Agronomy

13 pages, 1037 KB

Open AccessArticle

Screening of Positive Controls for Environmental Safety Assessment of RNAi Products

by Kaixuan Ding, Xiaowei Yang, Qinli Zhou, Geng Chen, Fengping Chen, Yao Tan, Jing Li and Lanzhi Han

Agronomy 2025, 15(10), 2399; https://doi.org/10.3390/agronomy15102399 - 16 Oct 2025

Abstract

RNA interference (RNAi) represents a promising pest control strategy, applicable to both insect-resistant genetically modified (IRGM) crops and sprayable RNAi insecticides. These products can achieve sequence-specific gene silencing and require rigorous environmental risk assessment (ERA) prior to approval. However, current environmental safety assessments [...] Read more.

RNA interference (RNAi) represents a promising pest control strategy, applicable to both insect-resistant genetically modified (IRGM) crops and sprayable RNAi insecticides. These products can achieve sequence-specific gene silencing and require rigorous environmental risk assessment (ERA) prior to approval. However, current environmental safety assessments of RNAi products and other RNAi experiments frequently use double-stranded EGFP (dsEGFP) as a negative control, while suitable RNAi-based positive controls are lacking. Sometimes conventional chemical toxins (e.g., chlorpyrifos) or protein inhibitors (e.g., trypsin inhibitors) are used as substitutes, but their distinct mechanisms, persistence, and metabolism make them inappropriate for RNAi-specific evaluations. In this study, we evaluated the suitability of RNAi-based positive controls for assessing non-target effects on Harmonia axyridis, a widely distributed predatory beetle used as a bioindicator in biosafety assessments. Under laboratory conditions, we tested one microRNA (miR-92a) and two double-stranded RNAs (dsHaSnf7 and dsHaDiap1) for their effects on H. axyridis. Injection of miR-92a showed no significant difference in mortality compared to controls, whereas dsHaSnf7 and dsHaDiap1 significantly reduced survival rates and target gene expression, as confirmed by qPCR. These findings suggest that HaSnf7 and HaDiap1 are suitable candidate genes for establishing RNAi-specific positive controls in environmental risk assessments of RNAi-based products. Full article

(This article belongs to the Special Issue Genetically Modified (GM) Crops and Pests Management)

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16 pages, 351 KB

Open AccessCommunication

Exploratory Field Case Study of Microbial and Resistance Genes Dynamics in the Maize Phyllosphere Following Fertigation with Anaerobic Digestate

by Camila Fabiani, María V. Valero, Jessica Basualdo, Marco Allegrini, Gastón A. Iocoli, María B. Villamil and María C. Zabaloy

Agronomy 2025, 15(10), 2398; https://doi.org/10.3390/agronomy15102398 - 16 Oct 2025

Abstract

Anaerobic digestate from manure, a byproduct of biogas production, is increasingly used as an organic fertilizer in circular agriculture systems. This study assessed the microbiological impact of maize fertigation with anaerobic digestate, focusing on fecal indicators (Escherichia coli, Salmonella), antibiotic [...] Read more.

Anaerobic digestate from manure, a byproduct of biogas production, is increasingly used as an organic fertilizer in circular agriculture systems. This study assessed the microbiological impact of maize fertigation with anaerobic digestate, focusing on fecal indicators (Escherichia coli, Salmonella), antibiotic resistance genes (ARGs), and integrons. The trial was conducted in a commercial maize field, where on-site manure-based anaerobic digestate was applied via center-pivot irrigation. Leaf samples were collected two days (2 dai) and four weeks (4 wai) after the last fertigation. E. coli and Salmonella were assessed by culturable methods, while ARGs and integrons were analyzed by qPCR. Results showed that E. coli (3 MPN/g) and Salmonella were detected at 2 dai but were undetectable at 4 wai and in the control condition, suggesting transient contamination. The abundance of tetW was approximately tenfold higher in digestate-treated plants than in the control, while no consistent changes were observed for the other genes. Overall, fertigation with anaerobic digestate appears to pose minimal microbiological impact within the specific conditions of this study, although it may act as a source of specific resistance determinants. Although limited by the use of single treated and control plots, this study offers preliminary insight into microbial and resistance gene dynamics in the phyllosphere, providing a basis for future replicated hypothesis-driven studies. Full article

(This article belongs to the Special Issue Sustainable Agricultural Systems: Enhancing Efficiency and Reducing Environmental Impact)

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23 pages, 2444 KB

Open AccessArticle

Agronomic, Nutritional, and Sensory Characterization and Horticultural Quality of Two Jerusalem Artichoke Biotypes from Northern Argentine Patagonia

by Susana Diez, Daniela Marisol Salvatori and Lorena Franceschinis

Agronomy 2025, 15(10), 2397; https://doi.org/10.3390/agronomy15102397 - 15 Oct 2025

Abstract

Despite its high inulin content, Jerusalem artichoke (Helianthus tuberosus L.) remains an underutilized vegetable for human consumption. Organic field trials of two biotypes adapted to Northern Patagonia, Argentina, were conducted. Since no cultivars are formally registered in the country, two biotypes, “elongated” [...] Read more.

