Agronomy

26 pages, 5496 KB

Open AccessArticle

Integrative Metabolomic and Transcriptomic Analyses Reveal Mechanisms of Hexavalent Chromium Toxicity in Contrasting Rapeseed Cultivars

by Wan Xu, Ahsan Ayyaz, Fakhir Hannan, Mujeeb Ur Rehman Khan, Tongjun Qin, Wenjian Song, Muhammad Shahbaz Naeem, Ling Xu, Weijun Zhou and Iram Batool

Agronomy 2025, 15(12), 2892; https://doi.org/10.3390/agronomy15122892 - 16 Dec 2025

Abstract

Brassica napus is a key oilseed crop with potential for cultivation in contaminated soils. However, the molecular mechanisms underlying chromium (Cr) toxicity and tolerance are not well-defined. This study aimed to elucidate these mechanisms by analyzing two contrasting cultivars, ZS758 and ZD622, under [...] Read more.

Brassica napus is a key oilseed crop with potential for cultivation in contaminated soils. However, the molecular mechanisms underlying chromium (Cr) toxicity and tolerance are not well-defined. This study aimed to elucidate these mechanisms by analyzing two contrasting cultivars, ZS758 and ZD622, under 50 μM Cr stress using a hydroponic experiment for physiological assessments, transcriptomics, and metabolomics. Cr exposure significantly increased tissue Cr content and severely inhibited plant growth, photosynthesis, and mineral nutrient uptake. Multi-omics analysis revealed extensive transcriptional and metabolic reprogramming. Specifically, we identified 15,882 and 13,371 differentially expressed genes (DEGs) and 256 and 136 differentially expressed metabolites (DEMs) identified in ZS758 and ZD622, respectively. These changes were primarily enriched in carbohydrate and amino acid metabolism pathways. The tolerant cultivar ZS758 exhibited more robust activation of defense-related pathways, including cell wall biosynthesis, hormone signaling, and transporter activity. Our integrative analysis reveals that Cr tolerance in rapeseed associated with cultivar-specific physiological and molecular adaptations. These insights provide potential targets and pathways for developing Cr-resistant varieties for sustainable agriculture in contaminated environments. Full article

(This article belongs to the Special Issue Regulatory Network of Crop to Environmental Stress: Genetic and Biochemical Characterization)

► Show Figures

Figure 1

18 pages, 2412 KB

Open AccessArticle

Effects of Cassava Brown Streak Disease and Harvest Time on Two Cassava Mosaic Disease-Resistant Varieties in Eastern Democratic Republic of the Congo

by Clerisse M. Casinga, Rudolph R. Shirima, Alain Kangela, Everlyne N. Wosula, Benoit Bashizi, Henry U. Ugentho, Leon N. Nabahungu, Godefroid Monde, Zoumana Bamba, Lava Kumar and James P. Legg

Agronomy 2025, 15(12), 2891; https://doi.org/10.3390/agronomy15122891 - 16 Dec 2025

Abstract

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are the two main viral diseases threatening cassava production in the Democratic Republic of the Congo (DRC). CMD can be effectively controlled using resistant varieties; however, currently, there are no cassava varieties that [...] Read more.

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are the two main viral diseases threatening cassava production in the Democratic Republic of the Congo (DRC). CMD can be effectively controlled using resistant varieties; however, currently, there are no cassava varieties that exhibit durable resistance to CBSD. As the deleterious effects of CBSD become more pronounced with the maturity of the cassava, we assessed the potential benefits of early harvesting on mitigating the impact of CBSD on the performance of two improved CMD-resistant cassava varieties, Nabana (MM 96/4653) and Sawasawa (MM 96/3920). The percentage yield reduction was calculated by comparing the yield of infected treatments to that of uninfected treatments. At 9 months after planting (MAP) and 12 MAP, overall fresh root yield from farmer-selected healthy planting material of varieties Nabana and Sawasawa was significantly higher than the yield of crops established using CBSD-infected cuttings of the same varieties. Fresh root yield losses due to CBSD for Nabana were 44% at 9 MAP and 86% at 12 MAP, while for Sawasawa, they were 40% at 9 MAP and 72% at 12 MAP. Healthy planting material of the two varieties yielded 5% more at 12 MAP than at 9 MAP, while infected planting material yielded 52.5% less at 12 MAP than at 9 MAP. These results highlight the benefits of using healthy planting material in conjunction with early harvesting to minimize losses among CBSD-susceptible cassava varieties. These results suggest the need for a robust seed system that can deliver disease-free planting material of market-preferred varieties to farmers, thereby promoting food security. Full article

(This article belongs to the Section Farming Sustainability)

► Show Figures

Figure 1

16 pages, 1423 KB

Open AccessArticle

Modeling the Relationship Between Autonomous Mower Trampling Activity and Turfgrass Green Cover Percentage

by Sofia Matilde Luglio, Christian Frasconi, Lorenzo Gagliardi, Mattia Fontani, Michele Raffaelli, Andrea Peruzzi, Marco Volterrani, Simone Magni and Marco Fontanelli

Agronomy 2025, 15(12), 2890; https://doi.org/10.3390/agronomy15122890 - 16 Dec 2025

Abstract

Autonomous mowers’ navigation pattern plays a crucial role in turfgrass quality, influencing both esthetic and functional performance. However, despite extensive research on mowing efficiency, the effects of different navigation patterns on turfgrass damage and visual quality remain inadequately investigated. This study aimed to [...] Read more.

