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27 pages, 3286 KB  
Article
Insights into the Significance of Nitrogen Fertiliser and Hydraulic Lift with Moisture Depletions in Cotton Quality and Nitrogen Distribution Under Topsoil Drought
by Jia Lu, Longjia Tian, Dan Xu and Guangcheng Shao
Agronomy 2025, 15(9), 2094; https://doi.org/10.3390/agronomy15092094 - 30 Aug 2025
Viewed by 37
Abstract
Dry topsoil restricts root growth and nutrient uptake in arid regions, thereby significantly reducing crop yield. Hydraulic lift occurs due to the dry topsoil and wet deep soil. This study investigates the effects of topsoil drought intensity (three field capacities in topsoil: 60–70% [...] Read more.
Dry topsoil restricts root growth and nutrient uptake in arid regions, thereby significantly reducing crop yield. Hydraulic lift occurs due to the dry topsoil and wet deep soil. This study investigates the effects of topsoil drought intensity (three field capacities in topsoil: 60–70% (W1), 50–60% (W2), and 40–50% (W3)) and nitrogen application rate (N1: 120, N2: 240, and N3: 360 kg ha−1) on cotton quality and the distribution of nitrogen in soil and plant under hydraulic lift using a root-splitting device. The upper pot of the root-splitting device was 22 cm high, with a 26 cm top diameter and a 23 cm bottom diameter; the lower pot of the root-splitting device was 45 cm high, with a 48 cm top diameter and a 36 cm bottom diameter. Topsoil moisture was maintained at W1 without nitrogen application under the control treatment (CK). The W2 and W3 treatments (representing different topsoil drought intensities) were designed to compare the interactive effects of water and nitrogen fertiliser on nitrogen distribution and cotton quality with the CK treatment. Results indicate that the concentrations of nitrate nitrogen (NO3-N) in the 10–20 cm soil were generally higher than those in the 0–10 cm soil. The topsoil drought intensity and nitrogen application rate had significant impacts on nitrogen concentrations in cotton organs. The W2 treatment produced the maximum nitrogen concentration, except for the root nitrogen concentration in 2021. The nitrogen concentration in the roots and stems peaked at 240 kg ha−1 of nitrogen application rate. The topsoil drought intensity and nitrogen application rate had considerable influences on the cotton dry matter. The nitrogen application rate had a significant impact on the following indexes: internal nitrogen-fertiliser use efficiency (INUE), physiological nitrogen-fertiliser use efficiency (PNUE), and nitrogen-fertiliser recovery efficiency (NRE), except for PNUE in 2020. The INUE of other treatments decreased by 13.82–43.44% compared with CK treatment. In 2021, fibre length and elongation were significantly impacted by the topsoil drought intensity, nitrogen application rates, and their interactions. The nitrogen application rate’s effects on the uniformity index were significant in 2020 and 2021. The hydraulic lift magnitude, NRE, and NO3-N in the 0–10 cm soil were significantly correlated with each other. There were correlations among cotton quality indexes: fibre length and strength, uniformity index and micronaire, and micronaire and elongation. These findings provide a reference for future research on the mechanism by which hydraulic lift participates in nitrogen distribution in soil and crops and also offer a new direction to utilize deep water to improve the utilization rate of water resources. Full article
(This article belongs to the Section Water Use and Irrigation)
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24 pages, 11302 KB  
Article
Systematic Calibration and Validation of Discrete Element Model Parameters for Cotton Root Systems
by Yong Yue, Rensheng Xing, Yasenjiang Baikeli, Haodong Xu, Weibin Ma and Liehong Guo
Agriculture 2025, 15(17), 1827; https://doi.org/10.3390/agriculture15171827 - 27 Aug 2025
Viewed by 203
Abstract
Aiming at the problem of lacking accurate and reliable contact and bonding parameters in the discrete element simulation of whole cotton stalk harvesting equipment, this study proposed a reverse modeling method for cotton roots combining the Discrete Element Method (DEM) with 3D laser [...] Read more.
