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16 pages, 1313 KiB  
Article
Mycorrhizas Promote Total Flavonoid Levels in Trifoliate Orange by Accelerating the Flavonoid Biosynthetic Pathway to Reduce Oxidative Damage Under Drought
by Lei Liu and Hong-Na Mu
Horticulturae 2025, 11(8), 910; https://doi.org/10.3390/horticulturae11080910 (registering DOI) - 4 Aug 2025
Abstract
Flavonoids serve as crucial plant antioxidants in drought tolerance, yet their antioxidant regulatory mechanisms within mycorrhizal plants remain unclear. In this study, using a two-factor design, trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings in the four-to-five-leaf stage were either inoculated with Funneliformis [...] Read more.
Flavonoids serve as crucial plant antioxidants in drought tolerance, yet their antioxidant regulatory mechanisms within mycorrhizal plants remain unclear. In this study, using a two-factor design, trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings in the four-to-five-leaf stage were either inoculated with Funneliformis mosseae or not, and subjected to well-watered (70–75% of field maximum water-holding capacity) or drought stress (50–55% field maximum water-holding capacity) conditions for 10 weeks. Plant growth performance, photosynthetic physiology, leaf flavonoid content and their antioxidant capacity, reactive oxygen species levels, and activities and gene expression of key flavonoid biosynthesis enzymes were analyzed. Although drought stress significantly reduced root colonization and soil hyphal length, inoculation with F. mosseae consistently enhanced the biomass of leaves, stems, and roots, as well as root surface area and diameter, irrespective of soil moisture. Despite drought suppressing photosynthesis in mycorrhizal plants, F. mosseae substantially improved photosynthetic capacity (measured via gas exchange) and optimized photochemical efficiency (assessed by chlorophyll fluorescence) while reducing non-photochemical quenching (heat dissipation). Inoculation with F. mosseae elevated the total flavonoid content in leaves by 46.67% (well-watered) and 14.04% (drought), accompanied by significantly enhanced activities of key synthases such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), 4-coumarate:coA ligase (4CL), and cinnamate 4-hydroxylase (C4H), with increases ranging from 16.90 to 117.42% under drought. Quantitative real-time PCR revealed that both mycorrhization and drought upregulated the expression of PtPAL1, PtCHI, and Pt4CL genes, with soil moisture critically modulating mycorrhizal regulatory effects. In vitro assays showed that flavonoid extracts scavenged radicals at rates of 30.07–41.60% in hydroxyl radical (•OH), 71.89–78.06% in superoxide radical anion (O2•−), and 49.97–74.75% in 2,2-diphenyl-1-picrylhydrazyl (DPPH). Mycorrhizal symbiosis enhanced the antioxidant capacity of flavonoids, resulting in higher scavenging rates of •OH (19.07%), O2•− (5.00%), and DPPH (31.81%) under drought. Inoculated plants displayed reduced hydrogen peroxide (19.77%), O2•− (23.90%), and malondialdehyde (17.36%) levels. This study concludes that mycorrhizae promote the level of total flavonoids in trifoliate orange by accelerating the flavonoid biosynthesis pathway, hence reducing oxidative damage under drought. Full article
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21 pages, 6219 KiB  
Article
Semi-Supervised Density Estimation with Background-Augmented Data for In Situ Seed Counting
by Baek-Gyeom Sung, Chun-Gu Lee, Yeong-Ho Kang, Seung-Hwa Yu and Dae-Hyun Lee
Agriculture 2025, 15(15), 1682; https://doi.org/10.3390/agriculture15151682 - 4 Aug 2025
Viewed by 76
Abstract
Direct seeding has gained prominence as a labor-efficient and environmentally sustainable alternative to conventional transplanting in rice cultivation. In direct seeding systems, early-stage management is crucial for stable seedling establishment, with sowing uniformity measured by seed counts being a critical indicator of success. [...] Read more.
