Agronomy

18 pages, 13913 KB

Open AccessArticle

Comparative Transcriptome Analysis Reveals Molecular Indicators of Embryogenic Initiation Divergence Between Rice Varieties CXJ and 9311 During Microspore Culture

by Wenqi Zhang, Runhong Gao, Yingjie Zong, Yulu Tao, Yu Wang, Zhiwei Chen, Yingbo Li and Chenghong Liu

Agronomy 2025, 15(9), 2206; https://doi.org/10.3390/agronomy15092206 - 17 Sep 2025

Abstract

This study elucidates the key molecular features underlying the embryogenic initiation divergence between japonica rice Chongxiangjing (CXJ) and indica rice 9311 during isolated microspore culture. Comparative transcriptome analysis across critical timepoints (0, 5, and 10 days post-culture initiation) revealed that while both varieties [...] Read more.

This study elucidates the key molecular features underlying the embryogenic initiation divergence between japonica rice Chongxiangjing (CXJ) and indica rice 9311 during isolated microspore culture. Comparative transcriptome analysis across critical timepoints (0, 5, and 10 days post-culture initiation) revealed that while both varieties initially exhibit comparable microspore viability, CXJ maintains transcriptional stability and activates developmental programs (e.g., hormone signaling, DNA replication, cell morphogenesis), enabling sustained callus formation. In contrast, 9311 undergoes drastic transcriptome reorganization by 5 days, characterized by maladaptive activation of stress-response pathways (glutathione metabolism, MAPK signaling, ER stress) and futile metabolic reactivation (photosynthesis, starch degradation), culminating in near-total cell death and failed callus induction. Transcription factor dynamics further explain this divergence: CXJ specifically upregulates regulators coordinating development and stress resilience (NAC, ERF, HSF, GRAS, bZIP), while 9311 exhibits detrimental upregulation of FAR1 and B3, leading to catastrophic energy misallocation. These findings identify master transcriptional networks and stress-response pathways as pivotal indicators of embryogenic initiation efficiency, providing strategic targets for enhancing indica rice microspore culture technology. Full article

(This article belongs to the Special Issue Innovative Research on Rice Breeding and Genetics)

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33 pages, 8400 KB

Open AccessArticle

Biochar and Nitrogen Fertilizer Synergies: Enhancing Soil Properties and Jujube Fruit Quality in Saline–Alkali Orchards of Southern Xinjiang

by Haoyang Liu, Yunqi Ma, Yuxuan Wei, Cuiyun Wu and Yuyang Zhang

Agronomy 2025, 15(9), 2205; https://doi.org/10.3390/agronomy15092205 - 17 Sep 2025

Abstract

Saline–alkali soils in southern Xinjiang present significant challenges for sustainable jujube cultivation, necessitating innovative fertilization strategies to improve soil health and enhance fruit quality. This study investigated the synergistic effects of biochar–nitrogen (N) co-application on soil amelioration and the improvement of jujube quality [...] Read more.

Saline–alkali soils in southern Xinjiang present significant challenges for sustainable jujube cultivation, necessitating innovative fertilization strategies to improve soil health and enhance fruit quality. This study investigated the synergistic effects of biochar–nitrogen (N) co-application on soil amelioration and the improvement of jujube quality in saline–alkali jujube orchards. A field experiment was conducted using different biochar application rates (0, BC1, BC2) combined with various N fertilizer types (conventional nitrogen N1, N2, UI-N (urease inhibitor), and NI-N (nitrification inhibitor)), which systematically analyzed soil physicochemical properties, nutrient dynamics, enzyme activities, microbial community structure, and jujube fruit yield and quality parameters. The BC1 biochar application rate emerged as the optimal threshold for soil carbon and N sequestration, with BC1 + N2 treatment achieving the highest total carbon and total nitrogen concentrations, representing increases of 12.4% and 21.42%, respectively, compared to controls. Biochar–N co-application significantly enhanced soil available nutrients, with BC1 + UI-N treatment producing the greatest soil organic matter increase within the BC1 group (9.20–14.51% enhancement). Notably, the treatments modulated soil microelement profiles, suppressing potentially toxic Cu and Mn while enhancing the availability of beneficial Mg and Fe. Soil enzyme activities responded differently, with urease and sucrase activities reaching maximum levels under BC2 + N1 and BC1 + UI-N treatments, respectively. Microbial community analysis revealed that biochar–N combinations significantly restructured both bacterial and fungal communities, with BC1 + NI-N treatment demonstrating superior bacterial α-diversity across all indices. Soil enzyme activities exhibited distinct response patterns, with urease and sucrase activities reaching their peak under the BC2 + N1 and BC1 + UI-N treatments, respectively. Moreover, the co-application of biochar (BC1) with N fertilizer significantly improved fruit performance, increasing per-tree yield by 24.23% and fruit vitamin C content by 16.47%, compared to the control. This study demonstrates that moderate biochar application (BC1) combined with urease inhibitor- enhanced N fertilizer (UI-N) represents an optimal fertilization strategy for saline–alkali jujube orchards, achieving simultaneous soil amelioration and fruit quality enhancement through coordinated regulation of soil–microbe–plant interactions. The established quantitative relationships provide a scientific foundation for the implementation of precision agriculture in arid saline–alkali regions, offering significant implications for sustainable specialty fruit production and soil health restoration in environmentally challenged agricultural systems. Full article

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

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31 pages, 6233 KB

Open AccessArticle

Genome-Wide Identification of Flowering-Related Genes and Their Pleiotropic Roles in Regulating Flowering Time and Plant Height in Soybean

by Xiao Li, Hui Wang, Bei Liu, Yunhua Yang, Han Gou, Huan Du, Yuhao Chen, Huakun Yu, Mingqi Zhou, Jinming Zhao and Fengjie Yuan

Agronomy 2025, 15(9), 2204; https://doi.org/10.3390/agronomy15092204 - 17 Sep 2025

Abstract

Soybean (Glycine max (L.) Merr.) flowering time and plant height are critical agronomic traits that significantly influence yield and environmental adaptability. To clarify the regulatory mechanisms of flowering-related genes and their associations with plant height, a genome-wide identification of such genes in [...] Read more.