Aiming at the problem of lacking accurate and reliable contact and bonding parameters in the discrete element simulation of whole cotton stalk harvesting equipment, this study proposed a reverse modeling method for cotton roots combining the Discrete Element Method (DEM) with 3D laser scanning. This method systematically constructed a general discrete element model and completed its parameter calibration. Firstly, cotton root samples were collected and measured to obtain key morphological parameters, providing a basis for selecting representative roots and performing 3D reverse reconstruction. Subsequently, mechanical parameters and contact parameters of the cotton roots were measured and calibrated through mechanical tests and stacking angle tests. Furthermore, based on the Hertz–Mindlin with Bonding contact model, a structured root sample model was established using a layered particle combination strategy. The bonding parameters were then optimized and calibrated through shear and tensile mechanical simulation experiments. Finally, a discrete element model of the root–soil complex was established based on the optimal parameter set. The reliability of the model was validated by comparing the simulation results with physical field tests of root extraction force. The results indicated that in the contact parameter validation test, the relative error between the simulated stacking angle and the measured value was only 0.43%, demonstrating the high accuracy of the model in simulating contact characteristics. In the bonding parameter calibration validation tests, the relative errors between the simulation results and measured values for shear and tensile mechanics were 1.22% and 1.40%, respectively, indicating that the model parameters could accurately simulate shear strength and tensile strength. Finally, in the root extraction force validation test, the relative error between the simulated extraction force and the field-measured value was 3.76%, further confirming the model’s applicability for analyzing the complex interaction mechanisms between roots and soil. The findings of this study can provide key models and parameter support for the digital design, operation process simulation, and performance optimization of whole cotton stalk harvesting equipment. Full article
(This article belongs to the Section Agricultural Technology)
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21 pages, 6010 KB  
Article
Simulating Water Use and Yield for Full and Deficit Flood-Irrigated Cotton in Arizona, USA
by Elsayed Ahmed Elsadek, Said Attalah, Peter Waller, Randy Norton, Douglas J. Hunsaker, Clinton Williams, Kelly R. Thorp, Ethan Orr and Diaa Eldin M. Elshikha
Agronomy 2025, 15(9), 2023; https://doi.org/10.3390/agronomy15092023 - 23 Aug 2025
Viewed by 420
Abstract
Improved irrigation guidelines are needed to maximize crop water use efficiency. Combining field data with simulation models can provide information for better irrigation management. The objective of the present study was to evaluate the effects of two flood irrigation treatments on fiber yield [...] Read more.
Improved irrigation guidelines are needed to maximize crop water use efficiency. Combining field data with simulation models can provide information for better irrigation management. The objective of the present study was to evaluate the effects of two flood irrigation treatments on fiber yield (FY) and quality during the 2023 and 2024 growing seasons in Maricopa, Arizona, USA. Two irrigation treatments, denoted as F100% and F80%, were arranged in a randomized complete block design with three replicates. Then, AquaCrop was used to simulate cotton yield (YTot), water use (ETobs), and total soil water content (WCTot) for the two irrigation treatments. Six statistical metrics, including the coefficient of determination (R2), the normalized root-mean-square error (NRMSE), the mean absolute error (MAE), simulation error (Se), the index of agreement (Dindex), and the Nash–Sutcliffe efficiency coefficient (NSE), were employed to assess model performance. The results of the field trial demonstrated that reducing the irrigation rate to 80% of ETc negatively impacted cotton FY and ET water productivity (ETWP); the FY declined by 45.2% (ETWP = 0.097 kg·ha−1) in 2023 and by 38.1% (ETWP = 0.133 kg·ha−1) in 2024. Conversely, F100% produced a more uniform and stronger fiber than F80%, with the uniformity index (UI) and fiber strength (STR) measuring 81.7% and 29.5 g tex−1 in 2023 and 82.2% and 30.0 g tex−1 in 2024, indicating that UI and STR were well correlated with soil water during both growing seasons. AquaCrop showed an excellent performance in simulating cotton CC during the two growing seasons. The R2, NRMSE, Dindex, and NSE were between 0.97 and 0.99, 8.45% and 14.36%, 0.98 and 0.99, and 0.96 and 0.98, respectively. Moreover, the AquaCrop model accurately simulated YTot during these seasons, with R2, NRMSE, Dindex, and NSE for pooled yield data of 0.93, 8.05%, 0.95, and 0.78, respectively. The model consistently overestimated YTot, ETobs, and WCTot, but within an acceptable Se (Se < 15%) during both growing seasons, except for WCTot under the 80% treatment in 2023 (Se = 26.4%). Consequently, AquaCrop can be considered an effective tool for irrigation management and yield prediction in arid climates such as Arizona. Full article
(This article belongs to the Section Agricultural Biosystem and Biological Engineering)
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15 pages, 1361 KB  
Article
Biocontrol and Growth-Promoting Potential of Antagonistic Strain YL84 Against Verticillium dahliae
by Yuxin Tang, Qinyuan Xue, Jiahui Yu, Zhen Zhang, Zhe Wang, Lan Wang and Hongzu Feng
Agronomy 2025, 15(8), 1997; https://doi.org/10.3390/agronomy15081997 - 20 Aug 2025
Viewed by 332
Abstract
Cotton Verticillium wilt is a disease that significantly impacts the cotton industry, severely affecting cotton quality and the economic well-being of farmers. Bacillus atrophaeus YL84 is a biocontrol bacterium with broad-spectrum antagonistic and growth-promoting characteristics, previously isolated by our laboratory. This study aimed [...] Read more.
