Agronomy

24 pages, 5362 KiB

Open AccessArticle

Genomic Architecture of AP2/ERF Superfamily Genes in Marigold (Tagetes erecta) and Insights into the Differential Expression Patterns of AP2 Family Genes During Floral Organ Specification

by Hang Li, Guoqing Chen, Shirui Hu, Cuicui Liu, Manzhu Bao and Yanhong He

Agronomy 2025, 15(5), 1231; https://doi.org/10.3390/agronomy15051231 (registering DOI) - 18 May 2025

Abstract

The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, AP2/ERF genes remain uncharacterized in marigold (Tagetes erecta), [...] Read more.

The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, AP2/ERF genes remain uncharacterized in marigold (Tagetes erecta), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 AP2/ERF genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to AP2/ERF superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, TeAP2/ERF145 exhibited significantly higher expression in ray floret corollas compared to disc florets, while TeAP2/ERF103 showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that AP2 family genes may collaborate with MADS-box and CYC2 genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant. Full article

(This article belongs to the Section Horticultural and Floricultural Crops)

23 pages, 13662 KiB

Open AccessArticle

Adaptive SOM-GA Hybrid Algorithm for Grasping Sequence Optimization in Apple Harvesting Robots: Enhancing Efficiency in Open-Field Orchards

by Li Zhang, Zhihui He, Haobin Zhu, Zhanhong Wei, Juan Lu and Xiongkui He

Agronomy 2025, 15(5), 1230; https://doi.org/10.3390/agronomy15051230 (registering DOI) - 18 May 2025

Abstract

To address the challenge of low operational efficiency in apple harvesting robots, this study proposes an adaptive grasping sequence planning methodology that combines Self-Organizing Maps (SOMs) and genetic algorithms (GAs). The proposed adaptive SOM—GA hybrid algorithm aims to minimize cycle time by optimizing [...] Read more.

To address the challenge of low operational efficiency in apple harvesting robots, this study proposes an adaptive grasping sequence planning methodology that combines Self-Organizing Maps (SOMs) and genetic algorithms (GAs). The proposed adaptive SOM—GA hybrid algorithm aims to minimize cycle time by optimizing the path planning between the fruit detection and grasping phases. First of all, we propose a density-aware adaptive mechanism that dynamically adjusts planning strategies based on fruit count thresholds. In addition, the proposed grasping sequence planning framework for high-density dwarf cultivation (HDDC) orchards is validated through threshold sensitivity analysis and empirical analysis of over 500 real-world fruit distribution samples. Finally, comparative experiments demonstrate that our proposed method reduces path length in high-density scenarios. Statistical analysis reveals a bimodal fruit distribution, which aligns the algorithm’s adaptive thresholds with real-world operational demands. These advancements improve theoretical research and enhance the commercial viability in agricultural robotics. Full article

(This article belongs to the Special Issue Agricultural Environment and Intelligent Plant Protection Equipment—2nd Edition)

25 pages, 1383 KiB

Open AccessArticle

Optimizing Water and Nitrogen Application to Furrow-Irrigated Summer Corn Using the AquaCrop Model

by Yifei Zhao, Shunsheng Wang and Aili Wang

Agronomy 2025, 15(5), 1229; https://doi.org/10.3390/agronomy15051229 (registering DOI) - 18 May 2025

Abstract

Summer maize is an important grain crop in the North China Plain, but the problem of irrational application of water and fertilizer is becoming increasingly serious. Optimizing water and nitrogen management not only improves yield but also reduces water and fertilizer waste and [...] Read more.

Summer maize is an important grain crop in the North China Plain, but the problem of irrational application of water and fertilizer is becoming increasingly serious. Optimizing water and nitrogen management not only improves yield but also reduces water and fertilizer waste and environmental pollution. The Aquacrop model was calibrated and validated using a two-year summer maize field trial, and 16 different water and nitrogen scenarios were simulated and analyzed. In particular, the field trials were divided into 10 water–nitrogen treatments. The results showed that (1) the model has good applicability to the growth process of summer maize in the North China Plain. (2) Excessive water and nitrogen application would reduce yield by 5.6–33.7%, nitrogen bias productivity by 8.1–32.5%, and water use efficiency by 6.4–84.6%. (3) The optimal irrigation and nitrogen application program for furrow-irrigated summer maize is an irrigation quota of 360 mm in conjunction with nitrogen application of 240 kg/ha. This study provides a theoretical basis for a water-saving, fertilizer-saving, high-yield water and fertilizer management system for summer maize in the North China Plain. Full article

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

16 pages, 3314 KiB

Open AccessReview

Plant Aux/IAA Gene Family: Significance in Growth, Development and Stress Responses

by Zelong Zhuang, Jianwen Bian, Zhenping Ren, Wanling Ta and Yunling Peng

Agronomy 2025, 15(5), 1228; https://doi.org/10.3390/agronomy15051228 (registering DOI) - 18 May 2025

Abstract

Auxin plays a crucial role throughout the entire life cycle of plants. The auxin/indole-3-acetic acid (Aux/IAA) gene family serves as a negative regulator of auxin response and is one of the earliest auxin-responsive gene families. It regulates the expression of auxin-responsive [...] Read more.

Auxin plays a crucial role throughout the entire life cycle of plants. The auxin/indole-3-acetic acid (Aux/IAA) gene family serves as a negative regulator of auxin response and is one of the earliest auxin-responsive gene families. It regulates the expression of auxin-responsive genes by specifically binding to auxin response factors. This review summarizes the protein structural characteristics of the Aux/IAA gene family and its typical and atypical transduction mechanisms in auxin signaling. Additionally, it examines the role of Aux/IAA in regulating plant growth and development, as well as its function in modulating plant resistance to abiotic stress through hormonal signaling pathways. Our findings indicate that the Aux/IAA gene family plays a significant role in plant growth and development, as well as in abiotic stress resistance. However, research on the functional roles of the Aux/IAA gene family in crops such as rice, wheat, and maize remains relatively scarce. Furthermore, we identified key questions and proposed new research directions regarding the Aux/IAA gene family, aiming to provide insights for future research on plant hormone signaling and molecular breeding in crop design. Full article

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

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25 pages, 4506 KiB

Open AccessArticle

Optimizing Cropping Systems Using Biochar for Wheat Production Across Contrasting Seasons in Ethiopian Highland Agroecology

by Desalew Fentie, Fekremariam Asargew Mihretie, Yudai Kohira, Solomon Addisu Legesse, Mekuanint Lewoyehu, Tassapak Wutisirirattanachai and Shinjiro Sato

Agronomy 2025, 15(5), 1227; https://doi.org/10.3390/agronomy15051227 (registering DOI) - 18 May 2025

Abstract

Biochar has recently emerged as a promising resource for enhancing crop productivity by improving the soil quality. However, there is limited understanding of how varying application rates of biochar combined with inorganic fertilizers impact crop productivity across diverse biophysical contexts. This study investigated [...] Read more.