Soybean (Glycine max (L.) Merr.) flowering time and plant height are critical agronomic traits that significantly influence yield and environmental adaptability. To clarify the regulatory mechanisms of flowering-related genes and their associations with plant height, a genome-wide identification of such genes in soybean were performed. This analysis used Arabidopsis thaliana flowering genes as references, employing BLASTP searches and pathway classification. All of the identified flowering-related genes were classified into eight regulatory pathways, with the photoperiod pathway (Ph) being the most prominent. Evolutionary and expression analyses revealed that core regulators (e.g., GmFTs, GmSOC1s) are conserved across pathways and are preferentially expressed in shoot apical meristems (SAMs). Additionally, both flowering-related genes and key hormones (e.g., IAA, GA, ABA) exhibited rhythmic responses to light signals. CRISPR-Cas9-mediated validation confirmed that genes GmSAUR46b regulates both flowering time and plant height, as mutants of this gene showed early flowering and reduced height. Notably, a large proportion of previously mapped flowering genes overlapped with our identified ones, while some remained undetected, likely due to whole-genome duplication and adaptive evolution, which generate new regulatory networks. Most of the identified flowering-related genes, however, have not been mapped, which highlights substantial uncharacterized potential in soybean flowering and plant height regulation. This provides a valuable molecular framework to guide soybean molecular breeding for enhanced yield and environmental adaptability. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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16 pages, 563 KB

Open AccessArticle

Practical Test and Inference on the Inheritance of Dual Multi-Factors and Tri-Normal Distributions of Quantitative Characters

by Tingzhen Zhang, Xiaoming Jia, Zhao Xu and Zhiwu Cao

Agronomy 2025, 15(9), 2203; https://doi.org/10.3390/agronomy15092203 - 17 Sep 2025

Abstract

The multi-factorial hypothesis of quantitative trait inheritance originated from Nilson’s wheat hybridization experiments. It takes unit traits as the object and is based on the binomial distribution mathematically. Due to the requirement of the same distribution, it cannot include genes of other distributions. [...] Read more.

The multi-factorial hypothesis of quantitative trait inheritance originated from Nilson’s wheat hybridization experiments. It takes unit traits as the object and is based on the binomial distribution mathematically. Due to the requirement of the same distribution, it cannot include genes of other distributions. This is its limitation. Moreover, it does not incorporate the environmental effects that constitute the phenotype, so it is not comprehensive enough. This article started from the overallness of quantitative traits, was based on the central limit theorem, and was analyzed from both the genotype and the environment and proposed the assumption on the inheritance of dual multi-factors and tri-normal distributions of quantitative traits. This genetic model was tested with practical examples, and three inferences were made. Method and Results: Firstly, the overallness of quantitative traits was discussed, thus the above assumption was proposed. Next, using many examples of normal distribution of quantitative characters in the homogeneous populations, the research on the identification of the environments without GEI was carried out. Then, the examples of normal distribution of the same quantitative characters in the homogeneous populations and in the segregated populations of the same family were used. By means of normal distribution of quantitative characters in the homogeneous populations, it was indicated that the test locations were the environments without GEI. By utilizing the properties of normal distribution and variance, it was proven that normal distribution of phenotypic value for quantitative traits in a segregated population was formed by adding normal distribution of genotypic value and environmental effect, which enables the genetic model to be tested in practice. Three types of normal distribution of quantitative traits were inferred, indicating that the quantitative characters of a considerable number of organisms in nature obey a normal distribution, expressing continuous variation. Full article

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

22 pages, 5506 KB

Open AccessArticle

Design and Evaluation of a High-Speed Airflow-Assisted Seeding Device for Pneumatic Drum Type Soybean Precision Seed Metering Device

by Youqiang Ding, Gang Zheng, Wenyi Zhang, Bing Qi, Yunxia Wang, Qianqian Xia, Ruzheng Wang and Haojie Zhang

Agronomy 2025, 15(9), 2202; https://doi.org/10.3390/agronomy15092202 - 16 Sep 2025

Abstract

To improve the uniformity and precision of soybean seeding, this study designed a high-speed airflow-assisted seeding system for the pneumatic drum-type high-speed precision seed-metering device. The system accelerates seed delivery through airflow and ensures precise seed placement using a seed press wheel. Computational [...] Read more.