Autonomous mowers’ navigation pattern plays a crucial role in turfgrass quality, influencing both esthetic and functional performance. However, despite extensive research on mowing efficiency, the effects of different navigation patterns on turfgrass damage and visual quality remain inadequately investigated. This study aimed to evaluate the impact of three different autonomous mower navigation patterns (random, vertical, and chessboard) on operational performance and the effect of trampling activity on turfgrass. Each pattern was tested in terms of data on the number of passages, distance traveled (m), number of intersections and the percentage of area mowed using a remote sensing system and an updated custom-built software. Green coverage percentage was assessed weekly using image analysis (Canopeo app) to evaluate the turfgrass green coverage. The green coverage percentage, together with the number of passages, is analyzed and correlated. The random pattern generated the highest number of passages and intersections, leading to lower average green coverage (64%) compared with the chessboard (80%) and vertical (81%) patterns. Data of the green coverage percentage in the function of the average number of passages recorded using the custom-built software for each pattern fit the asymptotic regression model. The effective number of passages to reach 60% green cover (EP60) was 56.26, 87.30, and 155.32 for random, vertical, and chessboard, respectively. The model could be integrated into DSS, useful for the end user in turf management in order to maintain a high quality. Future studies should extend this approach to other species and environmental conditions, integrating the effective dose (in terms of passages) method for smart mowing management. Full article

(This article belongs to the Special Issue Innovations in Turfgrass Management for Enhanced Sustainability and Conservation)

► Show Figures

Figure 1

12 pages, 730 KB

Open AccessArticle

Assessment of Genetic Diversity Among Bulgarian Lavender Varieties Using Scot Markers

by Mariya Zhelyazkova, Veselina Badzhelova and Stanko Stanev

Agronomy 2025, 15(12), 2889; https://doi.org/10.3390/agronomy15122889 - 16 Dec 2025

Abstract

Lavender (Lavandula angustifolia Mill.) is a traditional and economically important crop in Bulgaria. The cultivated areas are primarily planted with seven Bulgarian varieties: ‘Hemus’, ‘Druzhba’, ‘Sevtopolis’, ‘Yubileina’, ‘Raya’, ‘Hebar’, and ‘Karlovo’. Except for ‘Karlovo’, these cultivars are widely grown due to their [...] Read more.

Lavender (Lavandula angustifolia Mill.) is a traditional and economically important crop in Bulgaria. The cultivated areas are primarily planted with seven Bulgarian varieties: ‘Hemus’, ‘Druzhba’, ‘Sevtopolis’, ‘Yubileina’, ‘Raya’, ‘Hebar’, and ‘Karlovo’. Except for ‘Karlovo’, these cultivars are widely grown due to their proven agronomic performance and adaptability across different regions of the country. However, their genetic diversity and relationships have not been deeply examined. In this study, 13 Start Codon Targeted (SCoT) markers were used to assess the genetic diversity of those seven Bulgarian cultivars. This research provides the first report on the application of SCoT markers in lavender accessions. The results revealed considerable polymorphism, confirming the effectiveness of the SCoT marker system for L. angustifolia. The obtained data indicate moderate genetic diversity among the cultivars, supported by the effective number of alleles and polymorphic information content. Cluster analysis (UPGMA) and Principal Coordinates Analysis (PCoA) demonstrated clear genetic differentiation, grouping the cultivars according to their genetic proximity. These findings provide valuable baseline information for future selection, conservation, and genetic evaluation of Bulgarian lavender. Full article

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

► Show Figures

Figure 1

18 pages, 4912 KB

Open AccessArticle

Sustained Inoculation of a Synthetic Microbial Community Engineers the Rhizosphere Microbiome for Enhanced Pepper Productivity and Quality

by Jiayuan Xu, Qiumei Liu, Zhigang Huang and Dejun Li

Agronomy 2025, 15(12), 2888; https://doi.org/10.3390/agronomy15122888 - 16 Dec 2025

Abstract

The effectiveness of microbial inoculants in agriculture is often limited by their unstable colonization in dynamic soil environments. We investigated the impact of application timing and continuity of a four-member synthetic microbial community (SynCom) on pepper (Capsicum annuum L.) productivity and rhizosphere [...] Read more.

The effectiveness of microbial inoculants in agriculture is often limited by their unstable colonization in dynamic soil environments. We investigated the impact of application timing and continuity of a four-member synthetic microbial community (SynCom) on pepper (Capsicum annuum L.) productivity and rhizosphere microbiome dynamics under greenhouse conditions. Four treatments were included: no inoculation (control), single inoculation at the seedling stage (T1; 5 days post-emergence), single inoculation at the potting stage (T2; 14 days post-transplant), and sustained inoculation at both stages (T3). T3 significantly enhanced plant dry weight (113.4%), root activity (267.8%), fruit sugar (43.9%), and yield (29.0%) relative to the control; and profoundly reshaped the rhizosphere microbiome, enriching functional pathways for nutrient cycling (e.g., phosphorus, nitrogen, and potassium metabolism) and phytohormone synthesis (e.g., indoleacetic acid pathway). Co-occurrence network analysis indicated a significant alteration in microbial interaction patterns, revealing a new community architecture with key taxa such as Neocosmospora, Dyella and the Rhizobium group emerging as central hubs in the T3 network. Our findings underscore that application continuity is a critical factor for optimizing bio-inoculant efficacy, providing a strategy to enhance crop productivity through microbiome engineering in sustainable agriculture. Full article