Biochar has recently emerged as a promising resource for enhancing crop productivity by improving the soil quality. However, there is limited understanding of how varying application rates of biochar combined with inorganic fertilizers impact crop productivity across diverse biophysical contexts. This study investigated the effects of different rates of water hyacinth-derived biochar and fertilizer application on wheat production during the rainy and dry seasons. Four biochar rates (0, 5, 10, and 20 t ha⁻¹), three NPS fertilizer rates (0, 100, and 200 kg ha⁻¹), and two irrigation levels (50% and 100%; for the dry season only) were evaluated for wheat yield and profitability with a randomized complete block design. Soil amendment with both biochar and fertilizer improved wheat grain yield by 6.4% in the dry season and by 173% in the rainy season. Optimal grain yields were achieved with 10 t ha⁻¹ of biochar and 200 kg ha⁻¹ of fertilizer in the rainy season, whereas in the dry season, the highest yield was observed with 20 t ha⁻¹ of biochar and 200 kg ha⁻¹ of fertilizer under the full water requirement. Specifically, for the dry season, plant height, leaf area, soil plant analysis development (SPAD) of leaf value, dry biomass, spike length, spikelet number, and grain number significantly improved due to biochar and fertilizer application. Furthermore, reducing irrigation to 50% did not significantly affect growth and yield components when the soil was amended with biochar. The highest net return (5351 and 3084 USD ha⁻¹) was achieved with 10 t ha⁻¹ of biochar and 200 kg ha⁻¹ of fertilizer during the rainy and dry seasons, respectively. This study suggests that maximum yield improvement and economic benefits can be obtained through the combination of biochar application, appropriate fertilizer rates, and water management strategies in rainfed and irrigated cropping systems. Full article

(This article belongs to the Special Issue Energy Crops in Sustainable Agriculture)

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23 pages, 1310 KiB

Open AccessArticle

Effects of Biochar on Soil Quality in a Maize Soybean Rotation on Mollisols

by Likun Hou, Yuchao Wang, Zhipeng Wang, Ruichun Gao, Xin Zhou, Siyu Yang, Xu Luo, Zhenfeng Jiang and Zhihua Liu

Agronomy 2025, 15(5), 1226; https://doi.org/10.3390/agronomy15051226 (registering DOI) - 18 May 2025

Abstract

Rotation and organic material addition (e.g., biochar) are major measures to improve soil quality, but the improvement effects and mechanisms of their combination on soil quality remain unclear; the relationship between the physical, chemical, and biological parameters was has not been adequately detected [...] Read more.

Rotation and organic material addition (e.g., biochar) are major measures to improve soil quality, but the improvement effects and mechanisms of their combination on soil quality remain unclear; the relationship between the physical, chemical, and biological parameters was has not been adequately detected in terms of the change in quality after biochar addition. This study selected corn straw biochar as the material and established two biochar application methods: biochar mixed in 0–20 cm soil depth (B1) and biochar mixed in 0–40 cm soil depth (B2). After 3 years of maize–bean rotation, soil samples from 0–20 cm and 20–40 cm were collected to determine the soil’s physical, chemical, and biological properties, as well as crop yields. Principal component analysis was used to establish a minimum data set for the systematic analysis of soil quality and its factors. The results showed that compared with the control (CK), biochar reduced soil bulk density by 3.1% and electrical conductivity by 19.5–28.25% while increasing soil organic matter content by 7.2%, ammonium nitrogen content by 6.7–12.0%, available nitrogen content by 6.7–18.5%, available phosphorus content by 15.6–23.8%, available potassium content by 11.6–17.3%, soil urease activity by 12.25–21.6%, soil sucrase activity by 6.8–30.8%, soil neutral phosphatase activity by 5.6–9.7%, and soil catalase activity by 13.6%. Four indicators, namely bulk density, water content, pH, and nitrate nitrogen, were selected from 16 soil-quality-related indicators to form the minimum data set (MDS), and the soil quality index was calculated. Biochar application significantly increased the soil quality index (SQI) of rotation soil by 14.6–63.3% and crop yields by 5.6–7.2%. A random forest analysis of soil indicators and crop yields, combined with partial least squares structural equation modeling, revealed that biological indicators—particularly catalase activity—showed significant positive correlations with crop yields. Based on these multi-dimensional analyses, the interaction between rotation systems and biochar application improves the quality of mollisol soil plow layers by reducing bulk density and increasing catalase activity. Full article

(This article belongs to the Section Innovative Cropping Systems)

20 pages, 3310 KiB

Open AccessArticle

CdGLK1 Transcription Factor Confers Low-Light Tolerance in Bermudagrass via Coordinated Upregulation of Photosynthetic Genes and Enhanced Antioxidant Enzyme Activity

by Peng Han, Jun Liu, Jingjin Yu, Zhongpeng Liu, Fahui He and Zhimin Yang

Agronomy 2025, 15(5), 1225; https://doi.org/10.3390/agronomy15051225 (registering DOI) - 17 May 2025

Abstract

As a widely cultivated warm-season turfgrass, bermudagrass (Cynodon spp.) faces significant challenges in shaded environments due to its inherent low-light sensitivity. While improving photosynthetic adaptation represents a promising strategy to address this limitation, the associated regulatory mechanisms remain insufficiently characterized. In this [...] Read more.

As a widely cultivated warm-season turfgrass, bermudagrass (Cynodon spp.) faces significant challenges in shaded environments due to its inherent low-light sensitivity. While improving photosynthetic adaptation represents a promising strategy to address this limitation, the associated regulatory mechanisms remain insufficiently characterized. In this study, we found that the overexpression of CdGLK1 significantly improved low-light tolerance in bermudagrass by increasing shoot weight, root weight, chlorophyll a, chlorophyll b, net photosynthetic rate (Pn), and maximum quantum yield of photosystem II (Fv/Fm). Furthermore, coordinated upregulation of both C₃ and C₄ pathway enzymes was observed under low-light stress, accompanied by enhanced antioxidant capacity and reduced photoxidative damage. Transcriptomic profiling further revealed CdGLK1-mediated activation of photosynthetic machinery components spanning light harvesting, electron transport, and carbon fixation modules. These findings establish CdGLK1 as a master integrator of photoprotection and metabolic adaptation under light-limiting conditions, providing both mechanistic insights and practical strategies for developing shade-resilient turfgrass cultivars. Full article

(This article belongs to the Special Issue New Strategies for Forage Breeding and Cultivation Under Challenging Conditions)

19 pages, 6793 KiB

Open AccessArticle

Identification and Analysis of Endoplasmic-Reticulum-Stress- and Salt-Stress-Related Genes in Solanum tuberosum Genome: StbZIP60 Undergoes Splicing in Response to Salt Stress and ER Stress

by Peiyan Guan, Dongbo Zhao, Chenxi Zhang, Zhennan Qiu, Qingshuai Chen, Inna P. Solyanikova, Peinan Sun, Peipei Cui, Ru Yu, Xia Zhang, Yanmei Li and Linshuang Hu

Agronomy 2025, 15(5), 1224; https://doi.org/10.3390/agronomy15051224 (registering DOI) - 17 May 2025

Abstract

Salt stress can trigger endoplasmic reticulum (ER) stress and affect potato yield. The endomembrane system is tightly regulated in response to salt stress for maintaining cellular homeostasis. However, little is known about the genes involved in the ER-mediated cytoprotective pathways in potato plants. [...] Read more.

Salt stress can trigger endoplasmic reticulum (ER) stress and affect potato yield. The endomembrane system is tightly regulated in response to salt stress for maintaining cellular homeostasis. However, little is known about the genes involved in the ER-mediated cytoprotective pathways in potato plants. Previously characterized genes involved in the ER stress signaling pathway in Arabidopsis were used as prototypes. We identified 29 genes involved in ER stress response in the potato genome. Transcriptome data analysis showed that the expression levels of related genes were significantly different in different tissues. Most genes can response to β-aminobutyric acid, benzothiadiazole, salt, and mannitol. qRT-PCR assay revealed that they could respond to NaCl and tunicamycin, which was consistent with the fact that the promoter region of related genes contained ER-stress- and abiotic-stress-related cis-elements. Furthermore, we found that StbZIP60 has a splicing form, StbZIP60s, under salt and ER stress, which can be spliced at the CxGxxG site in the C terminus to create a frame shift through the excision of 23 base pairs. StbZIP60 is localized in the cytoplasm and nucleus, whereas most of the StbZIP60s translocated to the nucleus. This study provides a basis for further analyses of the functions of salt-stress- and ER-stress-related genes in potato plants. Full article

(This article belongs to the Section Plant-Crop Biology and Biochemistry)

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21 pages, 7916 KiB

Open AccessReview

Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis

by Mengdi Tan, Tianjiao Feng, Cong Wang, Xiaozhen Hao and Hang Yu

Agronomy 2025, 15(5), 1223; https://doi.org/10.3390/agronomy15051223 (registering DOI) - 17 May 2025

Abstract

Microbial agents play a crucial role in improving soil quality, increasing soil fertility, enhancing crop yields, and reducing the incidence of diseases. The ecological benefits of these products contribute to environmental protection and to the promotion of sustainable agricultural development. Since the beginning [...] Read more.