To improve the uniformity and precision of soybean seeding, this study designed a high-speed airflow-assisted seeding system for the pneumatic drum-type high-speed precision seed-metering device. The system accelerates seed delivery through airflow and ensures precise seed placement using a seed press wheel. Computational Fluid Dynamics (CFD) and Discrete Element Method (DEM) coupling simulations were employed to analyze the seed motion trajectory, collision process, and velocity changes. Key design parameters of the airflow-assisted delivery system were optimized, including a tube diameter of 16 mm, a curved section radius of 80 mm, a seed delivery angle of 33.65°, and a press wheel diameter of 254 mm. The simulation results indicated that the relative position between the seed delivery tube and the seed drum significantly impacts seed trajectory and uniformity. Lowering the tube to align with the seed velocity direction minimized collisions and enhanced seed spacing consistency during high-speed operation. Increasing inlet air pressure improved seed distribution uniformity by accelerating seeds within the tube, reducing travel time and collisions; a 500 Pa pressure increase raised the maximum flow velocity by approximately 5 m/s. However, seed acceleration exhibited diminishing returns: pressure increase from 2.5 kPa to 3.5 kPa increased seed speed by 2.1 m/s, while a further increase to 4.5 kPa only added 1.1 m/s. The optimal inlet pressure for efficient energy transfer and seed acceleration was approximately 3.5 kPa. The press wheel played a crucial role by dispersing the impact force when seeds contact the soil, which achieved high capture rates above 94.0% across the seed drum rotary speed range of 11 to 19 rpm. This research provides theoretical and experimental support for the optimization of high-speed airflow-assisted seeding systems, offering significant practical value for large-scale agricultural production by enhancing seeding efficiency and quality. Full article

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

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14 pages, 3321 KB

Open AccessArticle

Parental Origin Influences Seed Quality and Seedling Establishment in Kiwifruit Cultivars

by Edgar Manuel Bovio-Zenteno, Benito Hernández-Castellanos, Alejandro Antonio Castro-Luna, Norma Flores-Estévez, Juan Guillermo Cruz-Castillo and Juan Carlos Noa-Carrazana

Agronomy 2025, 15(9), 2201; https://doi.org/10.3390/agronomy15092201 - 16 Sep 2025

Abstract

Kiwifruit (Actinidia Lindl.) cultivation is restricted to climates similar to its native habitat in China. The seeds, a product of sexual reproduction, are used to produce rootstocks in commercial plantations, being an important source of genetic diversity for adaptation to variable conditions [...] Read more.

Kiwifruit (Actinidia Lindl.) cultivation is restricted to climates similar to its native habitat in China. The seeds, a product of sexual reproduction, are used to produce rootstocks in commercial plantations, being an important source of genetic diversity for adaptation to variable conditions and emerging challenges. It is known that obtaining kiwifruit plants from seeds is difficult due to their characteristic dormancy. However, the effect of habitat and parents on seed characteristics and their relationship to the seedlings produced is unknown. Here, we show that plants with tolerance to extreme conditions provide advantages to their offspring. We point out that Actinidia arguta cv. Passion Poppers (kiwiberry), capable of tolerating extreme temperatures below zero, has a larger seed size (volume over 15 mm³) and weight (100 seeds weigh nearly 200 mg), greater germination capacity (90.75 ± 1.03), and more robust seedlings (quotient of 20.28 ± 0.75) than classic green and golden kiwifruits, and one tropicalized commercial kiwifruit from Veracruz, Mexico. These findings highlight that parental origin influences seed quality and seedling establishment. We noted that A. arguta seeds offer opportunities for mass plant propagation. In addition, the use of parental plants adapted to extreme conditions could be an effective strategy to improve seed and seedling quality, with factors such as long-term survival and development in new environments awaiting to be explored in extent. Full article

(This article belongs to the Special Issue Tropical and Subtropical Fruit Production: Physiology, Breeding and Sustainability)

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21 pages, 5960 KB

Open AccessArticle

Improving the Quality of LiDAR Point Cloud Data in Greenhouse Environments

by Gaoshoutong Si, Peter Ling, Sami Khanal and Heping Zhu

Agronomy 2025, 15(9), 2200; https://doi.org/10.3390/agronomy15092200 - 16 Sep 2025

Abstract

Automated crop monitoring in controlled environments is imperative for enhancing crop productivity. The availability of small unmanned aerial systems (sUAS) and cost-effective LiDAR sensors present an opportunity to conveniently gather high-quality data for crop monitoring. The LiDAR-collected point cloud data, however, often encounter [...] Read more.

Automated crop monitoring in controlled environments is imperative for enhancing crop productivity. The availability of small unmanned aerial systems (sUAS) and cost-effective LiDAR sensors present an opportunity to conveniently gather high-quality data for crop monitoring. The LiDAR-collected point cloud data, however, often encounter challenges such as occlusions and low point density that can be addressed by acquiring additional data from multiple flight paths. This study evaluated the performance of using an Iterative Closest Point (ICP)-based algorithm for registering sUAS-based LiDAR point clouds collected in the greenhouse environment. To address the issue of objects that may cause ICP or local feature-based registration to mismatch correspondences, this study developed a robust registration pipeline. First, the geometric centroid of the ground floor boundary was leveraged to improve the initial alignment, and then piecewise ICP was implemented to achieve fine registration. The evaluation of point cloud registration performance included visualization, root mean square error (RMSE), volume estimation of reference objects, and the distribution of point cloud density. The best RMSE dropped from 20.4 cm to 2.4 cm, and point cloud density improved after registration, and the volume-estimation error for reference objects dropped from 72% (single view) to 6% (post-registration). This study presents a promising approach to point cloud registration that outperforms conventional ICP in greenhouse layouts while eliminating the need for artificial reference objects. Full article

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

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33 pages, 13243 KB

Open AccessArticle

Maize Yield Prediction via Multi-Branch Feature Extraction and Cross-Attention Enhanced Multimodal Data Fusion

by Suning She, Zhiyun Xiao and Yulong Zhou

Agronomy 2025, 15(9), 2199; https://doi.org/10.3390/agronomy15092199 - 16 Sep 2025

Abstract

This study conducted field experiments in 2024 in Meidaizhao Town, Tumed Right Banner, Baotou City, Inner Mongolia Autonomous Region, adopting a plant-level sampling design with 10 maize plots selected as sampling areas (20 plants per plot). At four critical growth stages—jointing, heading, filling, [...] Read more.