Direct seeding has gained prominence as a labor-efficient and environmentally sustainable alternative to conventional transplanting in rice cultivation. In direct seeding systems, early-stage management is crucial for stable seedling establishment, with sowing uniformity measured by seed counts being a critical indicator of success. However, conventional manual seed counting methods are time-consuming, prone to human error, and impractical for large-scale or repetitive tasks, necessitating advanced automated solutions. Recent advances in computer vision technologies and precision agriculture tools, offer the potential to automate seed counting tasks. Nevertheless, challenges such as domain discrepancies and limited labeled data restrict robust real-world deployment. To address these issues, we propose a density estimation-based seed counting framework integrating semi-supervised learning and background augmentation. This framework includes a cost-effective data acquisition system enabling diverse domain data collection through indoor background augmentation, combined with semi-supervised learning to utilize augmented data effectively while minimizing labeling costs. The experimental results on field data from unknown domains show that our approach reduces seed counting errors by up to 58.5% compared to conventional methods, highlighting its potential as a scalable and effective solution for agricultural applications in real-world environments. Full article
(This article belongs to the Section Artificial Intelligence and Digital Agriculture)
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14 pages, 6927 KiB  
Article
Physiological and Transcriptomic Mechanisms Underlying Vitamin C-Mediated Cold Stress Tolerance in Grafted Cucumber
by Panpan Yu, Junkai Wang, Xuyang Zhang, Zhenglong Weng, Kaisen Huo, Qiuxia Yi, Chenxi Wu, Sunjeet Kumar, Hao Gao, Lin Fu, Yanli Chen and Guopeng Zhu
Plants 2025, 14(15), 2398; https://doi.org/10.3390/plants14152398 - 2 Aug 2025
Viewed by 266
Abstract
Cucumbers (Cucumis sativus L.) are highly sensitive to cold, but grafting onto cold-tolerant rootstocks can enhance their low-temperature resilience. This study investigates the physiological and molecular mechanisms by which exogenous vitamin C (Vc) mitigates cold stress in grafted cucumber seedlings. Using cucumber [...] Read more.
Cucumbers (Cucumis sativus L.) are highly sensitive to cold, but grafting onto cold-tolerant rootstocks can enhance their low-temperature resilience. This study investigates the physiological and molecular mechanisms by which exogenous vitamin C (Vc) mitigates cold stress in grafted cucumber seedlings. Using cucumber ‘Chiyu 505’ as the scion and pumpkin ‘Chuangfan No.1’ as the rootstock, seedlings were grafted using the whip grafting method. In the third true leaf expansion stage, seedlings were foliar sprayed with Vc at concentrations of 50, 100, 150, and 200 mg L−1. Three days after initial spraying, seedlings were subjected to cold stress (8 °C) for 3 days, with continued spraying. After that, morphological and physiological parameters were assessed. Results showed that 150 mg L−1 Vc treatment was most impactive, significantly reducing the cold damage index while increasing the root-to-shoot ratio, root vitality, chlorophyll content, and activities of antioxidant enzymes (SOD, POD, CAT). Moreover, this treatment enhanced levels of soluble sugars, soluble proteins, and proline compared to control. However, 200 mg L−1 treatment elevated malondialdehyde (MDA) content, indicating potential oxidative stress. For transcriptomic analysis, leaves from the 150 mg L−1 Vc and CK treatments were sampled at 0, 1, 2, and 3 days of cold stress. Differential gene expression revealed that genes associated with photosynthesis (LHCA1), stress signal transduction (MYC2-1, MYC2-2, WRKY22, WRKY2), and antioxidant defense (SOD-1, SOD-2) were initially up-regulated and subsequently down-regulated, as validated by qRT-PCR. Overall, we found that the application of 150 mg L−1 Vc enhanced cold tolerance in grafted cucumber seedlings by modulating gene expression networks related to photosynthesis, stress response, and the antioxidant defense system. This study provides a way for developing Vc biostimulants to enhance cold tolerance in grafted cucumbers, improving sustainable cultivation in low-temperature regions. Full article
(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)
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25 pages, 1529 KiB  
Article
Native Flora and Potential Natural Vegetation References for Effective Forest Restoration in Italian Urban Systems
by Carlo Blasi, Giulia Capotorti, Eva Del Vico, Sandro Bonacquisti and Laura Zavattero
Plants 2025, 14(15), 2396; https://doi.org/10.3390/plants14152396 - 2 Aug 2025
Viewed by 154
Abstract
The ongoing decade of UN restoration matches with the European goal of bringing nature back into our lives, including in urban systems, and Nature Restoration Regulation. Within such a framework, this work is aimed at highlighting the ecological rationale and strategic value of [...] Read more.