Cotton Verticillium wilt is a disease that significantly impacts the cotton industry, severely affecting cotton quality and the economic well-being of farmers. Bacillus atrophaeus YL84 is a biocontrol bacterium with broad-spectrum antagonistic and growth-promoting characteristics, previously isolated by our laboratory. This study aimed to elucidate the antagonistic effects of sterilized fermentation filtrate from Bacillus atrophaeus YL84 on cotton Verticillium wilt pathogen Verticillium dahliae and its growth-promoting effects on cotton. The experiments were conducted in vitro and in vivo to assess these effects comprehensively. Using the dual culture method, it was found that Bacillus atrophaeus YL84 exhibited a high inhibition rate on mycelial growth of V. dahliae, with an inhibition rate of 84.11%. The undiluted YL84 sterilized fermentation filtrate and its 10% volume fraction dilution (fermentation filtrate diluted to 10%) exhibited inhibition rates of 80.25% and 72.16% for conidial germination and mycelial growth of V. dahliae, respectively. Scanning electron microscopy showed increased branching, swelling, and shortened internodes in the antagonized mycelia. Conductivity measurements revealed a significant enhancement caused by the YL84 filtrate, with conductivity increasing by 8.94 times compared to the control at a 250 μg/mL concentration. Similarly, protein leakage peaked at 9.47 times the control level at 250 μg/mL, demonstrating the filtrate’s potent impact on mycelial cell membrane permeability. The enzymatic activities of polygalacturonase (PG), cellulase (CL), and β-glucosidase (β-GC) were significantly reduced following treatment with YL84 sterilized fermentation filtrate, with reductions from control levels of 15.78, 10.11, and 5.01 U/mL to treatment levels of 11.81, 6.96, and 1.44 U/mL, respectively. Indoor pot experiments demonstrated that different concentrations of YL84 sterilized fermentation filtrate significantly suppressed the occurrence of cotton Verticillium wilt while promoting plant growth. Compared to the control group, application of 250 μg/mL YL84 sterilized fermentation filtrate resulted in a control efficacy of 66.69% for cotton Verticillium wilt, with increases in plant height, root length, fresh weight, and dry weight of 9.36–33.85%, 17.33–29.49%, 16.79–28.24%, and 25–58.33%, respectively. These findings underscore the potential of the YL84 filtrate as both a biocontrol agent and a promoter of cotton plant growth in agricultural settings. These results indicate that Bacillus atrophaeus YL84 sterilized fermentation filtrate possesses both disease-suppressing and growth-promoting activities, making it a promising candidate for development and use as a biocontrol agent and plant growth promoter. Full article
(This article belongs to the Section Pest and Disease Management)
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10 pages, 2301 KB  
Communication
GhNRPB3 Negatively Regulates Drought and Salt Tolerance in Cotton
by Yi Wang, Jiacong Zeng, Yuehua Yu and Zhiyong Ni
Plants 2025, 14(16), 2575; https://doi.org/10.3390/plants14162575 - 19 Aug 2025
Viewed by 326
Abstract
RNA polymerase II (Pol II) has been shown to participate in various biological processes in plants, but its function in response to abiotic stress in cotton remains unclear. This study aimed to elucidate the role of the third-largest subunit of Pol II (NRPB3) [...] Read more.