This study conducted field experiments in 2024 in Meidaizhao Town, Tumed Right Banner, Baotou City, Inner Mongolia Autonomous Region, adopting a plant-level sampling design with 10 maize plots selected as sampling areas (20 plants per plot). At four critical growth stages—jointing, heading, filling, and maturity—multimodal data, including that covering leaf spectra, root-zone soil spectra, and leaf chlorophyll and nitrogen content, were synchronously collected from each plant. In response to the prevalent limitations of the existing yield prediction methods, such as insufficient accuracy and limited generalization ability due to reliance on single-modal data, this study takes the acquired multimodal maize data as the research object and innovatively proposes a multimodal fusion prediction network. First, to handle the heterogeneous nature of multimodal data, a parallel feature extraction architecture is designed, utilizing independent feature extraction branches—leaf spectral branch, soil spectral branch, and biochemical parameter branch—to preserve the distinct characteristics of each modality. Subsequently, a dual-path feature fusion method, enhanced by a cross-attention mechanism, is introduced to enable dynamic interaction and adaptive weight allocation between cross-modal features, specifically between leaf spectra–soil spectra and leaf spectra–biochemical parameters, thereby significantly improving maize yield prediction accuracy. The experimental results demonstrate that the proposed model outperforms single-modal approaches by effectively leveraging complementary information from multimodal data, achieving an R² of 0.951, an RMSE of 8.68, an RPD of 4.50, and an MAE of 5.28. Furthermore, the study reveals that deep fusion between soil spectra, leaf biochemical parameters, and leaf spectral data substantially enhances prediction accuracy. This work not only validates the effectiveness of multimodal data fusion in maize yield prediction but also provides valuable insights for accurate and non-destructive yield prediction. Full article

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

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12 pages, 2069 KB

Open AccessArticle

GmSWEET46 Regulates Seed Oil and Protein Content in Soybean

by Dezhi Han, Huiyi Su, Qiuzhen Lai, Wei Li, Wencheng Lu and Tianxiao Lv

Agronomy 2025, 15(9), 2198; https://doi.org/10.3390/agronomy15092198 - 16 Sep 2025

Abstract

Seed oil and protein contents are critical agronomic traits that determine soybean quality. However, the key loci and corresponding genes controlling these quality traits remain to be elucidated. Here, we performed bulked segregant analysis by sequencing (BSA-seq) using an F4 population derived from [...] Read more.

Seed oil and protein contents are critical agronomic traits that determine soybean quality. However, the key loci and corresponding genes controlling these quality traits remain to be elucidated. Here, we performed bulked segregant analysis by sequencing (BSA-seq) using an F4 population derived from a cross between the cultivars Heinong 35 (HN35) and Dengke 3 (DK3). A major soybean oil and protein quantitative trait locus (QTL) designated as q-OP18 was identified on chromosome 18, and the sugar transporter gene GmSWEET46 was further cloned. Haplotype analysis revealed that a single-nucleotide polymorphism (SNP) in the sixth exon of GmSWEET46 results in an amino acid change between HN35 and DK3 and is associated with seed oil and protein content, suggesting its important role in determining seed quality in soybean. GmSWEET46 is expressed during the early stages of seed and pod development and localizes to the plasma membrane, indicating its potential function as a sugar transporter. Further studies demonstrated that GmSWEET46 can regulate seed protein content, oil content, and seed size in Arabidopsis and soybean. Collectively, this study provides a novel locus and gene for regulating soybean seed traits and offers valuable resources for the breeding of high-quality and high-yielding soybean cultivars. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics—2nd Edition)

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19 pages, 1246 KB

Open AccessArticle

Influence of LED Light Spectra on Morphogenesis, Secondary Metabolite Production and Antioxidant Potential in Eucomis autumnalis Cultured In Vitro

by Monika Cioć, Agnieszka Szopa, Barbara Prokopiuk, Bożena Pawłowska and Łukasz Łopusiewicz

Agronomy 2025, 15(9), 2197; https://doi.org/10.3390/agronomy15092197 - 15 Sep 2025

Abstract

Eucomis autumnalis is a bulbous ornamental species with ethnobotanical relevance. In vitro cultures offer a sustainable tool for biomass propagation and metabolite production. This study investigates the effects of nine LED light spectra: red (R), blue (B), red–blue (RB), RB with green (RBG), [...] Read more.