The ongoing decade of UN restoration matches with the European goal of bringing nature back into our lives, including in urban systems, and Nature Restoration Regulation. Within such a framework, this work is aimed at highlighting the ecological rationale and strategic value of an NRRP measure devoted to forest restoration in Italian Metropolitan Cities, and at assessing respective preliminary results. Therefore, the measure’s overarching goal (not to create urban parks or gardens, but activate forest recovery), geographic extent and scope (over 4000 ha and more than 4 million planted trees and shrubs across the country), plantation model (mandatory use of native species consistent with local potential vegetation, density of 1000 seedlings per ha, use of at least four tree and four shrub species in each project, with a minimum proportion of 70% for trees, certified provenance for reproductive material), and compulsory management activities (maintenance and replacement of any dead plants for at least five years), are herein shown and explained under an ecological perspective. Current implementation outcomes were thus assessed in terms of coherence and expected biodiversity benefits, especially with respect to ecological and biogeographic consistency of planted forests, representativity in relation to national and European plant diversity, biogeographic interest and conservation concern of adopted plants, and potential contribution to the EU Habitats Directive. Compliance with international strategic goals and normative rules, along with recognizable advantages of the measure and limitations to be solved, are finally discussed. In conclusion, the forestation model proposed for the Italian Metropolitan Cities proved to be fully applicable in its ecological rationale, with expected benefits in terms of biodiversity support plainly met, and even exceeded, at the current stage of implementation, especially in terms of the contribution to protected habitats. These promising preliminary results allow the model to be recognized at the international level as a good practice that may help achieve protection targets and sustainable development goals within and beyond urban systems. Full article
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16 pages, 1141 KiB  
Article
Coordinated Roles of Osmotic Adjustment, Antioxidant Defense, and Ion Homeostasis in the Salt Tolerance of Mulberry (Morus alba L. ‘Tailai Sang’) Seedlings
by Nan Xu, Tiane Wang, Yuan Wang, Juexian Dong and Yu Shaopeng
Forests 2025, 16(8), 1258; https://doi.org/10.3390/f16081258 - 1 Aug 2025
Viewed by 159
Abstract
Soil salinization severely limits plant growth and productivity. Mulberry (Morus alba L.), an economically and ecologically important tree, is widely cultivated, yet its salt-tolerance mechanisms at the seedling stage remain insufficiently understood. This study investigated the physiological and biochemical responses of two-year-old [...] Read more.
Soil salinization severely limits plant growth and productivity. Mulberry (Morus alba L.), an economically and ecologically important tree, is widely cultivated, yet its salt-tolerance mechanisms at the seedling stage remain insufficiently understood. This study investigated the physiological and biochemical responses of two-year-old mulberry (‘Tailai Sang’) seedlings subjected to six NaCl treatments (0, 50, 100, 150, 200, and 300 mmol L−1) for 28 days. Results showed that growth parameters and photosynthetic gas exchange exhibited dose-dependent declines. The reduction in net photosynthetic rate (Pn) was attributed to both stomatal limitations (decreased stomatal conductance) and non-stomatal limitations, as evidenced by a significant decrease in the maximum quantum efficiency of photosystem II (Fv/Fm) under high salinity. To cope with osmotic stress, seedlings accumulated compatible solutes, including soluble sugars, proteins, and proline. Critically, mulberry seedlings demonstrated effective ion homeostasis by sequestering Na+ in the roots to maintain a high K+/Na+ ratio in leaves, a mechanism that was compromised above 150 mmol L−1. Concurrently, indicators of oxidative stress—malondialdehyde (MDA) and H2O2—rose significantly with salinity, inducing the activities of antioxidant enzymes (SOD, CAT, APX, and GR), which peaked at 150 mmol L−1 before declining under extreme stress. A biomass-based LC50 of 179 mmol L−1 NaCl was determined. These findings elucidate that mulberry salt tolerance is a coordinated process involving three key mechanisms: osmotic adjustment, selective ion distribution, and a robust antioxidant defense system. This study establishes an indicative tolerance threshold under controlled conditions and provides a physiological basis for further field-based evaluations of ‘Tailai Sang’ mulberry for cultivation on saline soils. Full article
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15 pages, 1899 KiB  
Article
Heterologous Watermelon HSP17.4 Expression Confers Improved Heat Tolerance to Arabidopsis thaliana
by Yajie Hong, Yurui Li, Jing Chen, Nailin Xing, Wona Ding, Lili Chen, Yunping Huang, Qiuping Li and Kaixing Lu
Curr. Issues Mol. Biol. 2025, 47(8), 606; https://doi.org/10.3390/cimb47080606 - 1 Aug 2025
Viewed by 132
Abstract
Members of the heat shock protein 20 (HSP20) family of proteins play an important role in responding to various forms of stress. Here, the expression of ClaHSP17.4 was induced by heat stress in watermelon. Then, a floral dipping approach was used to introduce [...] Read more.