RNA polymerase II (Pol II) has been shown to participate in various biological processes in plants, but its function in response to abiotic stress in cotton remains unclear. This study aimed to elucidate the role of the third-largest subunit of Pol II (NRPB3) in the response of cotton to drought and salt stress through molecular biology and physiological methods. Real-time fluorescence quantitative PCR was used to analyze the expression pattern of GhNRPB3 in roots, stems, leaves, and cotyledons and to detect changes in its expression under drought, NaCl, and ABA treatments. Using virus-induced gene silencing (VIGS) technology, GhNRPB3-silenced plants were obtained, and their physiological indicators under drought and salt stress, as well as the expression levels of the drought stress-related genes GhRD22 and GhRD26, were measured. This study revealed that GhNRPB3 is widely expressed in roots, stems, leaves, and cotyledons and that its expression is significantly induced by drought, NaCl, and ABA treatments. Compared to wild-type plants, the drought resistance, survival rate, and peroxidase activity of the GhNRPB3-silenced plants significantly increased, whereas the malondialdehyde content significantly decreased. Moreover, the expression levels of the drought-responsive genes GhRD22 and GhRD26 significantly increased. The salt tolerance of the GhNRPB3-silenced plants also increased, as reflected by decreased leaf wilting and significant increases in root growth parameters (including root length, root area, and root volume). These results indicate that GhNRPB3 plays a crucial role in mediating the adaptation of cotton to drought and salt stress by regulating the expression of stress-related genes. Full article
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22 pages, 2597 KB  
Article
Interactive Effects of Mulching Width and Irrigation Management on Cotton Growth and Dynamic Changes in Soil Factors in Arid Regions
by Nanfang Li, Guang Yang, Yinping Song, Wenzhi Wang, Xianbo Zhang, Hao Liu and Huifeng Ning
Agronomy 2025, 15(8), 1964; https://doi.org/10.3390/agronomy15081964 - 14 Aug 2025
Viewed by 252
Abstract
Mulching and irrigation are key practices for improving cotton yield and soil conditions, especially in Xinjiang, China. This study investigated the combined effects of mulching width and irrigation depth on cotton growth and rhizosphere microorganisms. Two mulching widths—conventional (M1) and ultra-wide (M2)—and three [...] Read more.
Mulching and irrigation are key practices for improving cotton yield and soil conditions, especially in Xinjiang, China. This study investigated the combined effects of mulching width and irrigation depth on cotton growth and rhizosphere microorganisms. Two mulching widths—conventional (M1) and ultra-wide (M2)—and three irrigation depths, 0.8 ETc (W1), 1.0 ETc (W2), and 1.2 ETc (W3), were tested. The impacts on cotton growth, soil environment, and rhizosphere microbial communities were analyzed. Results showed that under the same irrigation depth, M2 significantly increased soil moisture and reduced salt accumulation. Soil temperature under M2 was higher than M1, with increases of 0.55 °C and 1.65 °C during the budding and flowering–boll stages. M2 also increased root length (3.52–10.72%) and root surface area (5.8–7.51%). The beneficial fungus Cladosporium was enriched, while the pathogen Fusarium was suppressed under M2. With the same mulching width, increasing irrigation improved soil moisture, reduced electrical conductivity, and decreased soil temperature. Root diameter and volume increased by 7.67–47% and 9.43–10.36%, respectively. Mulching width and irrigation depth significantly affected bacterial α-diversity. M2W3 showed the highest microbial richness and functional diversity. This study offers guidance for efficient cotton cultivation in southern Xinjiang. Full article
(This article belongs to the Special Issue Crop Management in Water-Limited Cropping Systems)
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21 pages, 5866 KB  
Article
Genome-Wide Identification and Expression Analysis of the GH19 Chitinase Gene Family in Sea Island Cotton
by Jingjing Ma, Yilei Long, Jincheng Fu, Nengshuang Shen, Le Wang, Shuaijun Wu, Jing Li, Quanjia Chen, Qianli Zu and Xiaojuan Deng
Curr. Issues Mol. Biol. 2025, 47(8), 633; https://doi.org/10.3390/cimb47080633 - 7 Aug 2025
Viewed by 311
Abstract
In this study, GH19 chitinase (Chi) gene family was systematically identified and characterized using genomic assemblies from four cotton species: Gossypium barbadense, G. hirsutum, G. arboreum, and G. raimondii. A suite of analyses was performed, including genome-wide gene identification, [...] Read more.