Despite its high inulin content, Jerusalem artichoke (Helianthus tuberosus L.) remains an underutilized vegetable for human consumption. Organic field trials of two biotypes adapted to Northern Patagonia, Argentina, were conducted. Since no cultivars are formally registered in the country, two biotypes, “elongated” (E) and “rounded” (R), defined according to tuber morphology, were planted and characterized. Agronomic performance was evaluated through soil analysis and crop yield. Tubers were analyzed for horticultural quality (e.g., respiration rate, inulin, firmness) and microstructure. A nutritional profile was determined, including protein, fat, dietary fiber, sugars, organic acids, minerals, phenolic content, and antioxidant capacity. Sensory evaluation (overall liking, free association, and penalty–reward analysis) was performed with 128 consumers, most of them unfamiliar with the tuber. The biotype R exhibited twice the yield and higher consumer preference, whereas E showed a higher respiration rate, a better nutritional profile, a harder texture, and lower overall liking. Initially, 76% of participants expressed willingness to incorporate it into their diet, which increased to 96.6% after they were informed of its health benefits. This multidimensional study, support the revalorization of Jerusalem artichoke and its inclusion in human diets as a fresh vegetable for biotype R or functional ingredient for biotype E. Full article

(This article belongs to the Special Issue New Insights in Crop Management to Respond to Climate Change)

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27 pages, 1493 KB

Open AccessArticle

Optimizing Crop Water Use with Saline Aquaculture Effluent: For Succesful Production of Forage Sorghum Hybrids

by Ildikó Kolozsvári, Ágnes Kun, Mihály Jancsó, Noémi J. Valkovszki, Csaba Bozán, Norbert Túri, Árpád Székely, Andrea Palágyi, Csaba Gyuricza and Gergő Péter Kovács

Agronomy 2025, 15(10), 2396; https://doi.org/10.3390/agronomy15102396 - 15 Oct 2025

Abstract

Hungary faces increasing water challenges, including frequent droughts and a growing dependence on irrigation, which necessitate alternative water sources for agriculture. This study evaluated the use of saline aquaculture effluent—characterized by elevated sodium (Na⁺) and chloride (Cl⁻) concentrations—as an [...] Read more.

Hungary faces increasing water challenges, including frequent droughts and a growing dependence on irrigation, which necessitate alternative water sources for agriculture. This study evaluated the use of saline aquaculture effluent—characterized by elevated sodium (Na⁺) and chloride (Cl⁻) concentrations—as an irrigation resource for forage sorghum (Sorghum bicolor L.) over four consecutive growing seasons. Three hybrids (‘GK Áron’, ‘GK Balázs’, and ‘GK Erik’) were tested under five irrigation regimes, including freshwater and aquaculture effluent applied via drip irrigation at weekly doses of 30 mm and 45 mm, alongside a non-irrigated control. Effluent irrigation at 30 mm weekly increased biomass yield by up to 61% and enhanced nitrogen uptake by 22% compared to the control. Soil electrical conductivity (EC) values remained below 475 µS/cm, with effluent treatments showing lower EC than non-irrigated plots. The effluent water also supported the recycling of nutrients, especially nitrogen and phosphorus. Unlike conventional saline water, aquaculture effluent contains organic compounds and microbial activity that may improve nutrient mobilization and uptake. Our results highlight how we can reuse aquaculture wastewater in irrigated crop production. The results demonstrate that moderate effluent irrigation (30 mm/week) can optimize crop water use while maintaining soil health, offering a viable strategy for forage sorghum production in water-limited environments. Full article

(This article belongs to the Special Issue Optimizing Crop Water Use: Advances and Applications in Deficit Irrigation Strategies)

16 pages, 1479 KB

Open AccessArticle

Transport of Phosphorus from Three Fertilizers Through High- and Low-Phosphorus Soils

by Lily DuPlooy, Joshua Heitman, Luke Gatiboni and Aziz Amoozegar

Agronomy 2025, 15(10), 2395; https://doi.org/10.3390/agronomy15102395 - 15 Oct 2025

Abstract

Chemical fertilizers are commonly used to supply phosphorus and other nutrients to crops, but due to high affinity of soils for P fixation, over-application of P fertilizer is common, which may result in groundwater and surface water pollution. To increase P use efficiency, [...] Read more.

Chemical fertilizers are commonly used to supply phosphorus and other nutrients to crops, but due to high affinity of soils for P fixation, over-application of P fertilizer is common, which may result in groundwater and surface water pollution. To increase P use efficiency, different strategies, including different fertilizer formulations and types, have been developed. Two struvite-based fertilizers, Crystal Green^® (CG) and Crystal Green Pearl^® (CGP), are touted as environmentally safe, because they are insoluble in water but soluble in organic acids exuded from crop roots. The objective of this study was to assess fate and transport of P from diammonium phosphate (DAP), CG, and CGP through two loam soils with a significant difference in their initial P content. Two loamy soils, one collected from an experimental field receiving fertilizer continuously since 1985 and one from an adjacent area receiving no fertilizer, and a pure sand control were packed in 5 cm diameter and 5 cm long columns. Several grains equivalent to approximately 80 mg P from each fertilizer were imbedded at the bottom of the column. Distilled water was passed through the soil columns from the bottom at a relatively constant rate, and the outflow was collected every two hours using a fraction collector. Outflow samples from each treatment combination were analyzed for P by the colorimetric method, and the amount of P retained by the soils along the column at the end of the water application was determined by the nitric acid digestion method. Approximately 91% of P in DAP, 34% in CG, and only 3.8% in CGP was transported through the sand column. In contrast, the amounts of P transported were approximately 42.2% for DAP, 6.4% for CG, and 0.4% for CGP through the high-P soil and 22.4% for DAP, 0.6% for CG, and almost zero for CGP through the low-P soil. Overall, the results show a high solubility and transport for DAP, very low transport for CGP, and somewhat low to medium transport for CG fertilizers. In addition, the results show that even the high-P soil that has received fertilizer for about 40 years has the capacity to fix significant amounts of P. Full article