Microbial agents play a crucial role in improving soil quality, increasing soil fertility, enhancing crop yields, and reducing the incidence of diseases. The ecological benefits of these products contribute to environmental protection and to the promotion of sustainable agricultural development. Since the beginning of the 21st century, research in the academic community on the use of microbial agents for soil improvement has increased, yet a systematic summary of the progress in this field is lacking. In this paper, we review trends in microbial agent applications, focusing on their classification, mechanisms of action, and practical implementations. To achieve this, we conduct a bibliometric analysis based on the SCI-EXPANDED database of the Web of Science, using tools such as VOSviewer for visualization. We focus on microbial agents for soil improvement and analyze publication trends, research hotspots, and annual variations in relevant studies published between 2003 and 2024. The results show that (1) the number of publications on microbial soil improvement has steadily increased over the years, indicating that the academic community has maintained a high level of interest in this field. Keywords such as “soil”, “diversity”, “carbon”, and “nitrogen” have been central research hotspots in the past 20 years. The research has been highly concentrated in a few countries, including China and the United States, as well as in key institutions such as the Chinese Academy of Sciences and the United States Department of Agriculture. (2) We further analyze the principles governing microbial agent efficacy, address limitations in their application, and propose strategies to advance research in this field. Finally, several suggestions are proposed to promote the further development of research on microbial agents for soil improvement. Full article

(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)

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17 pages, 1159 KiB

Open AccessArticle

Optimization of Subsurface Drainage Parameters in Saline–Alkali Soils to Improve Salt Leaching Efficiency in Farmland in Southern Xinjiang

by Han Guo, Guangning Wang, Zhenliang Song, Pengfei Xu, Xia Li and Liang Ma

Agronomy 2025, 15(5), 1222; https://doi.org/10.3390/agronomy15051222 (registering DOI) - 17 May 2025

Abstract

In arid regions, soil salinization and inefficient water use are major challenges to sustainable agricultural development. Optimizing subsurface drainage system layouts is critical for improving saline soil reclamation efficiency. This study conducted field experiments from 2023 to 2024 to evaluate the effects of [...] Read more.

In arid regions, soil salinization and inefficient water use are major challenges to sustainable agricultural development. Optimizing subsurface drainage system layouts is critical for improving saline soil reclamation efficiency. This study conducted field experiments from 2023 to 2024 to evaluate the effects of varying subsurface drainage configurations—specifically, burial depths (1.0–1.5 m) and pipe spacings (20–40 m)—on drainage and salt removal efficiency in silty loam soils of southern Xinjiang, aiming to develop an optimized scheme balancing water conservation and desalination. Five treatments (A1–A5) were established to measure evaporation, drainage, and salt discharge during both spring and winter irrigation. These variables were analyzed using a water balance model and multifactorial ANOVA to quantify the interactive effects of drainage depth and spacing. The results indicated that treatment A5 (1.5 m depth, 20 m spacing) outperformed all the others in terms of both the drainage-to-irrigation ratio (R_d/i) and the drainage salt efficiency coefficient (DSEC), with a two-year average R_d/i of 32.35% across two spring and two winter irrigation events, and a mean DSEC of 3.28 kg·m⁻³. The 1.5 m burial depth significantly improved salt leaching efficiency by increasing the salt control volume and reducing capillary rise. The main effect of burial depth on both R_d/i and DSEC was highly significant (p < 0.01), whereas the effect of spacing was not statistically significant (p > 0.05). Although the limited experimental duration and the use of a single soil type may affect the generalizability of the findings, the recommended configuration (1.5 m burial depth, 20 m spacing) shows strong potential for broader application in silty loam regions of southern Xinjiang and provides technical support for subsurface drainage projects aimed at reclaiming saline soils in arid regions. Full article

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

19 pages, 3797 KiB

Open AccessArticle

The Influence of Unmanned Aerial Vehicle Wind Field on the Pesticide Droplet Deposition and Control Effect in Cotton Fields

by Haoran Li, Ying Li, Muhammad Zeeshan, Longfei Yang, Zhishuo Gao, Yuting Yang, Guoqiang Zhang, Chunjuan Wang and Xiaoqiang Han

Agronomy 2025, 15(5), 1221; https://doi.org/10.3390/agronomy15051221 (registering DOI) - 17 May 2025

Abstract

Unmanned aerial vehicles (UAVs) offer significant advantages in agricultural pest control. The present study investigated the influence of rotor-induced wind fields from multirotor UAVs (six-rotor T30, eight-rotor T40, eight-rotor T50, and four-rotor T60) on pesticide droplet deposition and control efficacy in cotton fields. [...] Read more.

Unmanned aerial vehicles (UAVs) offer significant advantages in agricultural pest control. The present study investigated the influence of rotor-induced wind fields from multirotor UAVs (six-rotor T30, eight-rotor T40, eight-rotor T50, and four-rotor T60) on pesticide droplet deposition and control efficacy in cotton fields. The results revealed that UAVs with stronger wind fields (e.g., T60) significantly improved droplet deposition in the middle and lower canopy layers, with penetration rates of 54.09–56.04% which were notably higher than the penetration rate observed for the T30 (45.83–44.76%). UAVs exhibited a pesticide utilization efficiency of 75.47–77.86% indicating a 32.2% improvement over the boom sprayers, which achieved a utilization efficiency of 58.88%. While the boom sprayers initially showed a better pest control efficacy, the efficacy gap narrowed after 7 days, with T40 achieving 91.55%, comparable to the efficacy of boom sprayers (93.36%). Following a second spraying, UAVs achieved defoliation rates exceeding 93% and boll opening rates exceeding 90%, similar to that of boom sprayers. This study underscores the critical role of wind field intensity in influencing the spraying performance, with UAVs featuring stronger wind fields exhibiting superior droplet penetration and distribution uniformity. These findings provide valuable scientific insights for optimizing UAV spraying in cotton fields. Full article

(This article belongs to the Special Issue Novel Studies in High-Performance and Precision Plant Protection Products Application—2nd Edition)

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20 pages, 3521 KiB

Open AccessArticle

Using Constrained K-Means Clustering for Soil Texture Mapping with Limited Soil Samples

by Fubin Zhu, Changda Zhu, Zihan Fang, Wenhao Lu and Jianjun Pan

Agronomy 2025, 15(5), 1220; https://doi.org/10.3390/agronomy15051220 (registering DOI) - 17 May 2025

Abstract

Soil texture is one of the most important physical properties of soil and plays a crucial role in determining its suitability for crop cultivation. Currently, supervised classification machine learning methods are most commonly used in digital soil mapping. However, these methods may not [...] Read more.