In this study, GH19 chitinase (Chi) gene family was systematically identified and characterized using genomic assemblies from four cotton species: Gossypium barbadense, G. hirsutum, G. arboreum, and G. raimondii. A suite of analyses was performed, including genome-wide gene identification, physicochemical property characterization of the encoded proteins, subcellular localization prediction, phylogenetic reconstruction, chromosomal mapping, promoter cis-element analysis, and comprehensive expression profiling using transcriptomic data and qRT-PCR (including tissue-specific expression, hormone treatments, and Fusarium oxysporum infection assays). A total of 107 GH19 genes were identified across the four species (35 in G. barbadense, 37 in G. hirsutum, 19 in G. arboreum, and 16 in G. raimondii). The molecular weights of GH19 proteins ranged from 9.9 to 97.3 kDa, and they were predominantly predicted to localize to the extracellular space. Phylogenetic analysis revealed three well-conserved clades within this family. In tetraploid cotton, GH19 genes were unevenly distributed across 12 chromosomes, often clustering in certain regions, whereas in diploid species, they were confined to five chromosomes. Promoter analysis indicated that GH19 gene promoters contain numerous stress- and hormone-responsive motifs, including those for abscisic acid (ABA), ethylene (ET), and gibberellin (GA), as well as abundant light-responsive elements. The expression patterns of GH19 genes were largely tissue-specific; for instance, GbChi23 was predominantly expressed in the calyx, whereas GbChi19/21/22 were primarily expressed in the roots and stems. Overall, this study provides the first comprehensive genomic and functional characterization of the GH19 family in G. barbadense, laying a foundation for understanding its role in disease resistance mechanisms and aiding in the identification of candidate genes to enhance plant defense against biotic stress. Full article
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20 pages, 3604 KB  
Article
Analysis of the Differences in Rhizosphere Microbial Communities and Pathogen Adaptability in Chili Root Rot Disease Between Continuous Cropping and Rotation Cropping Systems
by Qiuyue Zhao, Xiaolei Cao, Lu Zhang, Xin Hu, Xiaojian Zeng, Yingming Wei, Dongbin Zhang, Xin Xiao, Hui Xi and Sifeng Zhao
Microorganisms 2025, 13(8), 1806; https://doi.org/10.3390/microorganisms13081806 - 1 Aug 2025
Viewed by 420
Abstract
In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. [...] Read more.
In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article
(This article belongs to the Section Microbiomes)
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17 pages, 2789 KB  
Article
GhSPX1s Interact with GhPHR1A and GhPHL1A in Regulating Phosphate Starvation Response in Cotton
by Nuerkaimaier Mulati, Miaomiao Hao, Yuxin Yang, Yanping Shi, Guanghui Xiao and Liping Zhu
Biology 2025, 14(8), 916; https://doi.org/10.3390/biology14080916 - 23 Jul 2025
Viewed by 342
Abstract
SPX (SYG1/Pho81/XPR1) family genes play a pivotal role in phosphorus signaling, phosphorus uptake, and phosphorus translocation in plants. However, to date, the SPX family genes have not been systematically investigated in cotton. In this study, we conducted a genome-wide analysis and [...] Read more.
SPX (SYG1/Pho81/XPR1) family genes play a pivotal role in phosphorus signaling, phosphorus uptake, and phosphorus translocation in plants. However, to date, the SPX family genes have not been systematically investigated in cotton. In this study, we conducted a genome-wide analysis and identified 44 SPX family genes in Gossypium hirsutum, classifying them into four subfamilies (SPX, SPX-MFS, SPX-EXS, and SPX-RING) based on conserved domains. An expression analysis revealed that the majority of SPX family genes were highly expressed in the root and stem. We identified hormone response, stress response, low-temperature response, and PHR1 binding sequence (P1BS) cis-elements in the promoters of the SPX genes. Additionally, the expression of GhPHO1-4, GhSPX1-1/1-2/1-3, and GhSPX-MFS2-1/2-2 was significantly altered under phosphorus-deficient conditions and may be involved in the regulation of Pi response. A Y2H assay suggested that GhSPX1-1 interacts with GhPHR1A and GhSPX1-2 interacts with GhPHL1A. Our findings provide a basis for further cloning and functional verification of genes related to the regulatory network of low phosphorus tolerance in cotton. Full article
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18 pages, 21045 KB  
Article
Genome-Wide Characterization of the ABI3 Gene Family in Cotton
by Guoyong Fu, Yanlong Yang, Tahir Mahmood, Xinxin Liu, Zongming Xie, Zengqiang Zhao, Yongmei Dong, Yousheng Tian, Jehanzeb Farooq, Iram Sharif and Youzhong Li
Genes 2025, 16(8), 854; https://doi.org/10.3390/genes16080854 - 23 Jul 2025
Viewed by 351
Abstract
Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted [...] Read more.
Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted a comprehensive genome-wide investigation of the ABI3 gene family across 26 plant species, with a focus on 8 Gossypium species. Analyses included phylogenetics, chromosomal localization, synteny assessment, gene duplication patterns, protein domain characterization, promoter cis-regulatory element identification, and tissue-specific/spatiotemporal expression profiling under different organizations of Gossypium hirsutum. Results: Phylogenetic and chromosomal analyses revealed conserved ABI3 evolutionary patterns between monocots and dicots, alongside lineage-specific expansion events within Gossypium spp. Syntenic relationships and duplication analysis in G. hirsutum (upland cotton) indicated retention of ancestral synteny blocks and functional diversification driven predominantly by segmental duplication. Structural characterization confirmed the presence of conserved B3 domains in all G. hirsutum ABI3 homologs. Promoter analysis identified key stress-responsive cis-elements, including ABA-responsive (ABRE), drought-responsive (MYB), and low-temperature-responsive (LTRE) motifs, suggesting a role in abiotic stress regulation. Expression profiling demonstrated significant tissue-specific transcriptional activity across roots, stems, leaves, and fiber developmental stages. Conclusions: This study addresses a significant knowledge gap by elucidating the evolution, structure, and stress-responsive expression profiles of the ABI3 gene family in cotton. It establishes a foundational framework for future functional validation and targeted genetic engineering strategies aimed at developing stress-resilient cotton cultivars with enhanced fiber quality. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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16 pages, 6878 KB  
Article
Cotton STARD Gene Family: Characterization, Evolution, and Expression Profiles During Salt Stress
by Ruifeng Cui, Jiuguang Sun, Shuyan Li, Yupeng Cui, Cun Rui, Minshan Sun and Wuwei Ye
Genes 2025, 16(7), 813; https://doi.org/10.3390/genes16070813 - 11 Jul 2025
Viewed by 401
Abstract
Background: Cotton, a key global economic crop, suffers yield and quality losses due to salt stress. This study aims to analyze the cotton STARD gene family and its role in salt stress responses. Methods: We conducted a genome-wide analysis of the [...] Read more.
Background: Cotton, a key global economic crop, suffers yield and quality losses due to salt stress. This study aims to analyze the cotton STARD gene family and its role in salt stress responses. Methods: We conducted a genome-wide analysis of the STARD gene family in four cotton species, using phylogenetic trees, chromosomal mapping, and collinearity analyses to explore their evolutionary relationships and expansion mechanisms. We also examined gene structures, conserved motifs, and promoter cis-elements. ResultsSTARD genes are evenly distributed across the four cotton species. Segmental duplication was found to be the main driver of gene expansion, with most pairs undergoing purifying selection. Distinct structural features and potential roles in plant growth and stress responses were identified. Notably, 11 GhSTARD genes showed significant expression changes under salt stress, especially GhSTARD45 in root tissues. Conclusions: This study provides new insights into the function and salt stress response mechanisms of the cotton STARD gene family, suggesting GhSTARD45 plays a key role in root-mediated salt tolerance and highlighting the potential of STARD genes in enhancing cotton’s salt tolerance. Full article
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24 pages, 12214 KB  
Article
Brazilian Green Propolis Carried in Lipid-Based Nanostructures: A Potent Adjuvant Therapy to Non-Surgical Periodontal Treatment in the Management of Experimental Periodontitis
by Glauco Rodrigues Carmo Silveira, Vinícius Franzão Ganzaroli, Luan Felipe Toro, Leandro Lemes da Costa, Rodrigo Isaias Lopes Pereira, André Bueno da Silva, Iasmin Rosane Silva Ferreira, João Martins de Mello-Neto, Valdir Gouveia Garcia, Letícia Helena Theodoro, Priscyla Daniely Marcato and Edilson Ervolino
Biomedicines 2025, 13(7), 1643; https://doi.org/10.3390/biomedicines13071643 - 4 Jul 2025
Viewed by 777
Abstract
Objective: This study aimed to evaluate the effects of local use of Brazilian Green Propolis (BGP), either as an ethanolic extract (the most common formulation) or incorporated into lipid-based nanostructures, as an adjuvant therapy for non-surgical periodontal treatment in managing experimental periodontitis [...] Read more.