Eucomis autumnalis is a bulbous ornamental species with ethnobotanical relevance. In vitro cultures offer a sustainable tool for biomass propagation and metabolite production. This study investigates the effects of nine LED light spectra: red (R), blue (B), red–blue (RB), RB with green (RBG), yellow (RBY), far-red (RBfR), ultraviolet (RBUV), white (WLED), and fluorescent light (Fl, control), on the morphogenesis, polyphenol production, and antioxidant potential of E. autumnalis shoot cultures. Cultures were maintained on MS medium with 5 µM BA and 0.5 µM NAA. HPLC-DAD analysis identified 11 phenolic acids and 4 flavonoids, including eucomic acid, characteristic of the genus. Light quality impacted compound-specific accumulation and antioxidant activity, with responses varying among compounds and treatments. R and B light increased catechin, gentisic acid and hesperidin (289, 195, 245 mg/100 g DW), while UV suppressed flavonoids by ca. 2-fold for catechin and flavanones compared to other lights. RBG and RBfR induced the highest eucomic acid accumulation (424 mg/100 g DW), ferulic acid and epicatechin, correlating strongly with ABTS•+ activity (18–19% higher than other lights; r > 0.6–0.8). These findings highlight LED spectral modulation as a tool to enhance the phytochemical quality of E. autumnalis in vitro and provide a foundation for future biotechnological applications. Full article

(This article belongs to the Special Issue Light Environment Regulation of Crop Growth)

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14 pages, 2185 KB

Open AccessArticle

Impact of Future Climate Change on the Climatic Suitability of Tea Planting on Hainan Island, China

by Qichun Zhu, Yuqing Shi, Yujie Yu, Xiaowei Wang, Yulun Tang, Lixuan Ren and Yunsheng Lou

Agronomy 2025, 15(9), 2196; https://doi.org/10.3390/agronomy15092196 - 15 Sep 2025

Abstract

Hainan Island is one of the main tea-producing regions in South China. Climate change has increased agricultural instability, causing fluctuations in tea yield and quality. Based on daily surface meteorological data from 19 national meteorological observation stations on the island from 1990 to [...] Read more.

Hainan Island is one of the main tea-producing regions in South China. Climate change has increased agricultural instability, causing fluctuations in tea yield and quality. Based on daily surface meteorological data from 19 national meteorological observation stations on the island from 1990 to 2019, as well as related factors such as topography, a spatial analysis model for climate zoning indicators was established. Zoning indicators were spatialized through GIS spatial analysis, and fuzzy logic was applied to construct membership functions based on climatic elements to assess climatic suitability for tea cultivation. This approach helped refine zoning for tea planting areas and assess potential future climate changes. Results show high climatic suitability for tea production in spring (March-May) and autumn (September–October), but low suitability in summer (June–August) due to high temperatures and strong sunlight. The most suitable zone for tea planting is centered in the northeastern parts of the island; the suitable zone is mainly distributed in the central mountainous areas and the western coastal region; the sub-suitable zone mainly includes central and southern parts of Dongfang; and the unsuitable zone mainly includes eastern and southern parts of Dongfang and southern parts of Changjiang. Under future climatic scenarios, the island’s temperatures will further increase, and suitable temperature areas will shrink from the periphery toward the central mountainous regions. Precipitation will also increase over time, leading to an expansion of suitable precipitation areas on the island. This study helps promote sustainable tea production and the rational utilization of agricultural climate resources on Hainan Island. Full article

(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)

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24 pages, 12392 KB

Open AccessArticle

A Robust and High-Accuracy Banana Plant Leaf Detection and Counting Method for Edge Devices in Complex Banana Orchard Environments

by Xing Xu, Guojie Liu, Zihao Luo, Shangcun Chen, Shiye Peng, Huazimo Liang, Jieli Duan and Zhou Yang

Agronomy 2025, 15(9), 2195; https://doi.org/10.3390/agronomy15092195 - 15 Sep 2025

Abstract

Leaves are the key organs in photosynthesis and nutrient production, and leaf counting is an important indicator of banana plant health and growth rate. However, in complex orchard environments, leaves often overlap, the background is cluttered, and illumination varies, making accurate segmentation and [...] Read more.

Leaves are the key organs in photosynthesis and nutrient production, and leaf counting is an important indicator of banana plant health and growth rate. However, in complex orchard environments, leaves often overlap, the background is cluttered, and illumination varies, making accurate segmentation and detection challenging. To address these issues, we propose a lightweight banana leaf detection and counting method deployable on embedded devices, which integrates a space–depth-collaborative reasoning strategy with multi-scale feature enhancement to achieve efficient and precise leaf identification and counting. For complex background interference and occlusion, we design a multi-scale attention guided feature enhancement mechanism that employs a Mixed Local Channel Attention (MLCA) module and a Self-Ensembling Attention Mechanism (SEAM) to strengthen local salient feature representation, suppress background noise, and improve discriminability under occlusion. To mitigate feature drift caused by environmental changes, we introduce a task-aware dynamic scale adaptive detection head (DyHead) combined with multi-rate depthwise separable dilated convolutions (DWR_Conv) to enhance multi-scale contextual awareness and adaptive feature recognition. Furthermore, to tackle instance differentiation and counting under occlusion and overlap, we develop a detection-guided space–depth position modeling method that, based on object detection, effectively models the distribution of occluded instances through space–depth feature description, outlier removal, and adaptive clustering analysis. Experimental results demonstrate that our YOLOv8n MDSD model outperforms the baseline by 2.08% in mAP50-95, and achieves a mean absolute error (MAE) of 0.67 and a root mean square error (RMSE) of 1.01 in leaf counting, exhibiting excellent accuracy and robustness for automated banana leaf statistics. Full article

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

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24 pages, 6238 KB

Open AccessArticle

The XTH Gene Family in Cassava: Genomic Characterization, Evolutionary Dynamics, and Functional Roles in Abiotic Stress and Hormonal Response

by Wenke Zhang, Honggang Wang, Yuhua Chen, Man Liu, Xin Guo, Rui Zhang, Kai Luo and Yinhua Chen

Agronomy 2025, 15(9), 2194; https://doi.org/10.3390/agronomy15092194 - 15 Sep 2025

Abstract

Xyloglucan endotransglucosylases/hydrolases (XTHs) are key enzymes involved in cell wall remodeling that play roles in plant responses to environmental stress. Despite their importance, a comprehensive investigation of the XTH gene family in cassava (Manihot esculenta Crantz), a crucial drought-tolerant crop in tropical [...] Read more.

Xyloglucan endotransglucosylases/hydrolases (XTHs) are key enzymes involved in cell wall remodeling that play roles in plant responses to environmental stress. Despite their importance, a comprehensive investigation of the XTH gene family in cassava (Manihot esculenta Crantz), a crucial drought-tolerant crop in tropical and subtropical regions, has not yet been conducted. In the present study, we identified 37 XTH genes (MeXTH1-37) within the cassava genome, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). Phylogenetic analysis grouped 37 MeXTH genes into three distinct clades, a classification further supported by exon–intron organizations and the conserved protein motif architectures. Duplication events, particularly segmental duplication, were identified as the main driving force for MeXTH gene expansion in cassava. Comparative synteny analysis revealed orthologous relationships between MeXTH genes and XTH-related genes in seven other plant species, including soybean, poplar, tomato, Arabidopsis, maize, wheat, and rice. Global expression analysis revealed that MeXTH genes display different expression patterns in various cassava tissues, shedding light on their potential biological functions. Furthermore, quantitative real-time PCR (qRT-PCR) analysis of 12 representative MeXTH genes under salt and osmotic stress, as well as salicylic acid (SA) and methyl jasmonate (MeJA) treatments, demonstrated their differential responses to these stimuli. These results provide novel insights into the role of the MeXTH gene family in enhancing cassava’s tolerance to abiotic stress. Full article

(This article belongs to the Special Issue The Formation of Specialized Traits and the Regulation of Directional Development in Forage)

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18 pages, 1741 KB

Open AccessArticle

Mechanism of Modified Biochar in Mitigating Carbon and Nitrogen Loss in Drought Soil with Green Manure Application

by Ziyang Zhu, Lu Zhang, Fangyuan Chen, Wenyan Duan, Fangfang Li and Di Zhang

Agronomy 2025, 15(9), 2193; https://doi.org/10.3390/agronomy15092193 - 14 Sep 2025

Abstract

With the frequent occurrence of global droughts, modified biochar has demonstrated the potential to be an efficient soil amendment, which could affect carbon and nitrogen sequestration in arid soil. Therefore, this study investigated the co-application of pristine biochar (BC), Fe-modified biochar (FB) and [...] Read more.

With the frequent occurrence of global droughts, modified biochar has demonstrated the potential to be an efficient soil amendment, which could affect carbon and nitrogen sequestration in arid soil. Therefore, this study investigated the co-application of pristine biochar (BC), Fe-modified biochar (FB) and H₂O₂-modified biochar (HB) with green manure during a 70-day laboratory incubation under drought conditions and normal moisture conditions. The emissions were quantified using gas chromatography, while microbial necromass carbon and nitrogen were measured by quantifying the amino sugar content by gas chromatography–mass spectrometry, and other soil carbon and nitrogen fractions were determined through chemical analysis. The results revealed that under drought conditions, compared to BC co-application with green manure, the total carbon loss of FB and HB co-application with green manure was reduced from 24.38% to 13.14% and 14.27%, respectively, and the total nitrogen loss was also reduced from 14.61% to 7.23% and 7.27%, respectively. This reduction occurred because FB and HB protected soil organic matter through iron oxide binding and micropore adsorption, thereby increasing the content of soil total humus acid (>5%) and microbial necromass nitrogen (>16%). In addition, under normal moisture conditions, BC, FB and HB co-application with green manure enhanced microbial activity and promoted the formation of stable total humus acid, thereby enhancing carbon and nitrogen sequestration. In conclusion, this study provides crucial theoretical support for the optimization of the green manure return via modified biochar co-application in arid environments. Full article

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

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15 pages, 2687 KB

Open AccessArticle

Multi-Stage Salt Tolerance in Leymus chinensis: Contrasting Responses at Germination and Seedling Stages

by Mingxue Shi, Mengdan Sun, Dandan Zhao, Shaoyang Li, Wenwen Qi, Shiman Chen, Jushan Liu and Hongyuan Ma

Agronomy 2025, 15(9), 2192; https://doi.org/10.3390/agronomy15092192 - 14 Sep 2025

Abstract

Soil salinity poses a significant challenge for global agriculture and ecosystems, severely impacting plant growth and land-use efficiency. Leymus chinensis (L. chinensis) is a perennial grass with a high potential for saline soil restoration, yet little is known about whether its [...] Read more.

Soil salinity poses a significant challenge for global agriculture and ecosystems, severely impacting plant growth and land-use efficiency. Leymus chinensis (L. chinensis) is a perennial grass with a high potential for saline soil restoration, yet little is known about whether its salt tolerance during germination aligns with that during seedling development, which are considered the most salt-sensitive stages of its life cycle. Therefore, to investigate whether there is a correlation between salt tolerance during germination and the seedling stage, we evaluated the germination, growth, and survival of 10 genotypes of (G1–G10) L. chinensis under 0, 50, 100, and 150 mM NaCl stress over 12 weeks. Key indicators, including germination traits (germination percentage, radicle length, and shoot length), plant height, and survival rate, were integrated into stage-specific Comprehensive Evaluation Values (D value) to quantify salt tolerance. Salt stress significantly suppressed germination and seedling performance, with inter-genotypic variation. For example, G3 showed only an 18.0% reduction in germination percentage and 62.5% survival rate at 150 mM NaCl, while other genotypes had a 42.0–88.0% germination loss and over 90.0% mortality. However, a correlation analysis showed a positive yet non-significant correlation between D-Germination and D-Survival. Notably, D-Plant Height was negatively correlated with both D-Germination and D-Survival, with G3 and G8 displaying contrasting stress adaptation strategies. Collectively, these results indicate that salt tolerance in L. chinensis is both stage-specific and genotype-specific and that performance at germination does not reliably predict later survival. The findings of this study provide valuable germplasm resources and a theoretical basis for forage breeding and grassland restoration. The identified genotypes, G3 and G8, can serve as important materials for research on salt tolerance mechanisms and breeding programs. Full article