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

► Show Figures

Figure 1

15 pages, 640 KB

Open AccessArticle

Potential of Paenibacillus dendritiformis as a Plant Growth-Promoting Bacteria of Maize in Infertile Soil

by Jonathan Noé Rubio-Valdez, Jorge Armando Chávez-Simental, Rafael Jiménez Ocampo, José Rodolfo Goche Télles, Gerardo Antonio Pámanes Carrasco, Jaime Herrera Gamboa, Ixchel Abby Ortiz-Sánchez and Juan Pablo Cabral-Miramontes

Agronomy 2025, 15(12), 2887; https://doi.org/10.3390/agronomy15122887 - 16 Dec 2025

Abstract

Climate change and soil degradation represent a threat to essential crops such as maize. In Mexico, this grain is of strategic importance, yet yields are often low. Plant growth-promoting bacteria (PGPB) can help mitigate this problem. The potential of Paenibacillus dendritiformis, isolated [...] Read more.

Climate change and soil degradation represent a threat to essential crops such as maize. In Mexico, this grain is of strategic importance, yet yields are often low. Plant growth-promoting bacteria (PGPB) can help mitigate this problem. The potential of Paenibacillus dendritiformis, isolated from the “El Chichonal” volcano (Chiapas, Mexico), was evaluated as a PGPB under laboratory conditions using infertile soil. Its capacity for nitrogen fixation (NF), phosphate solubilization (PS), indole-3-acetic acid (IAA) production, biocontrol activity, and tolerance to different pH levels, temperature, and salinity were assessed. The effect of inoculation on maize seed germination and vigor was examined in vitro through morphological variables and dry weight. Completely randomized and randomized block designs were used, along with Duncan’s test (p < 0.05) for mean comparison. Cohen’s d was used to estimate the size of the treatment effect. P. dendritiformis demonstrated NF, PS, and IAA production, a wide range of environmental tolerance, and promoted root length and number of root hairs in maize at seven days, as well as increased leaf length and area and foliar and root dry weight at 14 days. It is concluded that P. dendritiformis has potential as a PGPB for infertile soils, based on laboratory evaluations. Full article

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

► Show Figures

Figure 1

20 pages, 1635 KB

Open AccessFeature PaperArticle

Influence of Long-Term Fertilization on Carbon, Nitrogen, and Phosphorus Allocation and Homeostasis in Cotton Under the Regulation of Phosphorus Availability

by Xihe Wang, Jinyu Yang, Hua Liu, Xiaohui Qu and Wanli Xu

Agronomy 2025, 15(12), 2886; https://doi.org/10.3390/agronomy15122886 - 16 Dec 2025

Abstract

Ecological stoichiometry offers critical insights into nutrient dynamics and soil–plant interactions in agroecosystems. To explore the effects of long-term fertilization on soil–cotton C, N, P stoichiometry and stoichiometric homeostasis in arid gray desert soils, this study was conducted at a national gray desert [...] Read more.

Ecological stoichiometry offers critical insights into nutrient dynamics and soil–plant interactions in agroecosystems. To explore the effects of long-term fertilization on soil–cotton C, N, P stoichiometry and stoichiometric homeostasis in arid gray desert soils, this study was conducted at a national gray desert soil monitoring station in Xinjiang (87°28′27″ E, 43°56′32″ N, elevation: 595 m a.s.l.)—an arid and semi-arid region with an annual mean temperature of 5–8 °C and annual precipitation of 100–200 mm. Established in 1989, the 31-year experiment adopted a wheat–maize–cotton annual rotation system with six treatments: CK (control, no fertilizer), N (nitrogen fertilizer alone), NK (nitrogen + potassium fertilizer), NP (nitrogen + phosphorus fertilizer), PK (phosphorus + potassium fertilizer), and NPK (nitrogen + phosphorus + potassium fertilizer). Key results showed that balanced NPK fertilization significantly increased soil organic carbon (SOC) by 22.7% and soil total phosphorus (STP) by 48.6% compared to CK, while the N-only treatment elevated soil N:P to 3.2 (a 68.4% increase vs. CK), indicating severe phosphorus limitation. For cotton, NPK increased seed phosphorus content by 68.2% (vs. N treatment) but reduced straw carbon content by 10.2% (vs. PK treatment), reflecting a carbon allocation trade-off from vegetative to reproductive organs under nutrient sufficiency. Stoichiometric homeostasis differed between organs: seeds maintained stricter carbon regulation (1/H = −0.40) than straw (1/H = −0.64), while straw exhibited more plastic N:P ratios (1/H = 1.95), highlighting organ-specific adaptive strategies to nutrient supply. Redundancy analysis confirmed that soil available phosphorus (AP) was the primary driver of cotton P uptake and yield formation. The seed cotton yield of NPK (5796.9 kg ha⁻¹) was 111.7% higher than CK, with NP (N-P co-application) achieving a 94.7% yield increase vs. CK—only 7.9% lower than NPK, whereas single N application showed the lowest straw yield (5995.0 kg ha⁻¹) and limited yield improvement. These findings demonstrate that long-term balanced NPK fertilization optimizes soil C-N-P stoichiometric balance by enhancing SOC sequestration and phosphorus retention, regulating cotton organ-specific stoichiometric homeostasis, and promoting efficient nutrient uptake and assimilate translocation. The study confirms that phosphorus is the key limiting factor in arid gray desert soil cotton systems, and balanced NPK supply is essential to mitigate stoichiometric imbalances and sustain soil fertility and productivity. This provides targeted practical guidance for rational fertilization management in arid agroecosystems, emphasizing the need to prioritize phosphorus supply and avoid single-nutrient application to maximize resource use efficiency. Full article