Objective: This study aimed to evaluate the effects of local use of Brazilian Green Propolis (BGP), either as an ethanolic extract (the most common formulation) or incorporated into lipid-based nanostructures, as an adjuvant therapy for non-surgical periodontal treatment in managing experimental periodontitis (EP) in ovariectomized rats. Methods: Fifty-six female Wistar rats underwent bilateral ovariectomies. After 10 weeks, a cotton ligature was placed around the lower first molar and remained in place for two weeks to induce EP. The ligature was removed, and the rats were randomly assigned in the groups NLT (n = 14), SRP (n = 14), SRP-BGPee (n = 14), and SRP-BGPlns (n = 14). In the NLT group, no local treatment was performed. The SRP group received scaling and root planing (SRP), along with irrigation using a physiological saline solution. The SRP-BGPee group underwent SRP and irrigation with ethanolic extract of BGP. The SRP-BGPlns group underwent SRP and irrigation with BGP-loaded lipid nanostructure (BGPlns). Each group received one SRP session followed by four irrigation sessions with the specified solutions, which were conducted immediately after SRP and subsequently after 2, 4, and 6 days. Euthanasia was performed at 7 and 28 days following the removal of the ligatures. The hemimandibles were processed for the following analyses: microtomographic analysis; histological analysis; histometric analysis of the percentage of bone tissue in the furcation region (PBT); and immunohistochemical analysis for tartrate-resistant acid phosphatase activity (TRAP), transforming growth factor beta 1 (TGFβ1), and osteocalcin (OCN). Results: The SRP-BGPlns group demonstrated superior periodontal tissue repair, reduced alveolar bone loss, fewer TRAP-positive cells (at 7 days), and higher levels of immunolabeling for TGFβ1 (at both 7 and 28 days) and OCN (at 28 days) compared to the other experimental groups. Conclusions: The irrigation with BGP is an effective adjuvant therapy for non-surgical periodontal treatment in managing EP in ovariectomized rats. Its application in lipid-based nanostructures proved to be more effective than the ethanolic extract form. Full article
(This article belongs to the Special Issue Periodontal Disease and Periodontal Tissue Regeneration)
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19 pages, 1898 KB  
Article
Reducing Nitrogen Input Increases the Efficacy of Soil Nitrogen Utilization by Regulating Cotton–Arbuscular Mycorrhizal Fungi–Soil Nitrogen Interactions
by Hushan Wang, Yunzhu He, Zihui Shen, Mengjuan Liu, Wangfeng Zhang and Xiaozhen Pu
Nitrogen 2025, 6(3), 55; https://doi.org/10.3390/nitrogen6030055 - 3 Jul 2025
Viewed by 416
Abstract
Crops and arbuscular mycorrhizal (AM) fungi can enhance nitrogen (N) transformation and utilization efficiency in the soil, and this effect is regulated by soil N application rates. However, it remains unclear whether the N utilization efficiency of cotton can be improved through the [...] Read more.
Crops and arbuscular mycorrhizal (AM) fungi can enhance nitrogen (N) transformation and utilization efficiency in the soil, and this effect is regulated by soil N application rates. However, it remains unclear whether the N utilization efficiency of cotton can be improved through the symbiosis of cotton with AM fungi under reduced N application rates. Therefore, we conducted 15N labeling experiments using a compartmentalized culture system with Gossypium hirsutum L. as the experimental plant. We established three N treatments (0.15 g·kg−1, 0.10 g·kg−1 and 0 g·kg−1) to investigate the effects of different fertilization rates on N utilization, soil N priming effects, and differences in N accumulation in various parts of cotton plants within the soil–AM fungi–cotton system. The results indicate that under reduced N application, symbiosis between cotton and AM fungi increased the N fertilizer utilization efficiency and the soil N priming effect. Specifically, reducing the fertilization dosage from 0.15 g·kg−1 to 0.10 g·kg−1 increased the N fertilizer utilization efficiency and soil N priming effect by 8.87% and 11.67%, respectively, and decreased the N loss rate by 7.02%. The symbiosis between cotton and AM fungi after N reduction significantly increased N accumulation in the roots and leaves. Moreover, the N fertilizer content accounted for 5.89% of the total N content in roots. Overall, when N application was reduced, symbiosis with AM fungi effectively promoted the rhizosphere N priming effect, which reconciled the conflict in N nutrient allocation within cotton and thus enabled the efficient utilization of soil N. Full article
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13 pages, 828 KB  
Article
Potential of Bacterial Inoculants to Mitigate Soil Compaction Effects on Gossypium hirsutum Growth
by Fausto Henrique Viera Araújo, Crislaine Alves da Conceição, Adriene Caldeira Batista, Gabriel Faria Parreiras de Andrade, Caique Menezes de Abreu, Paulo Henrique Grazziotti and Ricardo Siqueira da Silva
Plants 2025, 14(12), 1844; https://doi.org/10.3390/plants14121844 - 16 Jun 2025
Viewed by 547
Abstract
Aims: Soil compaction is one of the main challenges in agriculture, negatively affecting cotton growth (Gossypium hirsutum L.), nutrition, and productivity. This study evaluated the efficacy of plant growth-promoting bacteria (PGPB), Exiguobacterium sibiricum, and Pantoea vagans in mitigating the effects of different [...] Read more.