Soil texture is one of the most important physical properties of soil and plays a crucial role in determining its suitability for crop cultivation. Currently, supervised classification machine learning methods are most commonly used in digital soil mapping. However, these methods may not yield optimal predictive performance due to the limited number of soil samples. Therefore, we propose using Constrained K-Means Clustering to combine a small number of labeled samples with a large amount of unlabeled data, thereby achieving improved prediction in soil texture mapping. In this study, we focused on a typical hilly region in northern Jurong City, Jiangsu Province, China, and used Constrained K-Means Clustering as our mapping model. GF-2 remote sensing imagery and the ALOS digital elevation model (DEM), along with their derived variables, were employed as environmental variables. In Constrained K-Means Clustering, the choice of distance method is a key parameter. Here, we used four different distance methods (euclidean, maximum, manhattan, and canberra) and compared the results with those of the random forest (RF) and multilayer perceptron (MLP) models. Notably, the euclidean distance method within Constrained K-Means Clustering achieved the highest overall accuracy (

O A

),

K a p p a

coefficient, and

M a c r o F 1 S c o r e

, with values of 0.77, 0.68, and 0.75, respectively. These methods were higher than those obtained by the RF and MLP models by 0.12, 0.18, and 0.12, and 0.18, 0.26, and 0.18, respectively. This indicates that Constrained K-Means Clustering demonstrates strong predictive performance in soil texture mapping. Moreover, land use (LU), multi-resolution of ridge top flatness index (MRRTF), topographic position index (TPI), and plan curvature (PlC) emerged as the key environmental variables for predicting soil texture. Overall, Constrained K-Means Clustering proves to be an effective digital soil mapping approach, offering a novel perspective for soil texture mapping with limited samples. Full article

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

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18 pages, 998 KiB

Open AccessArticle

Optimizing the LED Light Spectrum for Enhanced Seed Germination of Lettuce cv. ‘Lollo Bionda’ in Controlled-Environment Agriculture

by Hamid Reza Soufi, Hamid Reza Roosta, Nazim S. Gruda and Mahdiyeh Shojaee Khabisi

Agronomy 2025, 15(5), 1219; https://doi.org/10.3390/agronomy15051219 (registering DOI) - 17 May 2025

Abstract

Light is crucial in controlled-environment agriculture (CEA), affecting germination, growth, and overall plant quality. Here, we explored the optimization of various LED light spectra on the germination traits such as germination percentage, mean germination time, germination index, vigor index, and early seedling growth [...] Read more.

Light is crucial in controlled-environment agriculture (CEA), affecting germination, growth, and overall plant quality. Here, we explored the optimization of various LED light spectra on the germination traits such as germination percentage, mean germination time, germination index, vigor index, and early seedling growth of ‘Lollo Bionda’ lettuce seedlings in a plant factory. A completely randomized design was implemented, involving three replications. LED lamps with different spectral compositions—red (R, peak at 656 nm), red/blue (3:1 ratio, R:B, peak at 656 nm), blue (B, peak at 450 nm), and white (400–700 nm)—were utilized in this study. The combination of red and blue LED lights, along with monochromatic red and blue treatments, significantly enhanced germination traits and early seedling growth compared to white and ambient lighting. The combined spectrum resulted in the highest seedling emergence, the longest shoot and root lengths, and the highest fresh weight. These findings underscore the potential of the LED technology to improve germination efficiency and enhance seedling quality in CEA. Future studies should refine multispectral LED strategies by examining factors such as light intensity and photoperiod, while also elucidating the molecular pathways involved in light-driven germination and early development in lettuce. Full article

(This article belongs to the Special Issue Advancement in Controlled Environment Agriculture (CEA) Automation and Crop Management)

16 pages, 2493 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing

by Huihong Liao, Fuping Liu, Xi Wang, Hongming Huang, Qichun Huang, Nina Wang and Chizhang Wei

Agronomy 2025, 15(5), 1218; https://doi.org/10.3390/agronomy15051218 (registering DOI) - 17 May 2025

Abstract

Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted [...] Read more.

Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and pathways involved in defense mechanisms. The transcriptome data showed that in the susceptible Ponkan Mandarin, there were 1519 upregulated genes and 700 downregulated genes, while in the resistant Punctate Wampee variety, there were 1611 upregulated genes and 1727 downregulated genes. Upon infection, 297 genes were upregulated in both varieties, while 211 genes were downregulated in both. These genes included transcription factors from different families such as WRKY, ERF, and MYB. Ponkan Mandarin primarily relies on pathways like lignin synthesis and cell wall modification to defend against HLB, whereas Punctate Wampee mainly resists HLB by regulating cellular homeostasis and metabolism. Weighted Gene Co-expression Network Analysis (WGCNA) identified ten potential key resistance genes in the resistant Punctate Wampee variety, including genes involved in lignin biosynthesis and genes related to cellular signaling pathways. These findings not only enhance our understanding of the distinct defense mechanisms employed by citrus species against HLB infection but also offer novel perspectives for developing effective prevention and management strategies against this disease. Full article

(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)

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19 pages, 7193 KiB

Open AccessArticle

Multimodal Deep Learning Models in Precision Agriculture: Cotton Yield Prediction Based on Unmanned Aerial Vehicle Imagery and Meteorological Data

by Chunbo Jiang, Xiaoshuai Guo, Yongfu Li, Ning Lai, Lei Peng and Qinglong Geng

Agronomy 2025, 15(5), 1217; https://doi.org/10.3390/agronomy15051217 (registering DOI) - 17 May 2025

Abstract

This study investigates a multimodal deep learning framework that integrates unmanned aerial vehicle (UAV) multispectral imagery with meteorological data to predict cotton yield. The study analyzes the impact of different neural network architectures, including the CNN feature extraction layer, the depth of the [...] Read more.

This study investigates a multimodal deep learning framework that integrates unmanned aerial vehicle (UAV) multispectral imagery with meteorological data to predict cotton yield. The study analyzes the impact of different neural network architectures, including the CNN feature extraction layer, the depth of the fully connected layer, and the method of integrating meteorological data, on model performance. Experimental results show that the model combining UAV multispectral imagery with weekly meteorological data achieved optimal yield prediction accuracy (RMSE = 0.27 t/ha; R² = 0.61). Specifically, models based on AlexNet (Model 9) and CNN2conv (Model 18) exhibited superior accuracy. ANOVA results revealed that deeper fully connected layers significantly reduced RMSE, while variations in CNN architectural complexity had no statistically significant effect. Furthermore, although the models exhibited comparable prediction accuracy (RMSE: 0.27–0.33 t/ha; R²: 0.61–0.69 across test datasets), their yield prediction spatial distributions varied significantly (e.g., Model 9 predicted a mean yield of 3.88 t/ha with a range of 2.51–4.89 t/ha, versus Model 18 at 3.74 t/ha and 2.33–4.76 t/ha), suggesting the need for further evaluation of spatial stability. This study underscores the potential of deep learning models integrating UAV and meteorological data for precision agriculture, offering valuable insights for optimizing spatiotemporal data integration strategies in future research. Full article

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

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22 pages, 1821 KiB

Open AccessArticle

Comparative Nutrient Study of Raphanus sativus L. Sprouts Microgreens, and Roots

by Dominika Kajszczak, Dorota Sosnowska, Radosław Bonikowski, Kamil Szymczak, Barbara Frąszczak, Katarzyna Pielech-Przybylska and Anna Podsędek

Agronomy 2025, 15(5), 1216; https://doi.org/10.3390/agronomy15051216 (registering DOI) - 17 May 2025

Abstract

Radish (Raphanus sativus L.) is an important vegetable crop worldwide. Four red radish cultivars (Carmen, Jutrzenka, Saxa 2, and Warta) were evaluated for their macronutrients (protein, fat, available carbohydrates), as well as ash, and dietary fiber at the sprout, microgreen, and mature [...] Read more.