Members of the heat shock protein 20 (HSP20) family of proteins play an important role in responding to various forms of stress. Here, the expression of ClaHSP17.4 was induced by heat stress in watermelon. Then, a floral dipping approach was used to introduce the pCAMBIA1391b-GFP overexpression vector encoding the heat tolerance-related gene ClaHSP17.4 from watermelon into Arabidopsis thaliana, and we obtained ClaHSP17.4-overexpressing Arabidopsis plants. Under normal conditions, the phenotypes of transgenic and wild-type (WT) Arabidopsis plants were largely similar. Following exposure to heat stress, however, the germination rates (96%) of transgenic Arabidopsis plants at the germination stages were significantly higher than those of wild-type idopsis (17%). Specifically, the malondialdehyde (MDA) content of transgenic Arabidopsis was half that of the control group, while the activities of peroxidase (POD) and superoxide dismutase (SOD) were 1.25 times those of the control group after exposure to high temperatures for 12 h at the seedling stages. The proline content in ClaHSP17.4-overexpressing transgenic Arabidopsis increased by 17% compared to WT plants (* p < 0.05), while the soluble sugar content rose by 37% (* p < 0.05). These results suggest that ClaHSP17.4 overexpression indirectly improves the antioxidant capacity and osmotic regulatory capacity of Arabidopsis seedlings, leading to improved survival and greater heat tolerance. Meanwhile, the results of this study provide a reference for further research on the function of the ClHSP17.4 gene and lay a foundation for breeding heat-tolerant watermelon varieties and advancing our understanding of plant adaptation to environmental stress. Full article
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14 pages, 31608 KiB  
Article
Primary Metabolic Variations in Maize Plants Affected by Different Levels of Nitrogen Supply
by The Ngoc Phuong Nguyen, Rose Nimoh Serwaa and Jwakyung Sung
Metabolites 2025, 15(8), 519; https://doi.org/10.3390/metabo15080519 - 1 Aug 2025
Viewed by 186
Abstract
Background/Objectives: Nitrogen (N) is an essential macronutrient that strongly influences maize growth and metabolism. While many studies have focused on nitrogen responses during later developmental stages, early-stage physiological and metabolic responses remain less explored. This study investigated the effect of different nitrogen-deficient [...] Read more.
Background/Objectives: Nitrogen (N) is an essential macronutrient that strongly influences maize growth and metabolism. While many studies have focused on nitrogen responses during later developmental stages, early-stage physiological and metabolic responses remain less explored. This study investigated the effect of different nitrogen-deficient levels on maize seedling growth and primary metabolite profiles. Methods: Seedlings were treated with N-modified nutrient solution, which contained 0% to 120% of the standard nitrogen level (8.5 mM). Results: Nitrogen starvation (N0) significantly reduced plant height (by 11–14%), shoot fresh weight (over 30%) compared to the optimal N supply (N100). Total leaf nitrogen content under N0–N20 was less than half of that in N100, whereas moderate N deficiency resulted in moderate reductions in growth and nitrogen content. Metabolite analysis revealed that N deficiency induced the accumulation of soluble sugars and organic acids (up to threefold), while sufficient N promoted the synthesis of amino acids related to nitrogen assimilation and protein biosynthesis. Statistical analyses (PCA and ANOVA) showed that both genotypes (MB and TYC) and tissue type (upper vs. lower leaves) influenced the metabolic response to nitrogen, with MB displaying more consistent shifts and TYC exhibiting greater variability under moderate stress. Conclusions: These findings highlight the sensitivity of maize seedlings to early nitrogen deficiency, with severity influenced by nitrogen level, tissue-specific position, and genotype; thus underscore the close coordination between physiological growth and primary metabolic pathways in response to nitrogen availability. These findings expand current knowledge of nitrogen response mechanisms and offer practical insights for improving nitrogen use efficiency in maize cultivation. Full article
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17 pages, 2601 KiB  
Article
Tree Selection of Vernicia montana in a Representative Orchard Cluster Within Southern Hunan Province, China: A Comprehensive Evaluation Approach
by Juntao Liu, Zhexiu Yu, Xihui Li, Ling Zhou, Ruihui Wang and Weihua Zhang
Plants 2025, 14(15), 2351; https://doi.org/10.3390/plants14152351 - 30 Jul 2025
Viewed by 318
Abstract
With the objective of identifying superior Vernicia montana trees grounded in phenotypic and agronomic traits, this study sought to develop and implement a comprehensive evaluation method which would provide a practical foundation for future clonal breeding initiatives. Using the Vernicia montana propagated from [...] Read more.