(This article belongs to the Section Grassland and Pasture Science)

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22 pages, 4402 KB

Open AccessArticle

Interactive Effects of Different Field Capacity and Nitrogen Levels on Soil Fertility and Microbial Community Structure in the Root Zone of Jujube (Ziziphus jujuba Mill.) Seedlings in an Arid Region of Southern Xinjiang, China

by Yunqi Ma, Haoyang Liu, Junpan Sun, Cuiyun Wu and Yuyang Zhang

Agronomy 2025, 15(9), 2191; https://doi.org/10.3390/agronomy15092191 - 14 Sep 2025

Abstract

Understanding the regulatory mechanisms of water–nitrogen coupling effects on soil–plant–microbe systems in arid regions is crucial for sustainable agricultural development. This study systematically investigated the interactive effects of field capacity (75% vs. 45%) and nitrogen application rates (100 vs. 300 kg ha⁻¹ [...] Read more.

Understanding the regulatory mechanisms of water–nitrogen coupling effects on soil–plant–microbe systems in arid regions is crucial for sustainable agricultural development. This study systematically investigated the interactive effects of field capacity (75% vs. 45%) and nitrogen application rates (100 vs. 300 kg ha⁻¹) combined with different enhanced-efficiency nitrogen fertilizers (EENFs) on rhizosphere soil fertility and microbial community structure of Jujube (Ziziphus jujuba Mill.) seedlings through a two-year pot experiment. Two-year-old jujube seedlings were employed with five treatments: NS (urea), NM (urease inhibitor), XH (nitrification inhibitor), W (microbial fertilizer), and CK (control), to analyze soil physicochemical properties and microbial community responses. Soil available N accumulated under high-N/adequate moisture but declined under drought. NM curbed NH₃ volatilization by 32.38–43.22%, while XH increased NH₄⁺-N by 35.76%. Drought raised microbial α-diversity (bacteria + 33.88–37.5%, fungi + 43.62–68.75%). NM demonstrated optimal performance in ammonia volatilization (32.38–43.22% reduction), while XH showed notable efficacy in ammonium-N regulation (35.76% enhancement). Microbial α-diversity exhibited enhanced responses under drought stress, with bacterial and fungal community improvements reaching 33.88–37.5% and 43.62–68.75%. Redundancy analysis showed environmental factors explained more community variance under water stress (bacteria: 79.19→88.76%; fungi: 64.64→92.52%). These findings provide theoretical support for jujube cultivation in arid zones, demonstrate the potential of targeted EENFs, and offer new insights for precision water–fertilizer and microbial management. Full article

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

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18 pages, 3748 KB

Open AccessArticle

Transcriptome Analysis of the Regulatory Mechanism of Exogenous Manganese Sulfate Application on Wheat Grain Yield and Carotenoids

by Na Yang, Ke Wang, Jiancheng Zhang, Xiaoyan Jiao, Zhiguo Yang, Jian Wang and Sha Yang

Agronomy 2025, 15(9), 2190; https://doi.org/10.3390/agronomy15092190 - 14 Sep 2025

Abstract

Given the critical role of manganese (Mn) as an essential micronutrient in wheat growth and development and the high efficiency of foliar fertilization in optimizing nutrient uptake and improving crop quality, this study aimed to elucidate the regulatory effects of exogenous manganese sulfate [...] Read more.

Given the critical role of manganese (Mn) as an essential micronutrient in wheat growth and development and the high efficiency of foliar fertilization in optimizing nutrient uptake and improving crop quality, this study aimed to elucidate the regulatory effects of exogenous manganese sulfate application on wheat grain yield and carotenoid accumulation. Methods: Field experiments were conducted from 2022 to 2024 at the Shuitou Experimental Station of the Cotton Research Institute, Shanxi Agricultural University (35°11′ N, 111°05′ E), using the wheat cultivar ‘Jinmai 110’. Foliar applications of manganese sulfate were administered at concentrations of 0.5 g/kg, 1.0 g/kg, and 1.5 g/kg, with water serving as the control (CTRL). Spraying was conducted on the upper canopy during the flowering and grain-filling stages, applied every 7 days for a total of three times. Samples for transcriptomic analysis were collected within 24 h of the final application. At maturity, yield-related traits and grain carotenoid contents were assessed. Results: Foliar application of 1.0 g/kg MnSO₄ significantly enhanced both grain yield and carotenoid content in wheat. Transcriptome sequencing revealed that treatment with 1.0 g/kg manganese sulfate (M2) resulted in 4761 differentially expressed genes (DEGs), including 2933 upregulated and 1828 downregulated genes, relative to CTRL. Gene Ontology (GO) analysis showed that in the M2 vs. CTRL comparison, 819 GO terms were significantly enriched among upregulated DEGs and 630 among downregulated DEGs. Specifically, upregulated genes were associated with 427 biological process terms and 299 cellular component terms, while downregulated genes were linked to 361 biological processes and 211 cellular components. Enriched functions primarily included cellular processes, metabolic processes, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 809 annotations for upregulated DEGs and 330 for downregulated DEGs, mainly related to photosynthesis, carotenoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction. In total, 43,395 alternative splicing (AS) events were identified from 17,165 genes, including 445 upregulated and 319 downregulated AS events, primarily enriched in photosynthesis and plant hormone-related pathways. Conclusion: Foliar application of manganese sulfate significantly modulates gene expression in wheat grains, thereby improving both yield and carotenoid accumulation. Key biological processes affected include photosynthesis, plant hormone signal transduction, and the carotenoid biosynthetic pathway. The interactions among these regulatory networks constitute a complex molecular mechanism through which exogenous Mn influences agronomic traits. These findings provide mechanistic insights and practical implications for enhancing wheat productivity and nutritional quality through foliar manganese application. Full article

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

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20 pages, 3085 KB

Open AccessArticle

Comparative Genomic and Transcriptomic Analysis Uncovers Metabolic Mechanisms Underlying Drought Tolerance Variation in Maize

by Yuxuan Li, Tianze Zhu, Yunyun Wang, Ye Sun, Pengcheng Li and Houmiao Wang

Agronomy 2025, 15(9), 2189; https://doi.org/10.3390/agronomy15092189 - 13 Sep 2025

Abstract

Drought stress severely limits maize (Zea mays L.) productivity worldwide, yet the molecular mechanisms underlying natural variation in drought tolerance remain poorly understood. We conducted a comprehensive comparative analysis using transcriptome sequencing (RNA-seq) and whole-genome resequencing of two inbred maize lines with [...] Read more.

Drought stress severely limits maize (Zea mays L.) productivity worldwide, yet the molecular mechanisms underlying natural variation in drought tolerance remain poorly understood. We conducted a comprehensive comparative analysis using transcriptome sequencing (RNA-seq) and whole-genome resequencing of two inbred maize lines with contrasting drought tolerance: drought-tolerant line A193 and drought-sensitive line MP23. Under drought stress, A193 exhibited superior photosynthetic performance and an 89% survival rate compared to only 11% for MP23. Transcriptome analysis identified substantial gene expression differences, with 7279 and 5991 differentially expressed genes (DEGs) between the two genotypes under control and drought conditions, respectively. Whole-genome resequencing identified 5,306,884 single-nucleotide polymorphisms and 1,133,400 insertions/deletions between the two lines. Integration of transcriptomic and genomic data revealed 2050 DEGs exhibiting genomic variations (DEVGs). Functional enrichment analysis revealed significant enrichment in starch and sucrose metabolism, benzoxazinoid biosynthesis, and amino acid metabolism pathways. Thirty DEVGs were identified in starch and sucrose metabolism, with 15 genes upregulated in A193, including beta-amylase, sucrose synthases, and starch synthase. Six DEVGs in benzoxazinoid biosynthesis showed stress-protective upregulation in A193. Additionally, 14 DEVGs in amino acid metabolism displayed genotype-specific expression patterns. Our findings demonstrate that superior drought tolerance in A193 is associated with enhanced metabolic reprogramming. Prioritized drought tolerance genes may provide direct targets for functional investigation or allelic mining. Full article

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

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13 pages, 2301 KB

Open AccessArticle

Transcriptome-Based Analysis of Mitochondrial Influence on Key Agronomic Traits and Nutritional Components in Auricularia heimuer

by Kaisheng Shao, Fangjie Yao, Ming Fang, Lixin Lu, Xiaoxu Ma, Wei Wang, Jingjing Meng, Xu Sun, Yuling Cui and Jian Sun

Agronomy 2025, 15(9), 2188; https://doi.org/10.3390/agronomy15092188 - 13 Sep 2025

Abstract

Mitochondria play a pivotal role in fungal growth, development, and metabolic regulation, yet their significance has often been overlooked in traditional breeding programs. Auricularia heimuer, the second most widely cultivated edible fungus in China, has attracted increasing attention due to its nutritional [...] Read more.

Mitochondria play a pivotal role in fungal growth, development, and metabolic regulation, yet their significance has often been overlooked in traditional breeding programs. Auricularia heimuer, the second most widely cultivated edible fungus in China, has attracted increasing attention due to its nutritional and health-promoting properties, underscoring the urgent need for the development of functional cultivars and the elucidation of mitochondrial regulatory mechanisms. In this study, we constructed isonuclear alloplasmic strains with identical nuclear genotypes but distinct mitochondrial backgrounds. Comparative analyses of mycelial growth, fruiting body morphology, and nutritional composition were conducted, alongside transcriptomic profiling. The results showed no significant morphological differences on sawdust-based medium; however, on PDA medium, the strains exhibited notable differences in growth rate, melanin content, β-glucan levels, iron ion concentration, and amino acid content. Transcriptomic analysis identified 3385 differentially expressed genes (DEGs), which were enriched in pathways related to lysine biosynthesis, purine metabolism, DNA replication, and repair. Key DEGs involved in lysine biosynthesis were found to encode aminoadipate reductase (AAR) and saccharine dehydrogenase (SDH), with AAR localized in the cytoplasm and potentially regulating lysine synthesis through its enzymatic activity. This study highlights the critical influence of mitochondrial genes on the metabolic composition and transcriptional landscape of A. heimuer, providing a theoretical foundation for genetic improvement and the development of functional fungal cultivars. Full article

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

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