Radish (Raphanus sativus L.) is an important vegetable crop worldwide. Four red radish cultivars (Carmen, Jutrzenka, Saxa 2, and Warta) were evaluated for their macronutrients (protein, fat, available carbohydrates), as well as ash, and dietary fiber at the sprout, microgreen, and mature (root) stages. Fatty acids, organic acids, and sugars were also profiled by using chromatographic methods. Radish roots are characterized by a good chemical composition due to a lower fat content, lower energy value, and higher available carbohydrate content compared to sprouts and microgreens. Microgreens outperformed other forms of radish in terms of organic acids, ash, and soluble dietary fiber, while sprouts contained the most protein. Both immature forms of radish proved to be better sources of fiber than their mature roots. In all radish samples analyzed, glucose, oxalic acid, and oleic acid or alpha-linolenic acid were the dominant sugar, organic acid, and fatty acid, respectively. The results indicate a diverse composition of radish sprouts, microgreens, and roots, and confirm the validity of using red radishes in various forms as valuable components of our diet. Full article

(This article belongs to the Section Horticultural and Floricultural Crops)

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18 pages, 4291 KiB

Open AccessArticle

Identification, Pathogenicity and Fungicide Sensitivity of Colletotrichum Species Causing Anthracnose on Polygonatum cyrtonema Hua

by Huixia Cai, Jinxin Li, Yanling Du, Di Wu, Jinyi Chen, Hong Chen, Kaili Qu, Yuhuan Miao and Dahui Liu

Agronomy 2025, 15(5), 1215; https://doi.org/10.3390/agronomy15051215 (registering DOI) - 16 May 2025

Abstract

Anthracnose significantly threatens the cultivation of Polygonatum cyrtonema, severely impacting its quality and yield. Between 2022 and 2023, 50 Colletotrichum isolates were obtained from diseased leaves collected in three P. cyrtonema production areas within the Two Lakes region of China (Hubei and [...] Read more.

Anthracnose significantly threatens the cultivation of Polygonatum cyrtonema, severely impacting its quality and yield. Between 2022 and 2023, 50 Colletotrichum isolates were obtained from diseased leaves collected in three P. cyrtonema production areas within the Two Lakes region of China (Hubei and Hunan provinces). Morphological and molecular analyses identified six Colletotrichum species as the causative agents of anthracnose: C. aenigma, C. siamense, C. gloeosporioides, C. spaethianum, C. fructicola, and C. karsti. Among these pathogens, C. fructicola and C. spaethianum were predominant (82%), while C. siamense and C. fructicola exhibited the highest aggressiveness. Physiological investigations revealed that the optimal temperature range for all six pathogens was 25–28 °C. C. spaethianum thrived under acidic conditions, whereas C. aenigma, C. siamense, and C. gloeosporioides preferred alkaline environments. In contrast, C. fructicola and C. karsti showed no significant response to pH variations. Fungicide screening demonstrated that pyraclostrobin, prochloraz, and carbendazim effectively inhibited the growth of Colletotrichum species. These findings elucidate the epidemiological factors, primary pathogens, and effective control agents for P. cyrtonema anthracnose in the Two Lakes region, providing a basis for developing targeted prevention and control strategies. Full article

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

24 pages, 5391 KiB

Open AccessArticle

Design and Implementation of an Intelligent Pest Status Monitoring System for Farmland

by Xinyu Yuan, Zeshen He and Caojun Huang

Agronomy 2025, 15(5), 1214; https://doi.org/10.3390/agronomy15051214 (registering DOI) - 16 May 2025

Abstract

This study proposes an intelligent agricultural pest monitoring system that integrates mechanical control with deep learning to address issues in traditional systems, such as pest accumulation interference, image contrast degradation under complex lighting, and poor balance between model accuracy and real-time performance. A [...] Read more.

This study proposes an intelligent agricultural pest monitoring system that integrates mechanical control with deep learning to address issues in traditional systems, such as pest accumulation interference, image contrast degradation under complex lighting, and poor balance between model accuracy and real-time performance. A three-axis coordinated separation device is employed, achieving a 92.41% single-attempt separation rate and 98.12% after three retries. Image preprocessing combines the Multi-Scale Retinex with Color Preservation (MSRCP) algorithm and bilateral filtering to enhance illumination correction and reduce noise. For overlapping pest detection, EfficientNetv2-S replaces the YOLOv5s backbone and is combined with an Adaptive Feature Pyramid Network (AFPN), achieving 95.72% detection accuracy, 94.04% mAP, and 127 FPS. For pest species recognition, the model incorporates a Squeeze-and-Excitation (SE) attention module and α-CIoU loss function, reaching 91.30% precision on 3428 field images. Deployed on an NVIDIA Jetson Nano, the system demonstrates a detection time of 0.3 s, 89.64% recall, 86.78% precision, and 1.136 s image transmission delay, offering a reliable solution for real-time pest monitoring in complex field environments. Full article

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

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35 pages, 2860 KiB

Open AccessArticle

Enhancing Soil Health, Growth, and Bioactive Compound Accumulation in Sunflower Sprouts Using Agricultural Byproduct-Based Soil Amendments

by Thidarat Rupngam, Patchimaporn Udomkun, Thirasant Boonupara and Puangrat Kaewlom

Agronomy 2025, 15(5), 1213; https://doi.org/10.3390/agronomy15051213 - 16 May 2025

Abstract

This study investigated the effects of organic soil amendments derived from agricultural byproducts—specifically cow manure (CM) at 0% and 1% w/w, and rice husk biochar (RHB) at 0%, 1%, 3%, and 5% w/w—on soil health, plant growth, [...] Read more.

This study investigated the effects of organic soil amendments derived from agricultural byproducts—specifically cow manure (CM) at 0% and 1% w/w, and rice husk biochar (RHB) at 0%, 1%, 3%, and 5% w/w—on soil health, plant growth, and the accumulation of bioactive compounds in sunflower sprouts. The application of 1% CM significantly improved the soil properties—enhancing macroaggregates (MaAs) by 54.5%, mesoaggregates (MeAs) by 16.7%, and soil organic carbon (SOC) by 27.2%. It also increased the shoot and root biomass by 22.3% and 25.8%, respectively, and boosted soil respiration by 67.0%, while reducing the nitrate (NO₃⁻) content by 33.7%. However, the CM also decreased the total phenolic content (TPC) by 21% and chlorophyll by 44.7%. The RHB, particularly at rates of 1–3% w/w, increased the MaAs by 62%, microaggregates (MiAs) by 3%, leaf area by up to 43.9%, root-to-shoot ratio by 26.5%, SOC by 13.1%, and DPPH antioxidant activity by 42.8%, while lowering the MeAs by 9% and NO₃⁻ content by up to 56.1%. In contrast, excessive RHB application (5% w/w) negatively impacted root development. The interaction effects revealed that the combination of 1% w/w CM with 1% w/w RHB maximized the MaAs by 12%, increased the root dry biomass by 101.9%, and also increased the TPC by 40.1% compared to the manure-only treatment. The Principal Component Analysis (PCA) indicated that CM primarily promoted plant growth and respiration, while RHB contributed to organic matter retention and nutrient availability. Applying 1% w/w CM and 1% w/w RHB showed promising effects and is recommended for short-cycle crop production. Full article

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

15 pages, 477 KiB

Open AccessArticle

Sodium Chloride Enhances Nitrogen Use Efficiency but Reduces Yield Benefits Under Elevated CO₂ in Upland Rice

by Daniel Amorim Vieira, Mayra Alejandra Toro-Herrera, João Paulo Pennacchi, Marília Mickaele Pinheiro Carvalho, Flavia Barbosa Silva Botelho, Paulo Eduardo Ribeiro Marchiori and João Paulo Rodrigues Alves Delfino Barbosa

Agronomy 2025, 15(5), 1212; https://doi.org/10.3390/agronomy15051212 - 16 May 2025

Abstract

Climate-change-driven elevation of atmospheric CO₂ (e[CO₂]) disrupts rice physiology by impairing nitrogen use efficiency (NUE) and leaf carbon balance. This study investigated how sodium chloride (NaCl) amendment modulates these processes in upland rice (Oryza sativa L. cv. CMG 2085) [...] Read more.