Aims: Soil compaction is one of the main challenges in agriculture, negatively affecting cotton growth (Gossypium hirsutum L.), nutrition, and productivity. This study evaluated the efficacy of plant growth-promoting bacteria (PGPB), Exiguobacterium sibiricum, and Pantoea vagans in mitigating the effects of different soil compaction levels (65%, 75%, 85%, and 95%) on cotton performance. Methods: Parameters such as plant height, stem diameter, number of leaves, shoot dry matter (SDM), and nutrient content in leaves, stems, and roots were assessed. The methodology included variance analysis and mean clustering to identify significant differences among treatments using R software. Results: The results indicated that PGPB inoculation improved plant growth and nutrition even under high compaction levels. Cotton height increased by up to 45% in compacted soils (95%), while stem diameter and SDM also showed significant gains. Foliar nutrient levels of N (37.2 g kg−1), Ca, and Mg remained within the adequate range for cotton cultivation, reflecting the efficiency of PGPB in enhancing nutrient absorption. Under severe compaction, Ca accumulation dropped to 18.2 g kg−1, highlighting the physical constraints imposed on the roots; however, the bacterial action mitigated this impact. Additionally, bacterial strains increased the availability of N and P in the soil due to their ability to fix nitrogen, solubilize phosphates, and produce exopolysaccharides that improve soil structure. Conclusions: In conclusion, inoculation with Exiguobacterium sibiricum and Pantoea vagans is an effective strategy to mitigate the impacts of soil compaction on cotton. These bacteria promote plant growth and nutrition and enhance the soil’s physical and biological properties. Full article
(This article belongs to the Special Issue Beneficial Effects of Bacteria on Plants)
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10 pages, 1657 KB  
Article
Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings
by Xianxu Wei, Siyu Yao, Jiangnuo Di, Jiaxin Guan, Aohan Wang, Jie Yang, Luyao Zhang, Yang Liu, Mengyao Liang, Zhihao Niu, Xuan Zhang, Jiarui Xue, Mengxue Shen, Lin Li, Yao Su and Zhengwen Sun
Plants 2025, 14(12), 1803; https://doi.org/10.3390/plants14121803 - 12 Jun 2025
Viewed by 518
Abstract
Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (Gossypium hirsutum L.) accessions genotyped with 2.97 [...] Read more.
Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (Gossypium hirsutum L.) accessions genotyped with 2.97 million single-nucleotide polymorphisms (SNPs). Phenotypic analysis reveals substantial variation under LP stress, with LP-SDW showing the highest coefficient of variation (33.69%). The GWASs identified thousands of significant SNPs, including pleiotropic loci associated with multiple traits. Chromosomes A08, D09, and D12 harbored novel associated signals. Multi-locus models significantly enhanced detection sensitivity, identifying 123 SNPs undetected by single-locus approaches. Functional annotations prioritized six candidate genes near associated SNPs, including GhM_A08G1315 (remorin protein) and GhM_D06G1152 (carotenoid cleavage dioxygenase), whose LP-induced expression patterns were validated by qRT-PCR. These genes are implicated in membrane signaling, root architecture modulation, and hormone metabolism. Our findings provide novel genetic insights into LP tolerance and establish a foundation for breeding phosphorus-efficient varieties through marker-assisted selection in cotton. Full article
(This article belongs to the Special Issue Genetic Analysis of Plant Adaptation to Abiotic Stresses)
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