(This article belongs to the Topic Carbon and Nitrogen Cycling in Agro-Ecosystems and Other Anthropogenically Maintained Ecosystems—2nd Edition)

► Show Figures

Figure 1

16 pages, 2630 KB

Open AccessArticle

A Canopy Height Model Derived from Unmanned Aerial System Imagery Provides Late-Season Weed Detection and Explains Variation in Crop Yield

by Fred Teasley, Alex L. Woodley and Robert Austin

Agronomy 2025, 15(12), 2885; https://doi.org/10.3390/agronomy15122885 - 16 Dec 2025

Abstract

Weeds pose a ubiquitous challenge to researchers as a source of unintended variation on crop yield and other metrics in designed experiments, creating a need for practical and spatially comprehensive techniques for weed detection. To that end, imagery acquired using unmanned aerial systems [...] Read more.

Weeds pose a ubiquitous challenge to researchers as a source of unintended variation on crop yield and other metrics in designed experiments, creating a need for practical and spatially comprehensive techniques for weed detection. To that end, imagery acquired using unmanned aerial systems (UASs) and classified using pixel-based, object-based, or neural network-based approaches provides researchers a promising avenue. However, in scenarios where spectral differences cannot be used to distinguish between crop and weed foliage, where physical overlap between crop and weed foliage obstructs object-based detection, or where large datasets are not available to train neural networks, alternative methods may be required. For instances where there is a consistent difference in height between crop and weed plants, a mask can be applied to a canopy height model (CHM) such that pixels are determined to be weed or non-weed based on height alone. The CHM Mask (CHMM) approach, which produces a measure of weed area coverage using UAS-acquired, red–green–blue imagery, was used to detect Palmer amaranth in Sweetpotato with an overall accuracy of 86% as well as explain significant variation in sweetpotato yield (p < 0.01). The CHMM approach contributes to the diverse methodologies needed to conduct weed detection in different agricultural settings. Full article

(This article belongs to the Section Weed Science and Weed Management)

► Show Figures

Figure 1

15 pages, 2051 KB

Open AccessArticle

Comparison of the Seed Germination Traits of Five Herbaceous Perennial Campanulaceae Species Native to the Korean Peninsula

by Hyeon Min Kim, Jun Hyeok Kim, Ji Yoon Park, Jae Hyeon Lee, Mi Hyun Lee, Gun Mo Kim and Chae Sun Na

Agronomy 2025, 15(12), 2884; https://doi.org/10.3390/agronomy15122884 - 15 Dec 2025

Abstract

Seed dormancy and germination traits of Campanulaceae species in relation to ecological factors remains unclear. Hence, we clarified the seed germination characteristics of five Campanulaceae species (Adenophora triphylla (Thunb.) A.DC., Asyneuma japonicum (Miq.) Briq., Campanula punctata Lam., Codonopsis pilosula (Franch.) Nannf., and [...] Read more.

Seed dormancy and germination traits of Campanulaceae species in relation to ecological factors remains unclear. Hence, we clarified the seed germination characteristics of five Campanulaceae species (Adenophora triphylla (Thunb.) A.DC., Asyneuma japonicum (Miq.) Briq., Campanula punctata Lam., Codonopsis pilosula (Franch.) Nannf., and Lobelia sessilifolia Lamb.) native to Korea. Seeds were subjected to varying temperatures, cold stratification (CS) durations, and gibberellic acid (GA₃) concentrations. Seeds of all species imbibed water readily, suggesting the absence of physical dormancy. For A. triphylla, A. japonicum, and L. sessilifolia, suitable seed germination occurred under elevated temperature conditions: 74.0 ± 6.2%, 37.0 ± 1.0%, and 26.0 ± 3.5% germination, respectively, at 25 °C, and 79.0 ± 3.8%, 38.0 ± 3.5%, and 62.0 ± 8.4% germination, respectively, at 25/15 °C (day/night) after 7 weeks after incubation. Germination of C. punctata and C. pilosula was consistently low across all temperatures. CS treatment resulted in significant final germination improvement to ~70.0% in four species, excluding C. pilosula. GA₃ application significantly enhanced seed germination by ~60.0% across all species, with the most notable effects observed at 1000 mg∙L⁻¹. Overall, Campanulaceae species seeds are permeable, and pre-treatment with CS and GA₃ is required for effective seed germination. Full article

(This article belongs to the Special Issue Effect of Agronomic Treatment on Seed Germination and Dormancy: 2nd Edition)

► Show Figures

Figure 1

18 pages, 1666 KB

Open AccessArticle

Identification of the Chalcone Synthase Gene Family: Revealing the Molecular Basis for Floral Colour Variation in Wild Aquilegia oxysepala in Northeast China

by Dan Chen, Yongli Cheng, Tingting Ma, Haihang Yu, Yun Bai, Yunwei Zhou and Yuan Meng

Agronomy 2025, 15(12), 2883; https://doi.org/10.3390/agronomy15122883 - 15 Dec 2025

Abstract

Aquilegia (Ranunculaceae), a genus of perennial herbs characterized by elegant leaves and unique flowers, exhibits promising application prospects in Northeast China. Chalcone synthase participates in the first enzymatic reaction of the anthocyanin biosynthesis pathway and plays a crucial role in flower color formation. [...] Read more.