With the objective of identifying superior Vernicia montana trees grounded in phenotypic and agronomic traits, this study sought to develop and implement a comprehensive evaluation method which would provide a practical foundation for future clonal breeding initiatives. Using the Vernicia montana propagated from seedling forests grown in the Suxian District of Chenzhou City in southern Hunan Province, we conducted pre-selection, primary selection, and re-selection of Vernicia montana forest stands and took the nine trait indices of single-plant fruiting quantity, single-plant fruit yield, disease and pest resistance, fruit ripening consistency, fruit aggregation, fresh fruit single-fruit weight, fresh fruit seed rate, dry seed kernel rate, and seed kernel oil content rate as the optimal evaluation indexes and carried out cluster analysis and a comprehensive evaluation in order to establish a comprehensive evaluation system for superior Vernicia montana trees. The results demonstrated that a three-stage selection process—consisting of pre-selection, primary selection, and re-selection—was conducted using a comprehensive analytical approach. The pre-selection phase relied primarily on sensory evaluation criteria, including fruit count per plant, tree size, tree morphology, and fruit clustering characteristics. Through this rigorous screening process, 60 elite plants were selected. The primary selection was based on phenotypic traits, including single-plant fruit yield, pest and disease resistance, and uniformity of fruit ripening. From this stage, 36 plants were selected. Twenty plants were then selected for re-selection based on key performance indicators, such as fresh fruit weight, fresh fruit seed yield, dry seed kernel yield, and oil content of the seed kernel. Then the re-selected optimal trees were clustered and analyzed into three classes, with 10 plants in class I, 7 plants in class II, and 3 plants in class III. In class I, the top three superior plants exhibited outstanding performance across key traits: their fresh fruit weight per fruit, fresh fruit seed yield, dry seed yield, and seed kernel oil content reached 41.61 g, 42.80%, 62.42%, and 57.72%, respectively. Compared with other groups, these figures showed significant advantages: 1.17, 1.09, 1.12, and 1.02 times the average values of the 20 reselected superior trees; 1.22, 1.19, 1.20, and 1.08 times those of the 36 primary-selected superior trees; and 1.24, 1.25, 1.26, and 1.19 times those of the 60 pre-selected trees. Fruits counts per plant and the number of fruits produced per plant of the best three plants in class I were 885 and 23.38 kg, respectively, which were 1.13 and 1.18 times higher than the average of 20 re-selected superior trees, 1.25 and 1.30 times higher than the average of 36 first-selected superior trees, and 1.51 and 1.58 times higher than the average of 60 pre-selected superior trees. Class I superior trees, especially the top three genotypes, are suitable for use as mother trees for scion collection in grafting. The findings of this study provide a crucial foundation for developing superior clonal varieties of Vernicia montana through selective breeding. Full article
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26 pages, 11108 KiB  
Article
Warming in the Maternal Environment Alters Seed Performance and Genetic Diversity of Stylosanthes capitata, a Tropical Legume Forage
by Priscila Marlys Sá Rivas, Fernando Bonifácio-Anacleto, Ivan Schuster, Carlos Alberto Martinez and Ana Lilia Alzate-Marin
Genes 2025, 16(8), 913; https://doi.org/10.3390/genes16080913 (registering DOI) - 30 Jul 2025
Viewed by 321
Abstract
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to [...] Read more.