(This article belongs to the Special Issue Conventional and Alternative Fertilization of Crops)

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23 pages, 7494 KB

Open AccessArticle

Genome-Wide Analysis of NAC Gene Family and Its Cold-Responsive Transcriptional Dynamics in Coffea arabica

by Jing Gao, Junjie Zhu, Zenan Lan, Feifei He and Xiangshu Dong

Agronomy 2025, 15(10), 2394; https://doi.org/10.3390/agronomy15102394 - 15 Oct 2025

Abstract

In numerous coffee-producing areas, coffee plants are routinely exposed to a low chilling temperature on a seasonal cycle. Despite the well-established significance of NAC transcription factors in mediating plant responses to abiotic stresses, their functions in Coffea arabica remain underexplored. This study identified [...] Read more.

In numerous coffee-producing areas, coffee plants are routinely exposed to a low chilling temperature on a seasonal cycle. Despite the well-established significance of NAC transcription factors in mediating plant responses to abiotic stresses, their functions in Coffea arabica remain underexplored. This study identified 161 CaNAC genes and classified them into 15 distinct subgroups distributed across 22 chromosomes, with chromosome 11 harboring the largest number of these genes. Furthermore, a total of 1077 cis-elements were detected in the promoter regions of the 161 CaNAC genes. Among these, MYB-binding sites and ABA-responsive elements (ABREs) were the most prevalent. RNA-seq analysis under chilling stress revealed 16,767 differentially expressed genes, which were grouped into four clusters. GO enrichment analysis highlighted biological processes such as the abscisic acid-activated signaling pathway, response to cold, and response to salicylic acid, providing fundamental insights into the transcriptional response of C. arabica to chilling stress. Expression pattern analysis of CaNACs under chilling stress showed that 38 CaNACs were differentially expressed; 15 genes, including CaNAC46/49/116/125, were downregulated, while 12 genes, including CaNAC56/64, were upregulated. This study enhances our understanding of the CaNAC gene family’s role in cold responses, potentially bolstering molecular breeding programs for C. arabica. Full article

(This article belongs to the Section Crop Breeding and Genetics)

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41 pages, 4704 KB

Open AccessReview

Integrative Genomics and Precision Breeding for Stress-Resilient Cotton: Recent Advances and Prospects

by Zahra Ghorbanzadeh, Bahman Panahi, Leila Purhang, Zhila Hossein Panahi, Mehrshad Zeinalabedini, Mohsen Mardi, Rasmieh Hamid and Mohammad Reza Ghaffari

Agronomy 2025, 15(10), 2393; https://doi.org/10.3390/agronomy15102393 - 15 Oct 2025

Abstract

Developing climate-resilient and high-quality cotton cultivars remains an urgent challenge, as the key target traits yield, fibre properties, and stress tolerance are highly polygenic and strongly influenced by genotype–environment interactions. Recent advances in chromosome-scale genome assemblies, pan-genomics, and haplotype-resolved resequencing have greatly enhanced [...] Read more.

Developing climate-resilient and high-quality cotton cultivars remains an urgent challenge, as the key target traits yield, fibre properties, and stress tolerance are highly polygenic and strongly influenced by genotype–environment interactions. Recent advances in chromosome-scale genome assemblies, pan-genomics, and haplotype-resolved resequencing have greatly enhanced the capacity to identify causal variants and recover non-reference alleles linked to fibre development and environmental adaptation. Parallel progress in functional genomics and precision genome editing, particularly CRISPR/Cas, base editing, and prime editing, now enables rapid, heritable modification of candidate loci across the complex tetraploid cotton genome. When integrated with high-throughput phenotyping, genomic selection, and machine learning, these approaches support predictive ideotype design rather than empirical, trial-and-error breeding. Emerging digital agriculture tools, such as digital twins that combine genomic, phenomic, and environmental data layers, allow simulation of ideotype performance and optimisation of trait combinations in silico before field validation. Speed breeding and phenomic selection further shorten generation time and increase selection intensity, bridging the gap between laboratory discovery and field deployment. However, the large-scale implementation of these technologies faces several practical constraints, including high infrastructural costs, limited accessibility for resource-constrained breeding programmes in developing regions, and uneven regulatory acceptance of genome-edited crops. However, reliance on highly targeted genome editing may inadvertently narrow allelic diversity, underscoring the need to integrate these tools with broad germplasm resources and pangenomic insights to sustain long-term adaptability. To realise these opportunities at scale, standardised data frameworks, interoperable phenotyping systems, robust multi-omic integration, and globally harmonised, science-based regulatory pathways are essential. This review synthesises recent progress, highlights case studies in fibre, oil, and stress-resilience engineering, and outlines a roadmap for translating integrative genomics into climate-smart, high-yield cotton breeding programmes. Full article

(This article belongs to the Special Issue Crop Genomics and Omics for Future Food Security)

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40 pages, 1415 KB

Open AccessArticle

A Decision-Support Grid for Evaluating Neonicotinoid Alternatives Based on Environmental and Human Health Impact

by Michael Raimondi, Edelbis Dávila López, Laura Peeters, Wim Reybroeck, Tim Belien, Dany Bylemans, Jeroen Buysse, Benny De Cauwer and Pieter Spanoghe

Agronomy 2025, 15(10), 2392; https://doi.org/10.3390/agronomy15102392 - 15 Oct 2025

Abstract

The European Union’s goal to reduce pesticide risk, exemplified by restrictions on insecticides like neonicotinoids, necessitates a shift from single-substance risk assessment to a holistic evaluation of pest control strategies. To address this, a novel decision-support grid was developed that integrates 13 environmental, [...] Read more.

The European Union’s goal to reduce pesticide risk, exemplified by restrictions on insecticides like neonicotinoids, necessitates a shift from single-substance risk assessment to a holistic evaluation of pest control strategies. To address this, a novel decision-support grid was developed that integrates 13 environmental, biodiversity, and human health risk indicators for multiple active substances across an entire crop season into a single Final Scenario Score (FSS), ranging from 0 to 1 (where 1 is the risk of the reference scenario). This framework was applied to three case studies in Belgium—sugar beet, apple, and pear cultivation—where neonicotinoid-based reference scenarios were compared with chemical and/or organic alternatives under low (best-case) and high (worst-case) pest pressure conditions. The results highlight the complexity of finding viable alternatives, with an FSS below 0.75 as the justification threshold. In sugar beet, only the best-case chemical alternative (FSS = 0.71) met the threshold, while worst-case chemical alternatives failed due to increased risk. For apple and pear, organic alternatives consistently showed low-risk scores (FSS 0.27–0.61) but faced important efficacy gaps against key insect. Chemical alternatives in orchards were justifiable in low-pressure scenarios (FSS 0.64–0.73) but failed under high pest pressure (FSS 0.91–0.93). This novel decision-support grid proves to be a valuable tool for guiding sustainable pest control strategies for regulators and field advisors. Full article

(This article belongs to the Section Pest and Disease Management)

16 pages, 963 KB

Open AccessArticle

Agronomic Assessment of Olive Mill Wastewater Sludge Derived Composts on Lactuca sativa and Zea mays: Fertilizing Efficiency and Potential Toxic Effect on Seed Germination and Seedling Growth

by Miguel Ángel Mira-Urios, José A. Sáez-Tovar, F. Javier Andreu-Rodríguez, Silvia Sánchez-Méndez, Luciano Orden, Lucía Valverde-Vozmediano, María Dolores Pérez-Murcia and Raúl Moral

Agronomy 2025, 15(10), 2391; https://doi.org/10.3390/agronomy15102391 - 15 Oct 2025

Abstract

Olive mill wastewater is a polluting residue generated from the olive oil industry and is one which constitutes an environmental concern in Mediterranean countries. Composting has been reported as a viable valorization alternative, as it reduces the volume and the phytotoxic characteristics of [...] Read more.

Olive mill wastewater is a polluting residue generated from the olive oil industry and is one which constitutes an environmental concern in Mediterranean countries. Composting has been reported as a viable valorization alternative, as it reduces the volume and the phytotoxic characteristics of OMW. In this study, several composts derived from OMW were evaluated under controlled conditions over two growing season pot experiments using Lactuca sativa as a test crop. The analysis focused on soil quality changes, crop yield, and plant development. Additionally, potential phytotoxicity was also evaluated through a direct acute toxicity plant growth test. Application of OMW composts improved soil fertility indicators, including oxidizable carbon, Kjeldahl total nitrogen, Olsen phosphorous, and plant availability. Crop yields were comparable to those obtained with other organic amendments such as vermicompost and fresh cattle manure in both growing seasons and plant development (in terms of chlorophyll content and canopy cover) was not negatively affected. Nutrient uptake (NPK) was consistent during both growing seasons, with similar nitrogen use efficiency to that achieved in other organic treatments. Regarding the potential toxic effect, the OMW composts tested enhanced seed germination when mixed with coconut fiber at weight ratios below 29.2%. No half-maximal effective concentration (EC50) values were detected, even at 100% compost concentration, while half-maximal inhibitory concentration (LC50) values ranged between 65–75%. These results indicate that OMW composts can serve as an effective short-term source of plant-available nitrogen and a medium-term source of phosphorus, without risk of finding inhibitory or phytotoxic effects on crops. Full article

(This article belongs to the Section Agricultural Biosystem and Biological Engineering)

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Graphical abstract

19 pages, 5496 KB

Open AccessFeature PaperArticle

Discrete Meta-Modeling and Parameter Calibration of Harvested Alfalfa Stalks

by Jianji Wang, Baolong Geng, Zhikai Yang, Jinlong Yang, Keping Zhang and Yangrong Meng

Agronomy 2025, 15(10), 2390; https://doi.org/10.3390/agronomy15102390 - 15 Oct 2025

Abstract

Addressing the problem of lacking accurate and reliable contact parameters and bonding parameters in the simulation of the mashing process during the harvesting of alfalfa, this study takes the stems of alfalfa at the harvesting stage as the research object. The geometric dimensions [...] Read more.

Addressing the problem of lacking accurate and reliable contact parameters and bonding parameters in the simulation of the mashing process during the harvesting of alfalfa, this study takes the stems of alfalfa at the harvesting stage as the research object. The geometric dimensions and related intrinsic parameters of the stems were measured. Using the Enhanced Discrete Element Method (EDEM) software, a multi-scale discrete element flexible bonding model of alfalfa stems was established based on region-specific parameters. The entire alfalfa stem was divided into three parts: the top, middle, and root sections. A multi-scale particle aggregation model of hollow stems was created using the Hertz-Mindlin with bonding model. The contact parameters between alfalfa stems at the harvesting stage and PU rubber were determined using a mathematical model based on quadratic polynomial fitting curves. The results showed that the shear modulus of the top, middle, and root sections of the alfalfa stems were 24.96 MPa, 29.60 MPa, and 10.48 MPa, respectively. The coefficients of restitution between the top, middle, and root sections of the alfalfa stems and PU rubber were 0.426, 0.375, and 0.386, respectively; the static friction coefficients were 0.613, 0.667, and 0.422, respectively; and the rolling friction coefficients were 0.213, 0.226, and 0.292, respectively. The relative error between the simulated and measured values of the angle of repose was less than 3%, effectively representing the mechanical characteristics of alfalfa stems at the harvesting stage bending and breaking under impact. This study aims to establish a discrete element flexible model of alfalfa stems at the harvesting stage and accurately calibrate the contact parameters with typical rubber materials, thereby addressing the lack of reliable bonding and contact parameters in existing simulations of the mashing process. Full article

(This article belongs to the Section Precision and Digital Agriculture)

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21 pages, 1489 KB

Open AccessArticle

Effects of Waterlogging at Different Developmental Stages on Growth, Yield and Physiological Responses of Forage Maize

by Chang-Woo Min, Il-Kyu Yoon, Min-Jun Kim, Jeong-Sung Jung, Md Atikur Rahman and Byung-Hyun Lee

Agronomy 2025, 15(10), 2389; https://doi.org/10.3390/agronomy15102389 - 15 Oct 2025

Abstract

Waterlogging (WL) is an abiotic stress that severely limits crop yield. However, limited research has addressed the effects of long-term WL stress at different developmental stages on the yield and physiological responses of forage maize. In this study, forage maize plants were subjected [...] Read more.

Waterlogging (WL) is an abiotic stress that severely limits crop yield. However, limited research has addressed the effects of long-term WL stress at different developmental stages on the yield and physiological responses of forage maize. In this study, forage maize plants were subjected to 14-day WL stress at the emergence (E), four-leaf (V4), eleven-leaf (V11), and tasseling (VT) stages. Plant height significantly decreased by 60% at the E stage and 48% at the V4 stage when exposed to 14-day WL. Leaf area decreased by 79% at the E stage, and the number of green leaves decreased most significantly at the VT stage. Chlorophyll fluorescence (Fv/Fm) and the relative chlorophyll content index (RCI) decreased most significantly at the V4 stage. The lysigenous aerenchyma formation rate of the roots increased significantly after 14-day WL at the V4 stage, whereas the number of adventitious roots increased most significantly at the V11 stage. The hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents, which are indicative of the root oxidation state, exhibited the highest increase at the E stage. In addition, at the E and V4 stages, the expression of genes related to energy metabolism and lysigenous aerenchyma formation in the roots was upregulated after 14-day WL. The total dry matter (DM) of maize after harvest decreased most significantly when exposed to 14-day WL at the V4 stage, while acid detergent fiber (ADF) and neutral detergent fiber (NDF) increased with the developmental stages. Consequently, total digestible nutrients (TDNs) and the relative feed value (RFV) decreased with advancing developmental stages, with the highest decrease at the VT stage. These results demonstrate that effective drainage management during the early developmental stage (V4) is more important to prevent forage maize yield loss due to prolonged WL stress, which is expected to increase in frequency due to climate change, and management during the later developmental stage (VT) is critical to prevent decreases in feed values. These findings provide valuable insights into the physiological responses of forage maize to WL stress. Full article

(This article belongs to the Section Crop Breeding and Genetics)

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29 pages, 12549 KB

Open AccessArticle

An Enhanced Faster R-CNN for High-Throughput Winter Wheat Spike Monitoring to Improved Yield Prediction and Water Use Efficiency

by Donglin Wang, Longfei Shi, Yanbin Li, Binbin Zhang, Guangguang Yang and Serestina Viriri

Agronomy 2025, 15(10), 2388; https://doi.org/10.3390/agronomy15102388 - 14 Oct 2025

Abstract

This study develops an innovative unmanned aerial vehicle (UAV)-based intelligent system for winter wheat yield prediction, addressing the inefficiencies of traditional manual counting methods (with approximately 15% error rate) and enabling quantitative analysis of water–fertilizer interactions. By integrating an enhanced Faster Region-Based Convolutional [...] Read more.

This study develops an innovative unmanned aerial vehicle (UAV)-based intelligent system for winter wheat yield prediction, addressing the inefficiencies of traditional manual counting methods (with approximately 15% error rate) and enabling quantitative analysis of water–fertilizer interactions. By integrating an enhanced Faster Region-Based Convolutional Neural Network (Faster R-CNN) architecture with multi-source data fusion and machine learning, the system significantly improves both spike detection accuracy and yield forecasting performance. Field experiments during the 2022–2023 growing season captured high-resolution multispectral imagery for varied irrigation regimes and fertilization treatments. The optimized detection model incorporates ResNet-50 as the backbone feature extraction network, with residual connections and channel attention mechanisms, achieving a mean average precision (mAP) of 91.2% (calculated at IoU threshold 0.5) and 88.72% recall while reducing computational complexity. The model outperformed YOLOv8 by a statistically significant 2.1% margin (p < 0.05). Using model-generated spike counts as input, the random forest (RF) model regressor demonstrated superior yield prediction performance (R² = 0.82, RMSE = 324.42 kg·ha⁻¹), exceeding the Partial Least Squares Regression (PLSR) (R² +46%, RMSE-44.3%), Least Squares Support Vector Machine (LSSVM) (R² + 32.3%, RMSE-32.4%), Support Vector Regression (SVR) (R² + 30.2%, RMSE-29.6%), and Backpropagation (BP) Neural Network (R²+22.4%, RMSE-24.4%) models. Analysis of different water–fertilizer treatments revealed that while organic fertilizer under full irrigation (750 m³ ha⁻¹) conditions achieved maximum yield benefit (13,679.26 CNY·ha⁻¹), it showed relatively low water productivity (WP = 7.43 kg·m⁻³). Conversely, under deficit irrigation (450 m³ ha⁻¹) conditions, the 3:7 organic/inorganic fertilizer treatment achieved optimal WP (11.65 kg m⁻³) and WUE (20.16 kg∙ha⁻¹∙mm⁻¹) while increasing yield benefit by 25.46% compared to organic fertilizer alone. This research establishes an integrated technical framework for high-throughput spike monitoring and yield estimation, providing actionable insights for synergistic water–fertilizer management strategies in sustainable precision agriculture. Full article

(This article belongs to the Section Water Use and Irrigation)

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18 pages, 1696 KB

Open AccessArticle

Recycling Reservoir Sediments and Rice Husk for Sustainable Rice Seedling Production

by Pei-Tzu Kao and Shan-Li Wang

Agronomy 2025, 15(10), 2387; https://doi.org/10.3390/agronomy15102387 - 14 Oct 2025

Abstract

Amending reservoir sediments with organic matter provides a sustainable alternative to conventional rice (Oryza sativa L.) seedling substrates, simultaneously reducing dependence on agricultural soils and promoting the recycling of dredged sediments and agricultural by-products. Preliminary tests showed that adding rice husk (RH) [...] Read more.

Amending reservoir sediments with organic matter provides a sustainable alternative to conventional rice (Oryza sativa L.) seedling substrates, simultaneously reducing dependence on agricultural soils and promoting the recycling of dredged sediments and agricultural by-products. Preliminary tests showed that adding rice husk (RH) improved the porosity and water retention of the sediments while preventing surface cracking. This study further examined the effects of RH and rice husk biochar (RHB) on sediment fertility and rice seedling growth. Seedlings were grown for 15 days in a fine- or coarse-texture sediment amended with 0, 5, 10, or 20% (w/w) RH or RHB. A 10% amendment was identified as the optimal ratio for promoting seedling growth (increasing ca. 20% biomass). Nitrogen (N) availability was the primary factor influencing seedling performance, outweighing the effects of salinity and phosphorus availability. Compared with RH, RHB amendment resulted in lower substrate available N, likely due to greater losses through denitrification and ammonia volatilization, leading to reduced growth. In contrast, RH amendment maintained higher levels of available N, resulting in greater shoot biomass and higher leaf chlorophyll concentrations. Overall, amending reservoir sediments with 10% RH provides the most effective substrate formulation, offering a practical and sustainable strategy for rice seedling production. Full article

(This article belongs to the Special Issue Circular Agriculture: Waste-to-Resource Innovations in Cropping Systems)

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23 pages, 4071 KB

Open AccessArticle

Functional Characterization of Glutathione Peroxidase Genes Reveals Their Contribution to the Rapid Range Expansion of Amaranthus palmeri Under Stress Conditions

by Siting Wang, Xiaoyu Liu, Daniel Bimpong, Yun Wang, Fulian Wang, Wang Chen, Linfeng Du and Dongfang Ma

Agronomy 2025, 15(10), 2386; https://doi.org/10.3390/agronomy15102386 - 14 Oct 2025

Abstract

Amaranthus palmeri is an aggressive, highly invasive weed that thrives across a wide range of adverse environments worldwide; nevertheless, the mechanisms underlying its rapid expansion remain largely unstudied. Glutathione peroxidase (GPX) is a crucial enzyme within the antioxidant defense system, belonging to the [...] Read more.

Amaranthus palmeri is an aggressive, highly invasive weed that thrives across a wide range of adverse environments worldwide; nevertheless, the mechanisms underlying its rapid expansion remain largely unstudied. Glutathione peroxidase (GPX) is a crucial enzyme within the antioxidant defense system, belonging to the phylogenetic conserved family of oxidoreductases present in all living organisms. Despite its significance, the role of GPX in A. palmeri has not been reported. This study identified eight GPX genes (ApGPXs) in A. palmeri through comprehensive bioinformatics and gene expression analyses. The research examined the characteristics, evolutionary relationships, chromosomal mapping, gene structure, subcellular localization, conserved motifs, and cis-acting elements of these genes, as well as their evolutionary conserved functions in relation to Arabidopsis thaliana GPXs and RT-qPCR analysis under various stress conditions. The ApGPXs were distributed across scaffolds (2, 4, and 12) of the A. palmeri genome. Phylogenetic analysis grouped GPX genes into four subgroups, and conserved motifs were found within certain phylogenetic subgroups. We identified Actin8 as the most stable internal reference gene for A. palmeri under diverse stress conditions. Gene expression analysis revealed that ApGPXs participate in both early and late regulatory responses to oxidative stress induced by NaCl, high temperature, osmotic pressure, and glufosinate ammonium. The Arabidopsis GPX mutant (AT4G31870) exhibited a stronger flg22-induced oxidative burst than the wild type, and qPCR confirmed that AtGPXs contribute significantly to glufosinate ammonium stress responses. Evolutionary analysis found high sequence similarity between ApGPX4 and AT1G63460, as well as ApGPX3 and AT4G11600. Also, ApGPX3 and AT4G11600 shared similar expression patterns under glufosinate ammonium stress. This research presents the first gene family study in A. palmeri and provides foundational insights for future studies in this economically critical species. Our findings establish a framework for mitigating A. palmeri’s impact on crop production and exploring ApGPXs in developing herbicide- and stress-tolerant cultivars. Full article

(This article belongs to the Special Issue Adaptive Evolution in Weeds: Molecular Basis and Management)

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17 pages, 7514 KB

Open AccessArticle

Biosynthesis of Selenium Nanoparticles from Rosa rugosa Extract: Mechanisms and Applications for Sustainable Crop Protection

by Le Song, Man Liang, Yingxiu Wang and Yanli Bian

Agronomy 2025, 15(10), 2385; https://doi.org/10.3390/agronomy15102385 - 13 Oct 2025

Abstract

Selenium nanoparticles (SeNPs) show great potential for sustainable agriculture, but their green synthesis and practical application still need further optimization. This study established a green synthesis method for SeNPs using lyophilized rose (Rosa rugosa Thunb.) powder as both a reducing and stabilizing [...] Read more.

Selenium nanoparticles (SeNPs) show great potential for sustainable agriculture, but their green synthesis and practical application still need further optimization. This study established a green synthesis method for SeNPs using lyophilized rose (Rosa rugosa Thunb.) powder as both a reducing and stabilizing agent to reduce sodium selenite (Na₂SeO₃), key parameters, including template concentration, Na₂SeO₃/VC ratio, and reaction temperature were systematically optimized. This process yielded stable, spherical SeNPs with optimal properties, exhibiting a diameter of 90 nm and a zeta potential of −35 mV. Structural characterization confirmed that selenium forms chelation complexes through carboxyl and hydroxyl oxygen-binding sites. The SeNPs exhibited exceptional stability (retained 426 days at 25 °C) and pH tolerance (pH 4–10), though divalent cations (Ca²⁺) triggered aggregation. In agricultural application tests, 5 mg/L SeNPs increased tomato plant biomass by 84% and antioxidant capacity by 152% compared to controls, and the biosynthesis pathways of salicylic acid and jasmonic acid were upregulated. Moreover, the SeNPs exhibited strong concentration-dependent antifungal activity against several major pathogens. Among these pathogens, tomato gray mold (Botrytis cinerea) was the most sensitive, as evidenced by its low EC₅₀ (4.86 mg/L) and sustained high inhibition rates, which remained substantial even at 1 mg/L and reached 94% at 10 mg/L. These findings highlight SeNPs as a friendly alternative for minimizing agrochemical use in sustainable agriculture. Full article

(This article belongs to the Special Issue Navigating Pesticide Residues: Safeguarding Agricultural Product Quality)

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18 pages, 5597 KB

Open AccessArticle

Evaluating the Performance of Winter Wheat Under Late Sowing Using UAV Multispectral Data

by Yuanyuan Zhao, Hui Wang, Wei Wu, Yi Sun, Ying Wang, Weijun Zhang, Jianliang Wang, Fei Wu, Wouter H. Maes, Jinfeng Ding, Chunyan Li, Chengming Sun, Tao Liu and Wenshan Guo

Agronomy 2025, 15(10), 2384; https://doi.org/10.3390/agronomy15102384 - 13 Oct 2025

Abstract

In the lower and middle sections of the Yangtze River Basin Region (YRBR) in China, challenges posed by climate change and delayed harvesting of preceding crops have hindered the timely sowing of wheat, leading to an increasing prevalence of late-sown wheat fields. This [...] Read more.

In the lower and middle sections of the Yangtze River Basin Region (YRBR) in China, challenges posed by climate change and delayed harvesting of preceding crops have hindered the timely sowing of wheat, leading to an increasing prevalence of late-sown wheat fields. This trend has emerged as a significant impediment to achieving high and stable production of wheat in this area. During the growing seasons of 2022–2023 and 2023–2024, an unmanned aerial vehicle (UAV)-based multispectral camera was used to monitor different wheat materials at various growth stages under normal sowing treatment (M1) and late sowing with increased plant density (M2). By assessing yield loss, the wheat tolerance to late sowing was quantified and categorized. The correlation between the differential vegetation indices (D-VIs) and late sowing resistance was examined. The findings revealed that the J2-Logistic model demonstrated optimal classification performance. The precision values of stable type, intermediate type, and sensitive type were 0.92, 0.61, and 1.00, respectively. The recall values were 0.61, 0.92, and 1.00. The mean average precision (mAP) of the model was 0.92. This study proposes a high-throughput and low-cost evaluation method for wheat tolerance to late sowing, which can provide a rapid predictive tool for screening suitable varieties for late sowing and facilitating late-sown wheat breeding. Full article

(This article belongs to the Special Issue Digital Twins in Precision Agriculture)

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26 pages, 4926 KB

Open AccessArticle

Synergistic Optimization of Root–Shoot Characteristics, Nitrogen Use Efficiency and Yield by Combining Planting Density with Nitrogen Level in Cotton (Gossypium hirsutum L.)

by Junwu Liu, Yuanqi Ma, Shulin Wang, Shuo Wang, Lingxiao Zhu, Ke Zhang, Yongjiang Zhang, Cundong Li, Liantao Liu and Hongchun Sun

Agronomy 2025, 15(10), 2383; https://doi.org/10.3390/agronomy15102383 - 13 Oct 2025

Abstract

To address low nitrogen use efficiency (NUE) derived from excessive fertilization in cotton production in the Yellow River Basin, a field study was conducted to evaluate the effects of two planting densities and six nitrogen (N) rate levels. Key results show that a [...] Read more.

To address low nitrogen use efficiency (NUE) derived from excessive fertilization in cotton production in the Yellow River Basin, a field study was conducted to evaluate the effects of two planting densities and six nitrogen (N) rate levels. Key results show that a N rate of 225 kg ha⁻¹ optimized root length density and root biomass density. High planting density (105,000 plants ha⁻¹) improved the population-level root traits, photosynthetic radiation interception, and boll number per unit area, though it reduced individual plant root development. Total dry matter peaked at 225 kg ha⁻¹ N, and density increased reproductive dry matter by 7.5–11.9%. Higher N rates reduced reproductive partitioning and root–shoot ratio. While the maximum seed cotton yield (SCY) was 225 kg ha⁻¹, near-maximum yield was achieved at 150 kg ha⁻¹. NUE declined with increasing N, but densification improved agronomic NUE and partial factor productivity by 1.5–6.6% and 3.3–39.3%, respectively. Under the “densification with N reduction” mode, combining a planting density of 105,000 plants·ha⁻¹ with an N rate of 150 kg·ha⁻¹ achieved conventional yield. At the same density, an N rate of 225 kg·ha⁻¹ not only enabled high yield and maintained relatively high NUE but also showed better adaptability to the simplified cultivation mode in Yellow River Basin cotton-growing regions. Full article

(This article belongs to the Section Soil and Plant Nutrition)

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16 pages, 3046 KB

Open AccessArticle

Combined Application of Organic Materials Regulates the Microbial Community Composition by Altering Functional Groups of Organic Matter in Coastal Saline–Alkaline Soils

by Qiaobo Song, Jian Ma, Xin Chen, Caiyan Lu, Huaihai Chen, Guangyu Chi and Yanyu Hu

Agronomy 2025, 15(10), 2382; https://doi.org/10.3390/agronomy15102382 - 13 Oct 2025

Abstract

Different types of organic materials demonstrate varying efficacy in ameliorating saline–alkali soils, while the combined application of organic materials can potentially enhance the remediation effects on saline–alkali land. To verify this assumption, our study conducted a pot experiment with spinach in saline–alkali soil, [...] Read more.

Different types of organic materials demonstrate varying efficacy in ameliorating saline–alkali soils, while the combined application of organic materials can potentially enhance the remediation effects on saline–alkali land. To verify this assumption, our study conducted a pot experiment with spinach in saline–alkali soil, observing the improvement effect of saline–alkali soil and the growth of crops when acid fermentation products of vegetables, humic acid-like substances, and corn straw were applied either individually or in combination. The results revealed that both the sole and combined application of organic materials could enhance the yield of spinach. Particularly, humic acid-like substances increased spinach yield to six times that of the chemical fertilizer treatment. Although the application of organic materials led to a decline in the diversity and richness indices of the microbial community in saline–alkali soil (except fungal richness), the combined use of organic materials contributed to a healthier trend in the soil microbial community structure. Beyond its effects on soil nutrients such as total carbon and total nitrogen, the improvement in soil organic matter activity caused by the joint application of organic materials was identified as the primary factor responsible for enhancing the health of the soil microbial community and the remediation effects on saline–alkali soil. Full article

(This article belongs to the Section Soil and Plant Nutrition)

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21 pages, 5231 KB

Open AccessArticle

Influence of Soil Temperature on Potential Evaporation over Saturated Surfaces—In Situ Lysimeter Study

by Wanxin Li, Zhi Li, Jinyue Cheng, Yi Wang, Fan Wang, Jiawei Wang and Wenke Wang

Agronomy 2025, 15(10), 2381; https://doi.org/10.3390/agronomy15102381 - 12 Oct 2025

Abstract

Potential evaporation (PE) from saturated bare surfaces is the basis for estimating actual evaporation (E_s) in agricultural and related disciplines. Most models estimate PE using meteorological data. Thus, the dependence of soil temperature (T) on PE is often simplified [...] Read more.

Potential evaporation (PE) from saturated bare surfaces is the basis for estimating actual evaporation (E_s) in agricultural and related disciplines. Most models estimate PE using meteorological data. Thus, the dependence of soil temperature (T) on PE is often simplified in applications. To address this gap, we conducted an in situ lysimeter experiment in the Guanzhong Basin, China, continuously measuring PE, T, and soil heat flux (G) at high temporal resolution over three fully saturated sandy soils. Results show that annual PE over fine sand was 7.1% and 11.0% higher than that of coarse sand and gravel. The observed PE differences across textures can be quantitatively explained using the surface energy balance equation and a radiatively coupled Penman-Monteith equation, accounting for the dependence of T on net radiation (R_n) and G. In contrast, PE estimates diverged from observations when R_n and G were assumed to be independent of T. We further evaluated the influence of T and other influencing variables on PE. The random forest model identified that near-surface heat storage variations (∆S) contribute most significantly to PE estimation (relative importance = 0.37), followed by surface temperature (0.24) and sensible heat flux (0.23). These findings highlight the critical role of near-surface temperature in PE estimation. Full article

(This article belongs to the Special Issue Agricultural Water Management in Arid, Semi-Arid and Drought Prone Areas—2nd Edition)

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