Aquilegia (Ranunculaceae), a genus of perennial herbs characterized by elegant leaves and unique flowers, exhibits promising application prospects in Northeast China. Chalcone synthase participates in the first enzymatic reaction of the anthocyanin biosynthesis pathway and plays a crucial role in flower color formation. In the present study, eight AoCHSs were identified and a comprehensive analysis of AoCHSs was then carried out, considering physical and chemical properties, conservative motifs, phylogenetic relationships, and cis-acting elements. The expression patterns of the AoCHSs were analyzed based on the transcriptome of A. oxysepala, which differs in sepal color between two species, to identify the candidate genes involved in flower color variation. AoCHS2/3/5 expression levels were found to be upregulated at PrA stage in A. oxysepala with dark purple sepals, while remaining consistently low in the pale-yellow species. Combining KEGG annotations and expression patterns, AoCHS5 was identified as a key gene for anthocyanin biosynthesis in Aquilegia that could play a role in the variation in flower color. The results of correlation network analysis showed that AoCHS5 was highly associated with MYB, bHLH, and WRKY. These results provided genetic resources for accelerating the molecular breeding of innovative Aquilegia flower colors. Full article

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

14 pages, 2954 KB

Open AccessArticle

Research on the Efficient Industrial Scale-Up Cultivation of a Novel Aromatic and Disease-Resistant Mushroom Rhodotus palmatus

by Xi Luo, Shaoxiong Liu, Fan Zhou, Jianying Li, Junbo Zhang, Qimeng Liu, Chunli Liu, Lei Wang, Rong Hua and Dafeng Sun

Agronomy 2025, 15(12), 2882; https://doi.org/10.3390/agronomy15122882 - 15 Dec 2025

Abstract

Rhodotus palmatus is commercially marketed as ‘fruity-scented mushroom’, a novel cultivar first brought into commercial cultivation in China at the end of 2023. It is characterized by a distinct pinkish pigmentation, a pileus with a distinct reticulated surface pattern, and an intense fruity [...] Read more.

Rhodotus palmatus is commercially marketed as ‘fruity-scented mushroom’, a novel cultivar first brought into commercial cultivation in China at the end of 2023. It is characterized by a distinct pinkish pigmentation, a pileus with a distinct reticulated surface pattern, and an intense fruity aroma. To date, only a few natural strains have been documented in China, and scientific research on this species remains scarce. This study successfully bred a new variety of Rhodotus palmatus and established corresponding efficient techniques for its industrial-scale cultivation. As a result, strain ZJGWG001, known for its short growth cycle (23 d), high yield potential (177.43 ± 10.08 g·bag⁻¹) and biological efficiency (59.1%), and distinctive, stable phenotypic traits, is well suited for industrial cultivation. This cultivar is the first newly registered Rhodotus palmatus variety in China to receive provincial-level certification and has been officially designated as ‘Zhongjunguoweigu No. 1’. It represents an important discovery in the collection and exploration of wild fungal germplasm resources in recent years. Full article

(This article belongs to the Special Issue Identification and Breeding of High-Quality, Disease-Resistance and High-Producing Varieties)

► Show Figures

Figure 1

17 pages, 6352 KB

Open AccessArticle

Genome-Wide Identification of AP2/ERF Family Genes in Rubber Tree: Two HbAP2/ERF Genes Regulate the Expression of Multiple Natural Rubber Biosynthesis Genes

by Xiaoyu Du, Yi Sun, Wenqing Cao, Shaohua Wu, Xiaomin Deng, Shuguang Yang, Minjing Shi, Hongmei Yuan and Jinquan Chao

Agronomy 2025, 15(12), 2881; https://doi.org/10.3390/agronomy15122881 - 15 Dec 2025

Abstract

The AP2/ERF (APETALA2/ethylene-responsive factor) superfamily is one of the largest transcription factor families in plants and is not only vital for plant growth and development but also participates in responding to various abiotic stresses. However, few studies have investigated the function of the [...] Read more.

The AP2/ERF (APETALA2/ethylene-responsive factor) superfamily is one of the largest transcription factor families in plants and is not only vital for plant growth and development but also participates in responding to various abiotic stresses. However, few studies have investigated the function of the AP2/ERF gene family in natural rubber (NR) biosynthesis in Hevea brasiliensis. Here, 174 HbAP2/ERF genes were identified genome-wide and classified into 18 subclades based on gene-conserved structure and phylogenetic analysis. Gene duplication analysis revealed that 7 tandem and 100 segmental duplication events were major drivers of this gene family. Cis-element analysis in HbAP2/ERF promoters identified light-, hormone-, stress-, and development-associated cis-elements. Tissue-specific expression profiles revealed that 160 HbAP2/ERFs were expressed in at least one tissue. The protein–protein interaction network identified 59 potential interactions among the HbAP2/ERFs. Critically, dual-luciferase reporter assays confirmed that two key regulators exhibit distinct regulatory modes on NR biosynthesis-related genes: HbAP2/ERF25 significantly repressed the transcriptional activities of HbMVD1, HbCPT7, and HbSRPP1, whereas HbAP2/ERF46 repressed HbMVD1 but activated HbHMGR1, HbFPS1, and HbSRPP1. These findings reveal the complex regulatory network of HbAP2/ERFs in NR biosynthesis, establish a comprehensive framework for understanding their evolution and functional diversification, and provide novel molecular targets for genetic improvement of NR yield in rubber tree breeding and metabolic engineering. Full article

► Show Figures

Figure 1

15 pages, 2151 KB

Open AccessArticle

Performance of Strip Intercropping of Genetically Modified Maize and Soybean Against Major Target Pests

by Wanxuan Zhao, Chen Zhang, Zhicheng Shen, Laipan Liu, Mohammad Shaef Ullah, Xiaowei Yang, Geng Chen and Lanzhi Han

Agronomy 2025, 15(12), 2880; https://doi.org/10.3390/agronomy15122880 - 15 Dec 2025

Abstract

The commercialization of genetically modified (GM) maize and soybean is advancing, with strip intercropping emerging as a promising model to enhance crop yields and resource efficiency. However, the impact of this system on target pests remains unclear. To address this, we evaluated eight [...] Read more.