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to warming and elevated CO2 on progeny physiology, genetic diversity, and population structure in Stylosanthes capitata, a resilient forage legume native to Brazil. Methods: Maternal plants were cultivated under controlled treatments, including ambient conditions (control), elevated CO2 at 600 ppm (eCO2), elevated temperature at +2 °C (eTE), and their combined exposure (eTEeCO2), within a Trop-T-FACE field facility (Temperature Free-Air Controlled Enhancement and Free-Air Carbon Dioxide Enrichment). Seed traits (seeds per inflorescence, hundred-seed mass, abortion, non-viable seeds, coat color, germination at 32, 40, 71 weeks) and abnormal seedling rates were quantified. Genetic diversity metrics included the average (A) and effective (Ae) number of alleles, observed (Ho) and expected (He) heterozygosity, and inbreeding coefficient (Fis). Population structure was assessed using Principal Coordinates Analysis (PCoA), Analysis of Molecular Variance (AMOVA), number of migrants per generation (Nm), and genetic differentiation index (Fst). Two- and three-way Analysis of Variance (ANOVA) were used to evaluate factor effects. Results: Compared to control conditions, warming increased seeds per inflorescence (+46%), reduced abortion (−42.9%), non-viable seeds (−57%), and altered coat color. The germination speed index (GSI +23.5%) and germination rate (Gr +11%) improved with warming; combined treatments decreased germination time (GT −9.6%). Storage preserved germination traits, with warming enhancing performance over time and reducing abnormal seedlings (−54.5%). Conversely, elevated CO2 shortened GSI in late stages, impairing germination efficiency. Warming reduced Ae (−35%), He (−20%), and raised Fis (maternal 0.50, progeny 0.58), consistent with the species’ mixed mating system; A and Ho were unaffected. Allele frequency shifts suggested selective pressure under eTE. Warming induced slight structure in PCoA, and AMOVA detected 1% (maternal) and 9% (progeny) variation. Fst = 0.06 and Nm = 3.8 imply environmental influence without isolation. Conclusions: Warming significantly shapes seed quality, reproductive success, and genetic diversity in S. capitata. Improved reproduction and germination suggest adaptive advantages, but higher inbreeding and reduced diversity may constrain long-term resilience. The findings underscore the need for genetic monitoring and broader genetic bases in cultivars confronting environmental stressors. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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18 pages, 3095 KiB  
Article
Investigating Seed Germination, Seedling Growth, and Enzymatic Activity in Onion (Allium cepa) Under the Influence of Plasma-Treated Water
by Sabnaj Khanam, Young June Hong, Eun Ha Choi and Ihn Han
Int. J. Mol. Sci. 2025, 26(15), 7256; https://doi.org/10.3390/ijms26157256 - 27 Jul 2025
Viewed by 340
Abstract
Seed germination and early seedling growth are pivotal stages that define crop establishment and yield potential. Conventional agrochemicals used to improve these processes often raise environmental concerns, highlighting the need for sustainable alternatives. In this study, we demonstrated that water treated with cylindrical [...] Read more.
Seed germination and early seedling growth are pivotal stages that define crop establishment and yield potential. Conventional agrochemicals used to improve these processes often raise environmental concerns, highlighting the need for sustainable alternatives. In this study, we demonstrated that water treated with cylindrical dielectric barrier discharge (c-DBD) plasma, enriched with nitric oxide (NO) and reactive nitrogen species (RNS), markedly enhanced onion (Allium cepa) seed germination and seedling vigor. The plasma-treated water (PTW) promoted rapid imbibition, broke dormancy, and accelerated germination rates beyond 98%. Seedlings irrigated with PTW exhibited significantly increased biomass, root and shoot length, chlorophyll content, and antioxidant enzyme activities, accompanied by reduced lipid peroxidation. Transcriptomic profiling revealed that PTW orchestrated a multifaceted regulatory network by upregulating gibberellin biosynthesis genes (GA3OX1/2), suppressing abscisic acid signaling components (ABI5), and activating phenylpropanoid metabolic pathways (PAL, 4CL) and antioxidant defense genes (RBOH1, SOD). These molecular changes coincided with elevated NO2 and NO3 levels and finely tuned hydrogen peroxide dynamics, underpinning redox signaling crucial for seed activation and stress resilience. Our findings establish plasma-generated NO-enriched water as an innovative, eco-friendly technology that leverages redox and hormone crosstalk to stimulate germination and early growth, offering promising applications in sustainable agriculture. Full article
(This article belongs to the Special Issue Plasma-Based Technologies for Food Safety and Health Enhancement)
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26 pages, 3811 KiB  
Article
Development and Validation of Multi-Locus GWAS-Based KASP Markers for Maize Ustilago maydis Resistance
by Tao Shen, Huawei Gao, Chao Wang, Yunxiao Zheng, Weibin Song, Peng Hou, Liying Zhu, Yongfeng Zhao, Wei Song and Jinjie Guo
Plants 2025, 14(15), 2315; https://doi.org/10.3390/plants14152315 - 26 Jul 2025
Viewed by 370
Abstract
Corn smut, caused by Ustilago maydis, significantly threatens maize production. This study evaluated 199 maize inbred lines at the seedling stage under greenhouse conditions for resistance to U. maydis, identifying 39 highly resistant lines. A genome-wide association study (GWAS) using the [...] Read more.