Climate-change-driven elevation of atmospheric CO₂ (e[CO₂]) disrupts rice physiology by impairing nitrogen use efficiency (NUE) and leaf carbon balance. This study investigated how sodium chloride (NaCl) amendment modulates these processes in upland rice (Oryza sativa L. cv. CMG 2085) under current (400 μmol mol⁻¹) and elevated (700 μmol mol⁻¹) CO₂ concentrations. Using a randomized block design with factorial treatments (CO₂ × NaCl), we analyzed leaf nutrients, gas exchange, chlorophyll fluorescence, and yield parameters. Our findings revealed that 3 mmol L⁻¹ NaCl under ambient CO₂ (1) reduced photorespiration by half, (2) increased grain yield, and (3) enhanced leaf area despite lower leaf N content, indicating improved NUE. Conversely, under e[CO₂], NaCl supplementation decreased rice yield by 15%, demonstrating CO₂-dependent reversal of sodium benefits. Photosynthetic modeling showed higher Vcmax and J values at ambient CO₂, while e[CO₂] increased J/Vcmax, suggesting altered nitrogen allocation to photosynthetic reactions. These results demonstrate that applying low-dose NaCl (3 mmol L⁻¹) can optimize carbon and nitrogen economy under current CO₂ concentrations, although its efficacy diminishes under e[CO₂]. These findings support climate-resilient cultivation strategies for upland rice in tropical and subtropical regions where mild salinity can be used to enhance nitrogen use efficiency and yield under present-day atmospheric conditions. Full article

(This article belongs to the Section Plant-Crop Biology and Biochemistry)

23 pages, 4299 KiB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Analyses Reveal the Positive Effects of 5-Aminolevulinic Acid (ALA) on Shading Stress in Peanut (Arachis hypogaea L.)

by Qi Wu, Liyu Yang, Haiyan Liang, Miao Liu, Dianxu Chen and Pu Shen

Agronomy 2025, 15(5), 1211; https://doi.org/10.3390/agronomy15051211 - 16 May 2025

Abstract

Shading stress is a major negative abiotic environmental factor seriously affecting peanut growth, development, and ultimately resulting in a yield decrease in peanut in peanut/maize intercropping systems. However, 5-aminolevulinic acid (ALA) is a potential plant growth regulator that can enhance its tolerance to [...] Read more.

Shading stress is a major negative abiotic environmental factor seriously affecting peanut growth, development, and ultimately resulting in a yield decrease in peanut in peanut/maize intercropping systems. However, 5-aminolevulinic acid (ALA) is a potential plant growth regulator that can enhance its tolerance to various abiotic stresses. However, there is limited information on how ALA affects plant physiology and molecular mechanisms under shading stress. To address this, field experiments were designed involving two shading conditions (CK and AS0, no shading; S40 and AS40, 40% shading) and two ALA foliar sprayed levels (CK and S40, no ALA application; AS0 and AS40, 20 mg L⁻¹ (0.15 mM) ALA application) to investigate the effects of the exogenous application of ALA under shading stress via the evaluation of both transcriptome and metabolome. The research results suggested that the exogenous ALA application under normal light conditions significantly enhanced photosynthesis, while exogenous ALA application could improve the stability of the cell membrane structure and biological function in response to shading stress and thereby enhance shading tolerance of the plant. The results also implied that exogenous ALA regulates the adaptability of peanuts under different light conditions by affecting the concentration of endogenous ALA. This finding improves the understanding of ALA’s regulatory molecular mechanisms and the metabolic pathways of peanuts under shading stress. Our results extend the application of ALA in agricultural production and will provide a reference for crop cultivation, especially for peanut/maize intercropping systems. Full article

(This article belongs to the Section Plant-Crop Biology and Biochemistry)

15 pages, 5843 KiB

Open AccessArticle

Genome-Wide Characterization and Haplotype Module Stacking Analysis of the KTI Gene Family in Soybean (Glycine max L. Merr.)

by Huilin Tian, Zhanguo Zhang, Shaowei Feng, Jia Song, Xue Han, Xin Chen, Candong Li, Enliang Liu, Linli Xu, Mingliang Yang, Qingshan Chen, Xiaoxia Wu and Zhaoming Qi

Agronomy 2025, 15(5), 1210; https://doi.org/10.3390/agronomy15051210 - 16 May 2025

Abstract

The Kunitz trypsin inhibitor (KTI) gene family encompasses a category of trypsin inhibitors, and the KTI proteins are important components of the 2S storage protein fraction in soybeans. In this study, fifty members of the GmKTI family were identified in the [...] Read more.

The Kunitz trypsin inhibitor (KTI) gene family encompasses a category of trypsin inhibitors, and the KTI proteins are important components of the 2S storage protein fraction in soybeans. In this study, fifty members of the GmKTI family were identified in the soybean genome, and their physicochemical properties, domain compositions, phylogenetic relationships, gene structures, and expression patterns were comprehensively analyzed to explore their impact on soybean seed protein content. The results revealed significant gene expansion within the GmKTI family in soybean. The gene structures and conserved motifs of GmKTI members exhibited both regularity and diversity, with distinct expression patterns across different soybean tissues. Haplotype analysis identified 7 GmKTI genes significantly associated with seed storage protein content, and the combination of superior haplotypes was found to enhance seed storage protein content. This is crucial for the improvement of soybean varieties and the enhancement of storage protein content. Additionally, the GmKTI family demonstrated evolutionary conservation, with its functions likely linked to light induction, biotic stress, and growth development. This study characterizes the structure, expression, genomic haplotypes, and molecular features of the soybean KTI domain for the first time, providing a foundation for functional analyses of the GmKTI domain in soybean and other plants. Full article

(This article belongs to the Special Issue Genetic Basis of Crop Selection and Evolution)

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22 pages, 5228 KiB

Open AccessArticle

An Analysis of Uncertainties in Evaluating Future Climate Change Impacts on Cotton Production and Water Use in China

by Ruixue Yuan, Keyu Wang, Dandan Ren, Zhaowang Chen, Baosheng Guo, Haina Zhang, Dan Li, Cunpeng Zhao, Shumin Han, Huilong Li, Shuling Zhang, De Li Liu and Yanmin Yang

Agronomy 2025, 15(5), 1209; https://doi.org/10.3390/agronomy15051209 - 16 May 2025

Abstract

Global Climate Models (GCMs) are a primary source of uncertainty in assessing climate change impacts on agricultural production, especially when relying on limited models. Considering China’s vast territory and diverse climates, this study utilized 22 GCMs and selected three representative cotton-producing regions: Aral [...] Read more.