The commercialization of genetically modified (GM) maize and soybean is advancing, with strip intercropping emerging as a promising model to enhance crop yields and resource efficiency. However, the impact of this system on target pests remains unclear. To address this, we evaluated eight different planting patterns (four different monocultures and four different strip intercropping integrations) of insect-resistant GM maize (‘RF88’) and soybean (CAL16) events and their non-transgenic parental lines (Xianyu 335 maize and Tianlong No. 1 soybean) in the Huang-Huai-Hai planting area from 2023 to 2025. Our results identified Helicoverpa armigera and Spodoptera exigua as the dominant pests on maize and soybean, respectively. We found that the GM trait significantly reduced the population density and plant damage caused by these pests. Strip intercropping also provided significant suppression across both crop lines. Furthermore, the integration of strip intercropping and the GM trait resulted in the most effective pest control. This study provides valuable insights for the top-level design and industrial layout of GM crop commercialization and contributes to promoting its safe application and sustainable pest management. Full article

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

► Show Figures

Figure 1

18 pages, 2808 KB

Open AccessArticle

Lightweight Structure and Attention Fusion for In-Field Crop Pest and Disease Detection

by Zijing Luo, Yunsen Liang, Naimin Kong, Lirui Liang, Wenjun Peng, Yujie Yao, Chi Qin, Xiaohan Lu, Mingman Xu, Yining Zhang, Chenyang Lin, Chengyao Jiang, Mengyao Li, Yangxia Zheng, Yameng Jiang and Wei Lu

Agronomy 2025, 15(12), 2879; https://doi.org/10.3390/agronomy15122879 - 15 Dec 2025

Abstract

In agricultural production, plant diseases and pests are among the major threats to crop yield and quality. Existing agricultural pest and disease identification methods have problems such as small target scales, complex background environments, and unbalanced sample distributions. This paper proposes a lightweight [...] Read more.

In agricultural production, plant diseases and pests are among the major threats to crop yield and quality. Existing agricultural pest and disease identification methods have problems such as small target scales, complex background environments, and unbalanced sample distributions. This paper proposes a lightweight improved target detection model, YOLOv5s-LiteAttn. Based on YOLOv5s, the model introduces GhostConv and Depthwise Conv to reduce the number of parameters and computational complexity, and it combines CBAM and Coordinate Attention mechanisms to enhance the network’s feature representation capability. Experimental results show that, compared with the basic YOLOv5s model, the number of parameters of the improved model is reduced by 22.75%, and the computational load is reduced by 16.77%. At the same time, mAP@0.5–0.95 is increased by 3.3 percentage points, and recall is improved by 1.1 percentage points. In addition, the inference speed increases from 121 FPS to 142 FPS at an input resolution of 640 × 640, further confirming that the proposed model achieves a favorable trade-off between accuracy and efficiency. The average precision of YOLOv5s-LiteAttn is 97.1%, which outperforms the existing mainstream lightweight detection models. Moreover, an independent test set containing 4328 newly collected field images was established to evaluate generalization and practical applicability. Despite a slight performance decrease compared with the validation results, the model maintained an mAP@0.5–0.95 of 95.8%, significantly outperforming the baseline model, thereby confirming its robustness and cross-domain adaptability. These results confirm that the model has high precision and is lightweight, making it effective for the detection of agricultural diseases and pests. Full article

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

► Show Figures

Figure 1

25 pages, 6042 KB

Open AccessArticle

Ridge-Furrow Planting with Nitrogen Application Enhanced Rainfed Maize Yield and Water Productivity by Improving Leaf Photosynthetic Capacity

by Zhenlin Lai, Hao Kong, Mahmood Hemat, Zhenqi Liao, Shengzhao Pei, Han Wang, Zhijun Li and Junliang Fan

Agronomy 2025, 15(12), 2878; https://doi.org/10.3390/agronomy15122878 - 15 Dec 2025

Abstract

Leaf photosynthesis plays an important role in maize growth and yield components due to its involvement in dry matter partitioning and organ formation. Nevertheless, how varying planting patterns affect maize leaf photosynthesis, chlorophyll fluorescence and subsequently maize yield remains poorly understood, particularly at [...] Read more.