Corn smut, caused by Ustilago maydis, significantly threatens maize production. This study evaluated 199 maize inbred lines at the seedling stage under greenhouse conditions for resistance to U. maydis, identifying 39 highly resistant lines. A genome-wide association study (GWAS) using the mrMLM model detected 19 significant single-nucleotide polymorphism (SNP) loci. Based on a linkage disequilibrium (LD) decay distance of 260 kb, 226 candidate genes were identified. Utilizing the significant loci chr1_244281660 and chr5_220156746, two kompetitive allele-specific PCR (KASP) markers were successfully developed. A PCR-based sequence-specific oligonucleotide probe hybridization technique applied to the 199 experimental lines and 60 validation lines confirmed polymorphism for both markers, with selection efficiencies of 48.12% and 43.33%, respectively. The tested materials were derived from foundational inbred lines of domestic and foreign origin. Analysis of 39 highly resistant lines showed that the advantageous alleles carrying thymine/cytosine (T/C) predominated at frequencies of 94.87% and 53.84%, respectively. The genotype TTCC conferred high resistance, while CCTT was highly susceptible. The resistance exhibited high heritability and significant gene-by-environment interaction. This work systematically dissects the genetic basis of common smut resistance in maize, identifies favorable alleles, and provides a novel KASP marker-based strategy for developing disease-resistant germplasm. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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14 pages, 1333 KiB  
Article
Reliable RT-qPCR Normalization in Polypogon fugax: Reference Gene Selection for Multi-Stress Conditions and ACCase Expression Analysis in Herbicide Resistance
by Yufei Zhao, Xu Yang, Qiang Hu, Jie Zhang, Sumei Wan and Wen Chen
Agronomy 2025, 15(8), 1813; https://doi.org/10.3390/agronomy15081813 - 26 Jul 2025
Viewed by 240
Abstract
Asia minor bluegrass (Polypogon fugax), a widespread Poaceae weed, exhibits broad tolerance to abiotic stresses. Validated reference genes (RGs) for reliable RT-qPCR normalization in this ecologically and agriculturally significant species remain unidentified. This study identified eight candidate RGs using transcriptome data [...] Read more.
Asia minor bluegrass (Polypogon fugax), a widespread Poaceae weed, exhibits broad tolerance to abiotic stresses. Validated reference genes (RGs) for reliable RT-qPCR normalization in this ecologically and agriculturally significant species remain unidentified. This study identified eight candidate RGs using transcriptome data from seedling tissues. We assessed the expression stability of these eight RGs across various abiotic stresses and developmental stages using Delta Ct, BestKeeper, geNorm, and NormFinder algorithms. A comprehensive stability ranking was generated using RefFinder, with validation performed using the target genes COR413 and P5CS. Results identified EIF4A and TUB as the optimal RG combination for normalizing gene expression during heat stress, cold stress, and growth stages. EIF4A and ACT were most stable under drought stress, EIF4A and 28S under salt stress, and EIF4A and EF-1 under cadmium (Cd) stress. Furthermore, EIF4A and UBQ demonstrated optimal stability under herbicide stress. Additionally, application of validated RGs revealed higher acetyl-CoA carboxylase gene (ACCase) expression in one herbicide-resistant population, suggesting target-site gene overexpression contributes to resistance. This work presents the first systematic evaluation of RGs in P. fugax. The identified stable RGs provide essential tools for future gene expression studies on growth and abiotic stress responses in this species, facilitating deeper insights into the molecular basis of its weediness and adaptability. Full article
(This article belongs to the Special Issue Adaptive Evolution in Weeds: Molecular Basis and Management)
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26 pages, 3318 KiB  
Article
Responses of Tomato Growth and Soil Environment Properties to Integrated Deficit Water-Biogas Slurry Application Under Indirect Subsurface Drip Irrigation
by Peng Xiang, Jian Zheng, Panpan Fan, Yan Wang and Fenyan Ma
Agriculture 2025, 15(15), 1601; https://doi.org/10.3390/agriculture15151601 - 25 Jul 2025
Viewed by 315
Abstract
To explore the feasibility of integrated deficit water-biogas slurry irrigation under indirect subsurface drip irrigation, three deficit irrigation levels (60%FC, 70%FC, and 80%FC; FC represents field capacity) were established during the three growth stages of tomatoes. The results indicated that biogas slurry irrigation [...] Read more.