Global Climate Models (GCMs) are a primary source of uncertainty in assessing climate change impacts on agricultural production, especially when relying on limited models. Considering China’s vast territory and diverse climates, this study utilized 22 GCMs and selected three representative cotton-producing regions: Aral (northwest inland region), Wangdu (Yellow River basin), and Changde (Yangtze River basin). Using the APSIM model, we simulated climate change effects on cotton yield, water consumption, uncertainties, and climatic factor contributions. Results showed significant variability driven by different GCMs, with uncertainty increasing over time and under radiation forcing. Spatial variations in uncertainty were observed: Wangdu exhibited the highest uncertainties in yield and phenology, while Changde had the greatest uncertainties in ET (evapotranspiration) and irrigation amount. Key factors affecting yield varied regionally—daily maximum temperature and precipitation dominated in Aral; precipitation was a major negative factor in Wangdu; and maximum temperature and solar radiation were critical in Changde. This study provides scientific support for developing climate change adaptation measures tailored to cotton production across different regions. Full article

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

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19 pages, 2471 KiB

Open AccessArticle

Optimizing Microbial Composition in Soil Macroaggregates Enhances Nitrogen Supply Through Long-Term Straw Return

by Lei Xu and Ganghua Li

Agronomy 2025, 15(5), 1208; https://doi.org/10.3390/agronomy15051208 - 16 May 2025

Abstract

Soil nitrogen (N) is critical for crop yield. Although previous studies have shown that straw return enhances soil mineral N availability, the response of soil aggregate microbes to straw return and its impact on soil mineral N availability remains unclear. We conducted a [...] Read more.

Soil nitrogen (N) is critical for crop yield. Although previous studies have shown that straw return enhances soil mineral N availability, the response of soil aggregate microbes to straw return and its impact on soil mineral N availability remains unclear. We conducted a 13-year experiment to explore how soil N mineralization potential, fungi, and bacteria within soil aggregates responded to straw return. Our findings indicated that straw return significantly increased mineral N concentrations in soil macroaggregates, with no statistically significant effect observed on microaggregate composition. We observed increased microbial community α-diversity, enhanced co-occurrence network stability, and an increase in functional groups associated with N (nitrate respiration, denitrification, nitrite denitrification) and carbon (saprotrophs, saprotroph–symbiotrophs, patho-saprotrophs) cycling within the aggregates. Additionally, microorganisms in macroaggregates were influenced by total N, while those in microaggregates were affected by soil total organic carbon and C–N ratio. A sensitivity network analysis identified specific microorganisms responding to straw return. Within macroaggregates, microbial community shifts explained 42.88% of mineral N variation, with bacterial and fungal β-diversity contributing 27.82% and 12.58%, respectively. Moreover, straw return upregulated N-cycling genes (N ammonification: sub, ureC, and chiA; nitrification: amoA-AOB; denitrification: nirK, nirS, nosZ, norB, and narG; and N fixation: nifH) in macroaggregates. Partial least squares path modeling revealed that N availability in macroaggregates was mainly driven by ammonification, with bacterial β-diversity explaining 23.22% and fungal β-diversity 15.16% of the variation. Our study reveals that macroaggregates, which play a crucial role in soil N supply, are highly sensitive to tillage practices. This finding provides a practical approach to reducing reliance on synthetic N fertilizers by promoting microbial-mediated N cycling, while sustaining high crop yields in intensive agricultural systems. Full article

(This article belongs to the Special Issue Effective Soil and Water Conservation Practices in Agriculture—2nd Edition)

24 pages, 1607 KiB

Open AccessReview

Research Progress and Prospects of Mechanized Planting Technology and Equipment for Wine Grapes

by Xiang Li, Fazhan Yang, Baogang Li, Yuhuan Li, Ruijun Sun and Baoju Li

Agronomy 2025, 15(5), 1207; https://doi.org/10.3390/agronomy15051207 - 16 May 2025

Abstract

This article systematically reviews the research progress and challenges in mechanized planting technology and equipment for wine grapes, with a particular focus on the current status and development of the wine grape industry in China. Studies show that the global wine grape cultivation [...] Read more.

This article systematically reviews the research progress and challenges in mechanized planting technology and equipment for wine grapes, with a particular focus on the current status and development of the wine grape industry in China. Studies show that the global wine grape cultivation area is extensive, and China, as one of the major producers, has made significant progress in planting scale and technology application in recent years. However, compared to developed countries such as France and the United States, China still lags behind in the full mechanization of wine grape cultivation, especially in winter cold protection and spring soil clearing. This paper provides a detailed analysis of mechanized operations in wine grape cultivation and compares the differences in related technologies and equipment between China and other countries. The study points out that the main problems faced by China in the mechanized production of wine grapes include a wide variety of equipment, complex winter cold protection procedures, diversified planting patterns, and inadequate technical standards. Future development directions should focus on the integration of advanced technologies with traditional equipment, the construction of a full mechanization technology system, the integration of intelligent and information technologies, and the development of multifunctional composite equipment. By addressing these issues, this article provides a theoretical basis and practical recommendations for the full mechanization development of China’s wine grape industry, aiming to enhance its international competitiveness. Full article

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

18 pages, 1956 KiB

Open AccessArticle

ABA Positively Regulates SlAPX2-Mediated Tolerance to Heat and Cold in Tomato Plants

by Kaimeng Liang, Xiulan Fan, Yuying Liu, Rongrong Tian, Meiling Wang, Zhihong Sun and Fei Ding

Agronomy 2025, 15(5), 1206; https://doi.org/10.3390/agronomy15051206 - 16 May 2025

Abstract

Tomato (Solanum lycopersicum) is highly susceptible to both high and low temperatures, which threaten its growth, yield, and quality. Ascorbate peroxidase (APX) plays a pivotal role in plant responses to abiotic stresses. In this study, we unveil the positive involvement of [...] Read more.

Tomato (Solanum lycopersicum) is highly susceptible to both high and low temperatures, which threaten its growth, yield, and quality. Ascorbate peroxidase (APX) plays a pivotal role in plant responses to abiotic stresses. In this study, we unveil the positive involvement of heat- and cold-induced SlAPX2 in bolstering tomato resilience to temperature extremes. Knockout of SlAPX2 using the CRISPR/Cas9 technique exacerbated oxidative stress under heat and cold conditions, as evidenced by reduced Fv/Fm and increased electrolyte leakage (REL), malondialdehyde (MDA) content, and hydrogen peroxide (H₂O₂) levels. Furthermore, SlAPX2 expression was modulated by abscisic acid (ABA), and the transcription factor ABF4 in the ABA signaling pathway positively regulated SlAPX2 transcription. Using yeast one-hybrid (Y1H) and dual luciferase (LUC) assays, we found that ABF4 directly bound to the SlAPX2 promoter, thereby activating its transcription. Additionally, silencing of SlABF4 compromised tomato’s tolerance to heat or cold. Collectively, these findings reveal a regulatory module, SlABF4–SlAPX2, that enhances tomato tolerance to temperature extremes by detoxifying excessive reactive oxygen species (ROS). This study advances our understanding of ABA-mediated stress responses and highlights the SlABF4–SlAPX2 module as a promising target for breeding temperature-resilient tomato cultivars. Full article

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

17 pages, 1820 KiB

Open AccessArticle

The Impact of Water Deficit at Various Growth Stages on Physiological Characteristics, Fruit Yield, and Quality of Drip-Irrigated Jujube Trees

by Wei Qiang, Pengrui Ai, Yingjie Ma and Jinghua Zhao

Agronomy 2025, 15(5), 1205; https://doi.org/10.3390/agronomy15051205 - 16 May 2025

Abstract

The long-term arid climate in Xinjiang poses a major challenge to sustainable jujube production. In this study, we systematically evaluated the impacts of deficit irrigation (DI) by comparing a full irrigation control (CK) with six DI treatments—mild DI (75% CK) and severe DI [...] Read more.