Leaf photosynthesis plays an important role in maize growth and yield components due to its involvement in dry matter partitioning and organ formation. Nevertheless, how varying planting patterns affect maize leaf photosynthesis, chlorophyll fluorescence and subsequently maize yield remains poorly understood, particularly at various nitrogen rates. A two-season field experiment was performed on rainfed maize in 2021 and 2022 to explore the responses of photosynthetic physiological characteristics, leaf N and chlorophyll contents, chlorophyll fluorescence parameters, grain yield and water productivity to various planting patterns and N rates. The experiment included six planting patterns, i.e., flat planting without mulching (CK), flat planting with straw mulching (SM), ridge mulched with transparent film and furrow without mulching (RP1), flat planting with full transparent film mulching (FM1), ridge mulched with black film and furrow without mulching (RP2), and flat planting with full black film mulching (FM2). Additionally, there were two nitrogen rates, i.e., 0 kg N ha⁻¹ (N0) and 180 kg N ha⁻¹. The results showed that nitrogen application significantly improved leaf physiological characteristics. Under various planting patterns, leaf photosynthetic pigments, leaf area duration, leaf nitrogen content, QYmax and ΦPSII ranked as RP2 > RP1(FM2) > FM1 > SM(CK) in 2021, and RP2(RP1) > FM1(FM2) > SM(CK) in 2022. No significant variations were observed in water productivity (WP) among different film colors, with overall performance of RP2(FM2) > RP1(FM1) > SM > CK. WP significantly improved by 36.14% and 25.15% under N1 compared to N0 in 2021 and 2022, respectively. This pattern paralleled the fluctuation in water consumption intensity. Compared to CK, RP significantly increased leaf nitrogen content (29.3%), total Chl content (16.0%), QYmax (6.39%), ΦPSII (32.01%), and net photosynthesis rate (14.2%), thereby significantly improving grain yield (46.35%) and WP (27.69%), while reducing evapotranspiration (6.84%). Yield performance ranked as RP2 > (RP1 and FM2) > FM1 > SM > CK in 2021 and RP2 > RP1 > (FM1 and FM2) > SM > CK in 2022. Overall, RP2N1 obtained the highest principal component scores in both years, suggesting great potential to improve leaf photosynthetic physiological characteristics, thereby increasing grain production and ensuring food security in rainfed maize cultivation areas. Full article

(This article belongs to the Collection Crop Physiology and Stress)

► Show Figures

Figure 1

19 pages, 3929 KB

Open AccessArticle

Application of Integrated Multi-Operation Paddy Field Leveling Machine in Rice Production

by Yangjie Shi, Jiawang Hong, Xingye Shen, Peng Xu, Jintao Xu, Xiaobo Xi, Qun Hu and Hui Shen

Agronomy 2025, 15(12), 2877; https://doi.org/10.3390/agronomy15122877 - 14 Dec 2025

Abstract

Paddy field leveling is the foundation of high-yield rice cultivation. In response to the current issues of low leveling accuracy and the lack of efficient multi-operation machinery, an Integrated Multi-operation Paddy Field Leveling Machine was designed in this study. This machine can complete [...] Read more.

Paddy field leveling is the foundation of high-yield rice cultivation. In response to the current issues of low leveling accuracy and the lack of efficient multi-operation machinery, an Integrated Multi-operation Paddy Field Leveling Machine was designed in this study. This machine can complete soil crushing, stubble burying, mud stirring, and leveling in a single pass. Combined with an adaptive control system based on Global Navigation Satellite System—Real-Time Kinematic (GNSS-RTK) technology, it enables adaptive and precise paddy field leveling operations. To verify the operational performance of the equipment, field tests were conducted. The results showed that the machine achieved an average puddling depth of 14.21 cm, a surface levelness of 2.16 cm, an average stubble burial depth of 8.15 cm, and a vegetation coverage rate of 89.33%, demonstrating satisfactory leveling performance. Furthermore, to clarify the feasibility and superiority of applying this equipment in actual rice production, experiments were conducted to investigate the effects of different field leveling methods on early rice growth, yield, and its components. One-way analysis of variance was employed to examine the differences in agronomic indicators between the different field leveling treatments. The results indicated that using this equipment for paddy field leveling, compared to traditional methods and dry land preparation, can improve the seedling emergence rate, thereby laying a solid population foundation for the formation of effective panicles. It also promoted root growth and development and increased the total dry matter accumulation at maturity, thereby contributing to high yield formation. Over the two-year experimental period, the rice yield remained above 9.8 t·hm⁻². This research provides theoretical support and practical guidance for the further optimization and development of subsequent paddy field preparation equipment, thereby promoting the widespread application of this technology in rice production. Full article

(This article belongs to the Special Issue Ecophysiological Principles for Sustainable Rice and Wheat Cultivation)

► Show Figures

Figure 1

18 pages, 1309 KB

Open AccessArticle

Seed Coating Synergies: Harnessing Plant Growth Regulators to Strengthen Soybean Nodulation and Stress Resilience

by Saranyapath Pairintra, Nantakorn Boonkerd, Neung Teaumroong and Kamolchanok Umnajkitikorn

Agronomy 2025, 15(12), 2876; https://doi.org/10.3390/agronomy15122876 - 14 Dec 2025

Abstract

Soybean (Glycine max) is a globally important crop, but its productivity is often limited by suboptimal nodulation and nitrogen fixation, particularly under stress conditions. Bradyrhizobium diazoefficiens strain USDA110 is widely applied to enhance nodulation, yet its efficiency can be further improved [...] Read more.