To explore the feasibility of integrated deficit water-biogas slurry irrigation under indirect subsurface drip irrigation, three deficit irrigation levels (60%FC, 70%FC, and 80%FC; FC represents field capacity) were established during the three growth stages of tomatoes. The results indicated that biogas slurry irrigation treatments increased the soil organic matter content in the root zone and water use efficiency (WUE) and reduced soil pH. As the degree of deficit increased, the plant height and stem diameter of tomatoes decreased significantly (p < 0.05), particularly during the seedling and flowering-fruiting stages. A mild deficit during the seedling stage was beneficial for subsequent plant growth, yielding maximum leaf area (6871.42 cm2 plant−1). Moderate deficit treatment at the seedling stage maximized yield, which was 19.79% higher than the control treatment in 2020 and 19.22% higher in 2021. The WUE of severe deficit treatment at the maturity stage increased by 26.6% (2020) and 31.04% (2021) compared to the control treatment. Comprehensive evaluation using TOPSIS combined with the weighted method revealed that severe deficit treatment at the maturity stage provided the best comprehensive benefits for tomatoes. In summary, deficit irrigation at different growth stages positively influenced tomato growth, quality, and soil environment in response to water-biogas slurry irrigation. Full article
(This article belongs to the Section Agricultural Water Management)
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21 pages, 94814 KiB  
Article
MaizeStar-YOLO: Precise Detection and Localization of Seedling-Stage Maize
by Taotao Chu, Hainie Zha, Yuanzhi Wang, Zhaosheng Yao, Xingwang Wang, Chenliang Wu and Jianfeng Liao
Agronomy 2025, 15(8), 1788; https://doi.org/10.3390/agronomy15081788 - 25 Jul 2025
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Abstract
Efficient detection and localization of maize seedlings in complex field environments is essential for accurate plant segmentation and subsequent three-dimensional morphological reconstruction. To overcome the limited accuracy and high computational cost of existing models, we propose an enhanced architecture named MaizeStar-YOLO. The redesigned [...] Read more.
Efficient detection and localization of maize seedlings in complex field environments is essential for accurate plant segmentation and subsequent three-dimensional morphological reconstruction. To overcome the limited accuracy and high computational cost of existing models, we propose an enhanced architecture named MaizeStar-YOLO. The redesigned backbone integrates a novel C2F_StarsBlock to improve multi-scale feature fusion, while a PKIStage module is introduced to enhance feature representation under challenging field conditions. Evaluations on a diverse dataset of maize seedlings show that our model achieves a mean average precision (mAP) of 92.8%, surpassing the YOLOv8 baseline by 3.6 percentage points, while reducing computational complexity to 3.0 GFLOPs, representing a 63% decrease. This efficient and high-performing framework enables precise plant–background segmentation and robust three-dimensional feature extraction for morphological analysis. Additionally, it supports downstream applications such as pest and disease diagnosis and targeted agricultural interventions. Full article
(This article belongs to the Section Precision and Digital Agriculture)
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21 pages, 1285 KiB  
Article
Stage-Specific Transcriptomic Insights into Seed Germination and Early Development in Camellia oleifera Abel.
by Zhen Zhang, Caixia Liu, Ying Zhang, Zhilong He, Longsheng Chen, Chengfeng Xun, Yushen Ma, Xiaokang Yuan, Yanming Xu and Rui Wang
Plants 2025, 14(15), 2283; https://doi.org/10.3390/plants14152283 - 24 Jul 2025
Viewed by 228
Abstract
Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. [...] Read more.
Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article
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