The long-term arid climate in Xinjiang poses a major challenge to sustainable jujube production. In this study, we systematically evaluated the impacts of deficit irrigation (DI) by comparing a full irrigation control (CK) with six DI treatments—mild DI (75% CK) and severe DI (50% CK) water deficits applied during either flowering + fruit setting or fruit enlargement stages. The key findings demonstrate that flowering + fruit setting DI effectively balances water conservation with productivity. Mild DI (75% CK) during flowering + fruit setting reduced irrigation by 72 mm while maintaining near-optimal photosynthesis (95% recovery post-rewatering) and significantly improving fruit quality (5.49–10.28% higher sugar content, 3.40–5.06% larger fruit volume), despite a moderate 4.22–11.36% yield reduction. In contrast, severe DI caused irreversible physiological stress (only 75% photosynthetic recovery), and fruit-enlargement-stage DI uniformly compromised both yield and fruit size. An economic analysis confirmed flowering + fruit setting mild DI as optimal, generating 17,139–20,550 RMB·ha⁻¹ profit through enhanced water use efficiency (WUE) and premium-quality fruit production. PLS-PM validation revealed that targeted flowering + fruit setting water deficit suppresses vegetative overgrowth while optimizing source–sink relationships, achieving a 23–31% WUE improvement without sacrificing marketable yield. Thus, mild DI during flowering + fruit setting is a climate-smart irrigation strategy for Xinjiang’s jujube industry, resolving water scarcity challenges with economic viability. Full article

(This article belongs to the Special Issue Irrigation and Fertilizer Requirements of Crop Tillage Systems Under Future Climate Change Scenarios)

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15 pages, 7279 KiB

Open AccessArticle

Genome-Wide Identification of BnaPDAT Family in Brassica napus and the Effect of BnaA02.PDAT1 on Seed Oil Content

by Hu Chen, Chunyun Guan and Mei Guan

Agronomy 2025, 15(5), 1204; https://doi.org/10.3390/agronomy15051204 - 16 May 2025

Abstract

Studies in multiple species have shown that phospholipid:diacylglycerol acyltransferase (PDAT) and oil bodies are important factors affecting plant oil accumulation. Although the PDAT gene family has been extensively studied in many plants, it has not yet been systematically analyzed in Brassica napus. [...] Read more.

Studies in multiple species have shown that phospholipid:diacylglycerol acyltransferase (PDAT) and oil bodies are important factors affecting plant oil accumulation. Although the PDAT gene family has been extensively studied in many plants, it has not yet been systematically analyzed in Brassica napus. In this study, we identified four PDAT family members in B. napus, which were divided into two subfamilies based on phylogenetic analysis. These members share conserved motifs and gene structures, with multiple cis-acting elements related to plant hormones and abiotic stress in their promoter regions. Transcriptome sequencing revealed that most BnaPDAT genes are highly expressed during the late stages of seed development, with expression differences under various abiotic stresses and in materials with varying oleic acid content. To further investigate the effects of the PDAT gene on seed oil content and fatty acid composition in Brassica napus, we constructed transgenic plants overexpressing BnaA02.PDAT1 under the control of the 35S promoter. The results showed that compared to wild type (WT), the thousand-seed weight of BnaA02.PDAT1 transgenic plants increased significantly by 12.95–14.76%. Additionally, the total oil content in transgenic seeds was 1.86–2.77% higher than that of WT. Furthermore, the fatty acid composition in the seeds was also altered. This study confirms the critical role of BnaPDAT genes in B. napus seed development and their impact on oil accumulation. Full article

(This article belongs to the Section Plant-Crop Biology and Biochemistry)

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15 pages, 739 KiB

Open AccessArticle

Advancing Research on Overlooked Invertebrates in Biological Control: A Case Study of Local Hoverflies and Wolf Spiders

by Rosemary A. Knapp, Robert McDougall and Paul A. Umina

Agronomy 2025, 15(5), 1203; https://doi.org/10.3390/agronomy15051203 - 16 May 2025

Abstract

Preserving natural enemies in agricultural landscapes is a cornerstone of biological pest control, and avoiding insecticides and miticides that harm non-target species is a key strategy to support naturally occurring populations in the field. Current research on the impacts of these chemicals is [...] Read more.

Preserving natural enemies in agricultural landscapes is a cornerstone of biological pest control, and avoiding insecticides and miticides that harm non-target species is a key strategy to support naturally occurring populations in the field. Current research on the impacts of these chemicals is often biased toward a small number of commercially cultured species, leaving important knowledge gaps for those groups that naturally occur at local scales. Hoverflies (Diptera: Syrphidae) and wolf spiders (Araneae: Lycosidae), both globally important invertebrates in agricultural systems, have been under-researched due to challenges in the field collection and laboratory cultivation of local species. This study helps to address these gaps by evaluating the effects of several widely used chemicals on Australian hoverflies (Melangyna sp.) and wolf spiders (Venatrix spp.) as case study species, with detailed descriptions of laboratory rearing and testing methodologies. The results from standardised chemical toxicity testing showed Venatrix spp. were relatively tolerant to various chemicals, highlighting their potential role in Integrated pest management (IPM) strategies that combine chemical and biological control methods. In contrast, Melangyna sp. was sensitive to numerous chemicals tested, including some that are widely regarded as safe for non-target species. These findings emphasise the need to expand research on underrepresented natural enemy groups to effectively support biological control efforts at local scales. Specifically, the methodologies developed in this study can be adapted to facilitate further research on locally occurring hoverfly and spider species in other regions. Full article

(This article belongs to the Special Issue Advances in Beneficial Insects Research for Conservation Biological Control)

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19 pages, 1250 KiB

Open AccessArticle

Mitigating Gas Emissions from the Dairy Slurry Management Chain: An Enhanced Solid–Liquid Separation Technology with Tannic Acid

by Zhiling Gao and Shanshan Wang

Agronomy 2025, 15(5), 1202; https://doi.org/10.3390/agronomy15051202 - 15 May 2025

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Abstract

Identifying novel flocculants to improve the separation efficiency of dairy slurries is important to facilitate slurry recycling with a low carbon footprint. Two microcosm experiments were conducted to differentiate ammonia (NH₃), nitrous oxide (N₂O), carbon dioxide (CO₂), [...] Read more.

Identifying novel flocculants to improve the separation efficiency of dairy slurries is important to facilitate slurry recycling with a low carbon footprint. Two microcosm experiments were conducted to differentiate ammonia (NH₃), nitrous oxide (N₂O), carbon dioxide (CO₂), and methane (CH₄) emissions from liquid and solid fractions obtained using conventional (mechanical separator) and enhanced (flocculant + mechanical separator) solid–liquid separation (SLS) methods during the storage and soil application phases. Tannic acid (TA) was investigated as a potential flocculant in order to explore its effectiveness in reducing greenhouse gas (GHG) emissions during the storage and soil phases. Compared to the conventional SLS method, the employment of the enhanced SLS method reduced GHG emissions during the storage and soil application phases by 53.64% and 31.63%, respectively, thereby leading to an integrative mitigation of GHG emissions across the storage and soil application chain; however, it strongly increased NH₃ emissions by 70.96% during the soil application phase, demonstrating a higher risk of gaseous N loss. Meanwhile, large trade-offs in N₂O, CH₄, and NH₃ emissions between the solid and liquid fractions during the storage phase were observed, and the reduced CH₄ and NH₃ emissions during the storage phase were also partly offset by increased emissions during the soil application phase. In conclusion, enhanced separation technology using tannic acid as a flocculant can reduce GHG emissions from the management chain, with synergistic mitigation of CH₄ and N₂O, but the risk of increased NH₃ emissions requires further attention. This study may be helpful in mitigating GHG emissions and recycling plant-derived tannic acid in the circular agriculture context. Full article

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

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