Soybean (Glycine max) is a globally important crop, but its productivity is often limited by suboptimal nodulation and nitrogen fixation, particularly under stress conditions. Bradyrhizobium diazoefficiens strain USDA110 is widely applied to enhance nodulation, yet its efficiency can be further improved by phytohormone modulation. This study examined the effects of seed coatings containing plant growth regulators (PGRs)—acetylsalicylic acid (ASA), aminoethoxyvinylglycine (AVG), Indole-3-butyric acid (IBA), and 6-benzylaminopurine (BAP)—at varying concentrations (5, 50, and 500 nM), in combination with USDA110, on nodulation, nitrogenase activity, ethylene emission, physiological traits, and yield of soybean cultivar CM60. Laboratory assays identified 50 nM AVG, 5 nM IBA, and 5 nM ASA as optimal treatments, significantly enhancing nodule number and nitrogenase activity more than 32% and 28%, as, respectively, compared to untreated seeds. Greenhouse trials in pots, both under well-watered and water stress conditions, showed that USDA110 + AVG/IBA significantly improved photosynthetic rate (+21 and +18% compared to USDA110 alone) and increased plant height. Notably, USDA110 + AVG/IBA treatments sustained higher seed weight under drought, increasing it by over 25%, indicating strong synergistic effects in mitigating stress impacts. These findings highlighted that integrating USDA110 with specific PGRs represented a promising strategy to optimize nitrogen fixation and enhanced soybean productivity under both favorable and challenging conditions. Full article

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

28 pages, 4180 KB

Open AccessArticle

Ecofriendly Application of Synthetic Zinc Oxide Nanoparticles as Stress Regulator Bio-Fertilizer for Zea mays

by Mostafa Ahmed, Zoltán Tóth, Roquia Rizk, Muhammad Waqar Nasir and Kincső Decsi

Agronomy 2025, 15(12), 2875; https://doi.org/10.3390/agronomy15122875 - 14 Dec 2025

Abstract

Agricultural production is consistently threatened by stressors such as salinity. Few studies have reported on the released antioxidative enzymes and the salinity-responsive genes identified using RNA sequencing and de novo assembly in maize. To further understand the harmony between stressing the maize with [...] Read more.

Agricultural production is consistently threatened by stressors such as salinity. Few studies have reported on the released antioxidative enzymes and the salinity-responsive genes identified using RNA sequencing and de novo assembly in maize. To further understand the harmony between stressing the maize with a NaCl solution as a compensatory water-irrigation method and spraying regulatory zinc oxide nanoparticles (ZnO/NPs), the salinity-responsive genes were analyzed using RNA sequencing and bioinformatics tools, and the antioxidant enzymatic activities were determined. Differential expression analysis was used to uncover genes that were up-/down-regulated during the experiment. The regulatory pathways and functions of differentially expressed genes (DEGs) were estimated. Glutathione reductase/-s-transferase (GR/GST), peroxidase (POX), superoxide dismutase (SOD), and catalase (CAT) enzymes were determined spectrophotometrically. Mitigating salinity stress with 150 mM NaCl led to significant oxidative stress, markedly elevating enzyme activities: POX and GST by 275% and 254%, GR by 166%, CAT by 91%, and SOD by 56%. Treatment with ZnO/NPs alleviated this stress, decreasing enzyme activity by 61% for GST, 55% for POX, 38% for CAT, 28% for SOD, and 25% for GR. The results of RNA-seq revealed candidate genes related to changes in stressed/non-stressed maize plants, regardless of whether they were sprayed with the nanoparticles or not. This study’s results offer novel insights into the genetic traits of maize subjected to salinity stress and ZnO/nanoparticle application, thereby advancing the comprehension of how ZnO/nanoparticles might alleviate the detrimental impacts of salinity on plants whose properties were enhanced to be used in the eco-friendly synthesis of nanoparticles that were used as a bio-fertilizer in priming plants. Full article

(This article belongs to the Special Issue Bio-Based Fertilizers and Soil Health: Innovations for Nutrient Recycling and Environmental Protection)

23 pages, 6247 KB

Open AccessArticle

Biochar Particle Size Modulates the Microbial Degradation of Petroleum Hydrocarbons in Contaminated Soil

by Yanjie Wang, Qiong Wang, Meijuan Wang, Haiqing Lei and Jiabo Chen

Agronomy 2025, 15(12), 2874; https://doi.org/10.3390/agronomy15122874 - 14 Dec 2025

Abstract

Petroleum hydrocarbons are pervasive soil pollutants that detrimentally affect the soil structure, nutrients, and microbial ecosystems. However, the effect of biochar particle size on the remediation effectiveness remains a critical, unresolved parameter. Here, a soil remediation experiment was conducted to evaluate the synergy [...] Read more.

Petroleum hydrocarbons are pervasive soil pollutants that detrimentally affect the soil structure, nutrients, and microbial ecosystems. However, the effect of biochar particle size on the remediation effectiveness remains a critical, unresolved parameter. Here, a soil remediation experiment was conducted to evaluate the synergy between biochars of different particle sizes and nutrient addition. Total petroleum hydrocarbons (TPHs) were quantified gravimetrically, and specific hydrocarbon fractions were analysed via gas chromatography mass spectroscopy (GC‒MS) while the microbial community composition was analysed via high-throughput sequencing. The results revealed that granular bulrush straw biochar (0.85 mm) with nutrients achieved the greatest TPH degradation (73.35%), significantly outperforming both powder biochar and soybean straw biochar. This enhanced remediation was associated with a significant shift in the microbial community (p < 0.05), characterized by substantial increases in hydrocarbon-degrading bacteria, particularly Actinobacteria and the genus Mycobacterium. This study revealed that the synergistic application of granular biochar and nutrients is a highly effective, nature-based strategy for petroleum-contaminated soil, which functions by resolving a critical biochar parameter to enhance key microbial degraders. Full article

(This article belongs to the Special Issue Soil Degradation and Restoration: Challenges and Prospects for Agroecological Development)

Journal Description

Agronomy

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI