li Chen and Ping Han
Molecules 2025, 30(8), 1803; https://doi.org/10.3390/molecules30081803 - 17 Apr 2025
Viewed by 158
Abstract
The global application of neonicotinoids (NEOs) has precipitated pervasive contamination of agricultural matrices, with China’s staple crop lands representing critical exposure hotspots. The occurrence and ecological risks of ten NEOs in the field soils of three major crops (i.e., rice, wheat and corn) [...] Read more.
The global application of neonicotinoids (NEOs) has precipitated pervasive contamination of agricultural matrices, with China’s staple crop lands representing critical exposure hotspots. The occurrence and ecological risks of ten NEOs in the field soils of three major crops (i.e., rice, wheat and corn) in China were investigated in the present study. Employing an optimized UPLC-MS/MS method (LOQ = 0.01–1.7 ng/g, RSD < 12.21%), ten NEOs across 69 representative field soils (rice: 23, corn: 18, wheat: 28) were quantified. It was found that the detection frequency (DF) of the NEOs was 100% in the soil. The DFs of NEOs in the soil followed the rule: imidacloprid (IMI, 100%) > thiamethoxam (TMX, 88.4%) > clothianidin (CLO, 87.0%) > acetamiprid (ACE, 46.4%) > dinotefuran (DIN, 7.2%) > nitenpyram (NIT, 1.4%). Mean total detected NEOs concentrations exhibited crop-dependent type: wheat (1.77–214.55 ng/g) > corn (0.79–97.53 ng/g) > rice (0.75–72.97 ng/g). The IMI, CLO and TMX triad constituted over 90% of the total contribution of detected NEOs. In addition, CLO and TMX in the rice soils, IMI, CLO and TMX in the corn soils and IMI, CLO and TMX in the wheat soils had medium ecological risks. Therefore, it is particularly important for agricultural ecological protection to strengthen monitoring and take effective measures to protect agricultural ecology. Full article
(This article belongs to the Special Issue Analysis of Pesticide Residues in Food and Environmental Samples)
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19 pages, 4066 KiB  
Review
Integrating Organic Fertilizers in Coconut Farming: Best Practices and Application Techniques
by Anjana J. Atapattu, Tharindu D. Nuwarapaksha, Shashi S. Udumann and Nuwandhya S. Dissanayaka
Crops 2025, 5(2), 17; https://doi.org/10.3390/crops5020017 - 3 Apr 2025
Viewed by 310
Abstract
Organic fertilizers are a revolutionary concept in coconut farming as they provide a package for sustainable coconut production. This review examines the multiple advantages of organic fertilization methods and types of organic fertilizers, which include compost, vermicompost, livestock manure, green manure, crop residues, [...] Read more.
Organic fertilizers are a revolutionary concept in coconut farming as they provide a package for sustainable coconut production. This review examines the multiple advantages of organic fertilization methods and types of organic fertilizers, which include compost, vermicompost, livestock manure, green manure, crop residues, and biofertilizers. The review focuses on the best practices, application methods, time of application, frequency and rate of application of nutrients for coconut palm at various developmental stages. The study provides a detailed and systematic review of the environmental, economic and social impacts of organic fertilization. Benefits include enhanced soil health, biodiversity promotion, carbon sequestration, cost effectiveness, quality improvement of the yield, food security and possibilities of creating rural income. Issues including resource accessibility difficulties, nutrient deficiencies, and intensive labor requirements are explored in detail, as well as future trends that focus on advanced technologies, new research areas, and policy approaches. Thus, the study reviews organic fertilization as a coherent concept that can be applied to coconut production and other goals of environmental protection, food security, and sustainable development of agriculture. Full article
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19 pages, 1149 KiB  
Article
The Potential Role of Precision Agriculture in Building Sustainable Livelihoods and Farm Resilience Amid Climate Change: A Stakeholders’ Perspective from Southern Punjab, Pakistan
by Aamir Raza, Ejaz Ashraf, Saima Sadaf, Nasir Abbas Khan, Ashfaq Ahmad Shah, Bader Alhafi Alotaib and Muhammad Rafay Muzamil
Land 2025, 14(4), 770; https://doi.org/10.3390/land14040770 - 3 Apr 2025
Viewed by 305
Abstract
This study explores the potential role of precision agricultural technologies (PATs) in enhancing the physical, natural, human, financial, and social capitals of farming communities in the southern Punjab region of Pakistan, specifically focusing on the districts of Bahawalpur, Rahim Yar Khan, Dera Ghazi [...] Read more.
This study explores the potential role of precision agricultural technologies (PATs) in enhancing the physical, natural, human, financial, and social capitals of farming communities in the southern Punjab region of Pakistan, specifically focusing on the districts of Bahawalpur, Rahim Yar Khan, Dera Ghazi Khan, and Multan. A stratified random sampling method with proportional allocation was employed to gather insights from four heterogeneous key stakeholder groups, including progressive farmers, researchers, extension agents, and academicians, yielding a total sample of 287 respondents. A structured questionnaire utilizing a five-point Likert scale was administered, allowing the respondents to assess the perceived potential impacts of the PATs on various livelihood assets. The findings reveal that while stakeholders recognized some potential for PATs to improve physical assets, natural resources, and human capital, the overall perceived impact remained limited across all dimensions. The highest-rated potential impact was noted in crop diversity, with an average score of 2.26 in the physical capital category. In the category of natural capital, precise plant protection practices were rated the highest, with an average score of 2.31 that showed little potential change. A reduction in labor displacement issues and generating skilful employment resources, with average scores of 2.12, were rated the highest in the human capital category. A slight increase in family income, with an average score of 2.28, was observed in the financial capital category, highlighting cautious optimism among respondents. Additionally, reducing family problems and social issues, with an average score of 2.20, was rated the highest, leading to a minimal perceived change in social capital, indicating a need for integrated approaches to foster stronger community ties. The results underscore the necessity for targeted interventions that combine technological adoption with community engagement to enhance the overall resilience of farming systems. This research contributes valuable insights into adopting PATs and their implications for sustainable livelihoods, emphasizing the importance of aligning technological advancements with the unique needs of farming communities in the face of a changing climate. Full article
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20 pages, 2553 KiB  
Article
Combined Mechanical–Chemical Weed Control Methods in Post-Emergence Strategy Result in High Weed Control Efficacy in Sugar Beet
by Jakob Berg, Helmut Ring and Heinz Bernhardt
Agronomy 2025, 15(4), 879; https://doi.org/10.3390/agronomy15040879 - 31 Mar 2025
Viewed by 420
Abstract
Against the backdrop of increasing herbicide resistance and societal and political objectives for reducing plant protection products, combinations of mechanical and herbicide weed control methods are gaining importance. In row crops such as sugar beet, the use of mechanical hoeing between crop rows [...] Read more.
Against the backdrop of increasing herbicide resistance and societal and political objectives for reducing plant protection products, combinations of mechanical and herbicide weed control methods are gaining importance. In row crops such as sugar beet, the use of mechanical hoeing between crop rows (interrow) combined with band spraying of herbicides within rows (intrarow) can lead to significant herbicide savings compared to standard broadcast herbicide applications. However, effective weed control remains crucial. In this study, a two-year field experiment was conducted to evaluate different combinations of band spraying, mechanical hoeing, and broadcast spraying in post-emergence weed control applications in sugar beet. The weed control efficacy of each treatment was assessed relative to an untreated control using weed counting to determine absolute weed density and image analysis to quantify weed cover. Compared to the untreated control, total weed control efficiencies of up to 90.8% (weed counting) and 99.5% (image analysis) were achieved. In comparison to three consecutive broadcast herbicide applications, the mechanical–chemical combinations resulted in a similar or even superior weed control efficacy while enabling herbicide reductions of up to 65.59%. These results highlight the valuable potential of mechanical–chemical weed control combinations for herbicide-reduced weed management within post-emergence application systems in sugar beet. They represent a key tool in the context of integrated weed management (IWM). Full article
(This article belongs to the Section Weed Science and Weed Management)
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23 pages, 3242 KiB  
Article
Profiling of Known and Novel microRNAs in an Oleaginous Crop Native to the Amazon Basin, Sacha Inchi (Plukenetia volubilis), Through smallRNA-Seq
by Richard Estrada, Lila Rodriguez, Yolanda Romero, Linda Arteaga, Domingo Ruelas-Calloapaza, Filiberto Oha-Humpiri, Nils Flores, Pedro Coila and Carlos I. Arbizu
Genes 2025, 16(4), 417; https://doi.org/10.3390/genes16040417 - 31 Mar 2025
Viewed by 297
Abstract
Background: MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in Plukenetia volubilis (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: [...] Read more.
Background: MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in Plukenetia volubilis (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: root, stem, and leaf. Methods: Small RNA libraries were sequenced on the Illumina Novaseq 6000 platform, yielding high-quality reads that facilitated the discovery of known and novel miRNAs using miRDeep-P. Results: A total of 277 miRNAs were identified, comprising 71 conserved and 206 novel miRNAs, across root, stem, and leaf tissues. In addition, differential expression analysis using DESeq2 identified distinct miRNAs exhibiting tissue-specific regulation. Notably, novel miRNAs like novel_1, novel_88, and novel_189 showed significant roles in processes such as auxin signaling, lignin biosynthesis, and stress response. Functional enrichment analysis of miRNA target genes revealed pathways related to hormonal regulation, structural reinforcement, and environmental adaptation, highlighting tissue-specific functions. The Principal Component Analysis and PERMANOVA confirmed clear segregation of miRNA expression profiles among tissues, underlining organ-specific regulation. Differential expression patterns emphasized unique regulatory roles in each organ: roots prioritized stress response and nutrient uptake, leaves focused on photosynthesis and UV protection, and stems contributed to structural integrity and nutrient transport, suggesting evolutionary adaptations in P. volubilis. Conclusions: This study identified novel miRNA-mediated networks that regulate developmental and adaptive processes in P. volubilis, underscoring its molecular adaptations for resilience and productivity. By characterizing both conserved and novel miRNAs, the findings lay a foundation for genetic improvement and molecular breeding strategies aimed at enhancing agronomic traits, stress tolerance, and the production of bioactive compounds. Full article
(This article belongs to the Special Issue Bioinformatics of Plant)
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19 pages, 299 KiB  
Review
Epigenetic Modifications, Immune Control Processes, and Plant Responses to Nematodes
by Seyedeh Najmeh Banihashemian and Seyed Mahyar Mirmajlessi
Agriculture 2025, 15(7), 742; https://doi.org/10.3390/agriculture15070742 - 30 Mar 2025
Viewed by 468
Abstract
Plants adapt to biotic and abiotic stresses through physiological, morphological, and genetic changes. In recent years, the fundamental roles of epigenetic mechanisms as regulators of various immune–biological processes in nematode–plant interactions have been increasingly recognized. Epigenetic control mechanisms include non-coding RNAs (ncRNAs), DNA [...] Read more.
Plants adapt to biotic and abiotic stresses through physiological, morphological, and genetic changes. In recent years, the fundamental roles of epigenetic mechanisms as regulators of various immune–biological processes in nematode–plant interactions have been increasingly recognized. Epigenetic control mechanisms include non-coding RNAs (ncRNAs), DNA methylation, and histone modifications. Gene expression and gene silencing play crucial roles in activated induced resistance during pathogen attacks. DNA methylation and histone modifications are linked to defense priming or immune memory, such as systemic acquired resistance (SAR). In addition, epigenetic processes play important roles in long-term defense priming, contributing to the development of immunological memory under future stress conditions. Therefore, advances in understanding epigenetic mechanisms hold considerable potential for future research on plant–nematode interactions. However, further development in the basic understanding of interactions among various stresses, the expansion of markers for epigenetic changes, and the permanence of priming are necessary to optimize its utilization in crop protection programs. In this paper, we focus on the function of epigenetic mechanisms in plant defense responses to nematode infection, specifically root-knot nematodes (RKNs). Understanding the adaptive ability of RKNs is important for developing suitable control methods. Additionally, we explore the role of epigenetic mechanisms in plant interactions with biological control agents. Full article
27 pages, 3184 KiB  
Review
The Good, the Bad, and the Epigenetic: Stress-Induced Metabolite Regulation and Transgenerational Effects
by Saida Ibragić, Sabina Dahija and Erna Karalija
Epigenomes 2025, 9(2), 10; https://doi.org/10.3390/epigenomes9020010 - 29 Mar 2025
Viewed by 326
Abstract
Background: Plants face a wide range of environmental stresses that disrupt growth and productivity. To survive and adapt, they undergo complex metabolic reprogramming by redirecting carbon and nitrogen fluxes toward the biosynthesis of protective secondary metabolites such as phenylpropanoids, flavonoids, and lignin. Recent [...] Read more.
Background: Plants face a wide range of environmental stresses that disrupt growth and productivity. To survive and adapt, they undergo complex metabolic reprogramming by redirecting carbon and nitrogen fluxes toward the biosynthesis of protective secondary metabolites such as phenylpropanoids, flavonoids, and lignin. Recent research has revealed that these stress-induced metabolic processes are tightly regulated by epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs. Methods: This review synthesizes current findings from studies on both model and crop plants, examining the roles of key epigenetic regulators in controlling secondary metabolism under stress. Special focus is placed on dynamic changes in DNA methylation, histone acetylation, and the action of small RNAs such as siRNAs and miRNAs in transcriptional and post-transcriptional regulation. Results: Evidence indicates that stress triggers rapid and reversible epigenetic modifications that modulate gene expression linked to secondary metabolic pathways. These modifications not only facilitate immediate metabolic responses but can also contribute to stress memory. In some cases, this memory is retained and transmitted to the next generation, influencing progeny stress responses. However, critical knowledge gaps remain, particularly concerning the temporal dynamics, tissue specificity, and long-term stability of these epigenetic marks in crops. Conclusions: Understanding how epigenetic regulation governs secondary metabolite production offers promising avenues to enhance crop resilience and productivity in the context of climate change. Future research should prioritize dissecting the stability and heritability of these modifications to support the development of epigenetically informed breeding strategies. Full article
(This article belongs to the Collection Epigenetic Control in Plants)
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27 pages, 13324 KiB  
Article
ShadeNet: Innovating Shade House Detection via High-Resolution Remote Sensing and Semantic Segmentation
by Yinyu Liang, Minduan Xu, Wuzhou Dong and Qingling Zhang
Appl. Sci. 2025, 15(7), 3735; https://doi.org/10.3390/app15073735 - 28 Mar 2025
Viewed by 234
Abstract
Shade houses are critical for modern agriculture, providing optimal growing conditions for shade-sensitive crops. However, their rapid expansion poses ecological challenges, making the accurate extraction of their spatial distribution crucial for sustainable development. The unique dark appearance of shade houses leads to low [...] Read more.
Shade houses are critical for modern agriculture, providing optimal growing conditions for shade-sensitive crops. However, their rapid expansion poses ecological challenges, making the accurate extraction of their spatial distribution crucial for sustainable development. The unique dark appearance of shade houses leads to low accuracy and high misclassification rates in traditional spectral index-based extraction methods, while deep learning approaches face challenges such as insufficient datasets, limited receptive fields, and poor generalization capabilities. To address these challenges, we propose ShadeNet, a novel method for shade house detection using high-resolution remote sensing imagery and semantic segmentation. ShadeNet integrates the Swin Transformer and Mask2Former frameworks, enhanced by a Global-Channel and Local-Spatial Attention (GCLSA) module. This architecture significantly improves multi-scale feature extraction and global feature capture, thereby enhancing extraction accuracy. Tested on a self-labeled dataset, ShadeNet achieved a mean Intersection over Union (mIOU) improvement of 2.75% to 7.37% compared to existing methods, significantly reducing misclassification. The integration of the GCLSA module within the Swin Transformer framework enhances the model’s ability to capture both global and local features, addressing the limitations of traditional CNNs. This innovation provides a robust solution for shade houses detection, supporting sustainable agricultural development and environmental protection. Full article
(This article belongs to the Special Issue Remote Sensing Image Processing and Application, 2nd Edition)
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19 pages, 3364 KiB  
Article
Responses of the Lipoxygenase Gene Family to Drought Stress in Broomcorn Millet (Panicum miliaceum L.)
by Lin Cong, Lin Deng, Hongfei Yao, Yaoyuan Zhang, Hongying Li, Haigang Wang, Bin Zhang, Yuanhuai Han and Junjie Wang
Genes 2025, 16(4), 368; https://doi.org/10.3390/genes16040368 - 23 Mar 2025
Viewed by 318
Abstract
Background: Broomcorn millet (Panicum miliaceum L.), a drought-tolerant C4 crop, is crucial for agricultural resilience in arid regions. Lipoxygenases (LOXs), key enzymes in plant stress responses, have not been studied in broomcorn millet. This study aimed to identify LOX genes in broomcorn [...] Read more.
Background: Broomcorn millet (Panicum miliaceum L.), a drought-tolerant C4 crop, is crucial for agricultural resilience in arid regions. Lipoxygenases (LOXs), key enzymes in plant stress responses, have not been studied in broomcorn millet. This study aimed to identify LOX genes in broomcorn millet and elucidate their role in drought tolerance. Methods: We employed bioinformatics and physiological analyses to identify LOX genes in broomcorn millet. Expression profiles were assessed in different organs, and drought stress responses were evaluated in tolerant (HSZ, YXDHM) and sensitive (YS10) varieties. Antioxidant enzyme activities (SOD, POD, CAT) and malondialdehyde (MDA) levels were measured. Results: Twelve LOX genes were identified, classified into three subfamilies, and mapped across seven chromosomes. These genes contained stress-responsive cis-elements and showed organ-specific expression, with PmLOX5 exhibiting no detectable expression. Under drought stress, tolerant varieties showed elevated antioxidant activities and reduced MDA accumulation. PmLOX2, a homolog of Arabidopsis AtLOX1/AtLOX5, was significantly induced in tolerant varieties, correlating with enhanced antioxidant capacity and reduced oxidative damage. Conclusions:PmLOX genes, particularly PmLOX2, play a pivotal role in drought tolerance by modulating ROS scavenging and membrane protection. This study provides a foundation for leveraging LOX genes to improve drought resilience in broomcorn millet and related crops. Full article
(This article belongs to the Section Bioinformatics)
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