Plants

16 pages, 1894 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of DNA Methyltransferase and Demethylase Gene Families in Sweet Potato and Its Diploid Relative

by Songtao Yang, Shuai Qiao, Yan Yang, Fang Wang, Wei Song, Wenfang Tan, Yongping Li and Youlin Zhu

Plants 2025, 14(11), 1735; https://doi.org/10.3390/plants14111735 - 5 Jun 2025

Viewed by 390

Abstract

DNA methylation is a conserved and vital epigenetic modification that plays essential roles in plant growth, development, and responses to environmental stress. Cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases) are key regulators of DNA methylation dynamics. However, a comprehensive characterization of these [...] Read more.

DNA methylation is a conserved and vital epigenetic modification that plays essential roles in plant growth, development, and responses to environmental stress. Cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases) are key regulators of DNA methylation dynamics. However, a comprehensive characterization of these gene families in sweet potato has remained elusive. In this study, we systematically identified and analyzed eight C5-MTase and five dMTase genes in the genomes of diploid (Ipomoea trifida, 2n = 2x = 30) and autohexaploid (Ipomoea batatas, 2n = 6x = 90) sweet potato. Phylogenetic, structural, and synteny analyses revealed a high degree of conservation among these genes, suggesting their essential roles during evolution. Promoter analysis uncovered multiple cis-acting elements, particularly those responsive to light and hormones. In addition, we examined the expression profiling of IbC5-MTases and IbdMTases genes during storage root development, revealing that several were highly expressed during the early and rapid expansion stages. These findings suggest that C5-MTases and dMTases may contribute to the regulation of storage root formation in sweet potato through epigenetic mechanisms, offering valuable insights for future functional studies and epigenetic breeding efforts. Full article

(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)

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26 pages, 7011 KiB

Open AccessArticle

Assessment of Different Irrigation Thresholds to Optimize the Water Use Efficiency and Yield of Potato (Solanum tuberosum L.) Under Field Conditions

by Rodrigo Mora-Sanhueza, Ricardo Tighe-Neira, Rafael López-Olivari and Claudio Inostroza-Blancheteau

Plants 2025, 14(11), 1734; https://doi.org/10.3390/plants14111734 - 5 Jun 2025

Viewed by 323

Abstract

The potato (Solanum tuberosum L.) is highly dependent on water availability, with physiological sensitivity varying throughout its phenological cycle. In the context of increasing water scarcity and greater climate variability, identifying critical periods where water stress negatively impacts productivity and tuber quality [...] Read more.

The potato (Solanum tuberosum L.) is highly dependent on water availability, with physiological sensitivity varying throughout its phenological cycle. In the context of increasing water scarcity and greater climate variability, identifying critical periods where water stress negatively impacts productivity and tuber quality is essential. This study evaluated the physiological response of potatoes under different deficit irrigation strategies in field conditions, and aimed to determine the irrigation reduction thresholds that optimize water use efficiency without significantly compromising yield. Five irrigation regimes were applied: well-watered (T1; irrigation was applied when the volumetric soil moisture content was close to 35% of total water available), 130% of T1 (T2, 30% more than T1), 75% of T1 (T3), 50% of T1 (T4), and 30% of T1 (T5). Key physiological parameters were monitored, including gas exchange (net photosynthesis, stomatal conductance, and transpiration), chlorophyll fluorescence (Fv’/Fm’, ΦPSII, electron transport rate), and photosynthetic pigment content, at three critical phenological phases: tuberization, flowering, and fruit set. The results indicate that water stress during tuberization and flowering significantly reduced photosynthetic efficiency, with decreases in stomatal conductance (gs), effective quantum efficiency of PSII (ΦPSII), and electron transport rate (ETR). In contrast, moderate irrigation reduction (75%) lowered the seasonal application of water by ~25% (≈80 mm ha⁻¹) while maintaining commercial yield and tuber quality comparable to the fully irrigated control. Intrinsic water use efficiency increased by 18 ± 4% under this regime. These findings highlight the importance of irrigation management based on crop phenology, prioritizing water supply during the stages of higher physiological sensitivity and allowing irrigation reductions in less critical phases. In a scenario of increasing water limitations, this strategy enhances water use efficiency while ensuring the production of tubers with optimal commercial quality, promoting more sustainable agricultural management practices. Full article

(This article belongs to the Special Issue Mitigation Strategies and Tolerance of Plants to Abiotic Stresses—2nd Edition)

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14 pages, 1184 KiB

Open AccessArticle

Quantification of Phenolic Compounds by HPLC/DAD and Evaluation of the Antioxidant, Antileishmanial, and Cytotoxic Activities of Ethanolic Extracts from the Leaves and Bark of Sarcomphalus joazeiro (Mart.)

by Natália Kelly Gomes de Carvalho, Débora Odília Duarte Leite, Aracélio Viana Colares, Fernando Almeida Souza, Kátia da Silva Calabrese, Gerson Javier Torres Salazar, Joice Barbosa do Nascimento, Mariana Pereira da Silva, Fabiola Fernandes Galvão Rodrigues and José Galberto Martins da Costa

Plants 2025, 14(11), 1733; https://doi.org/10.3390/plants14111733 - 5 Jun 2025

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Abstract

Sarcomphalus joazeiro (Mart.) is a promising candidate for the formulation of new therapies against parasitic infections. This study aimed to quantify the content of phenolic compounds and evaluate the antioxidant, antileishmanial, and cytotoxic potential of ethanolic extracts of the leaves (EELSJ) and bark [...] Read more.

Sarcomphalus joazeiro (Mart.) is a promising candidate for the formulation of new therapies against parasitic infections. This study aimed to quantify the content of phenolic compounds and evaluate the antioxidant, antileishmanial, and cytotoxic potential of ethanolic extracts of the leaves (EELSJ) and bark (EEBSJ) of S. joazeiro. Quantification of phenolic acids (caffeic acid, p-coumaric acid, ferulic acid, cinnamic acid) and flavonoids (naringenin, pinocembrin, and apigenin) was performed by high-performance liquid chromatography with a diode array detector (HPLC-DAD). The extracts were subjected to antioxidant assays, including Fe³⁺ reduction, Fe²⁺ chelation, and inhibition of oxidative degradation of deoxyribose (2-DR). The antileishmanial activity was evaluated against promastigote forms of Leishmania amazonensis, while cytotoxicity was assessed in J774.G8 macrophages. Among the biological effects evaluated, EELSJ showed potent hydroxyl radical (•OH) scavenging activity, with IC₅₀ < 10 µg/mL, which potentially correlates with its phenolic acid and flavonoid content (0.7066 mg/g). In comparison, EEBSJ showed a lower phenolic content (0.197 mg/g) and demonstrated Fe²⁺ chelating activity (IC₅₀ = 14.96 ± 0.0477 µg/mL). EELSJ also exhibited antileishmanial activity against L. amazonensis (IC₅₀ = 246.20 µg/mL), with low cytotoxicity (CC₅₀ = 343.3 µg/mL; SI = 1.39), whereas EEBSJ showed minimal antileishmanial effect and marked cytotoxicity toward J774.G8 macrophages (CC₅₀ = 5.866 µg/mL). The leaves of S. joazeiro stand out as the most promising plant organ for future investigations. Future studies should focus on investigating their action mechanisms in more detail. Full article

(This article belongs to the Special Issue Bioprospecting the Efficacy and Safety of Natural Products from Plants)

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19 pages, 2614 KiB

Open AccessArticle

Influence of Microclimatic Variations on Morphological Traits of Ferns in Urban Forests of Central Veracruz, Mexico

by Jessica G. Landeros-López, Thorsten Krömer, Jorge A. Gómez-Díaz, Noé Velázquez-Rosas and César I. Carvajal-Hernández

Plants 2025, 14(11), 1732; https://doi.org/10.3390/plants14111732 - 5 Jun 2025

Viewed by 347

Abstract

Urban forests are remnants of forest habitats within urban areas. Their structural alterations create stressful microclimatic conditions that can influence the morphology of sensitive plants, such as ferns. This study analyzed variations in the morphological traits of ferns in four urban forest sites [...] Read more.

Urban forests are remnants of forest habitats within urban areas. Their structural alterations create stressful microclimatic conditions that can influence the morphology of sensitive plants, such as ferns. This study analyzed variations in the morphological traits of ferns in four urban forest sites in central Veracruz, Mexico, considering the microclimatic differences arising from vegetation structure. Temperature, humidity, canopy openness, and radiation were measured, along with eight foliar traits, while assessing the impact of site and habit (terrestrial or epiphytic) on the response. Sites with greater alterations in vegetation structure exhibited increased canopy openness, solar radiation, temperature, and a higher number of days with lower relative humidity. In these sites, leaves showed an increase in dry matter content and vein density, indicating a greater investment in resource storage and structural resistance. In the less-disturbed sites, terrestrial ferns demonstrated larger leaf area and specific leaf area, suggesting greater growth potential. Conversely, epiphytes generally had smaller leaves, which could represent an adaptive advantage for these species. The results also suggest a process of biotic homogenization within this plant group, reflecting a similar morphological response, except for indicator species restricted to less disturbed sites. Thus, this study reveals that microclimatic variations induced by urbanization significantly affect plant morphology and, ultimately, species diversity. Full article

(This article belongs to the Special Issue Epiphytic Plants: Perspective on Their Diversity, Distribution, Systematics and Conservation in the Changing Environment)

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15 pages, 3853 KiB

Open AccessArticle

Enhanced Stress Tolerance in Rice Through Overexpression of a Chimeric Glycerol-3-Phosphate Dehydrogenase (OEGD)

by Jinhong Wu, Meiyao Chen, Fangwen Yang, Jing Han, Xiaosong Ma, Tianfei Li, Hongyan Liu, Bin Liang and Shunwu Yu

Plants 2025, 14(11), 1731; https://doi.org/10.3390/plants14111731 - 5 Jun 2025

Viewed by 188

Abstract

Crop productivity is severely constrained by abiotic and biotic stresses, necessitating innovative strategies to enhance stress resilience. Glycerol-3-phosphate (G3P) is a central metabolite in carbohydrate and lipid metabolism, playing crucial roles in stress responses. In this study, we engineered a novel glycerol-3-phosphate dehydrogenase [...] Read more.

Crop productivity is severely constrained by abiotic and biotic stresses, necessitating innovative strategies to enhance stress resilience. Glycerol-3-phosphate (G3P) is a central metabolite in carbohydrate and lipid metabolism, playing crucial roles in stress responses. In this study, we engineered a novel glycerol-3-phosphate dehydrogenase (GPDH) gene, designated OEGD, by fusing the N-terminal NAD-binding domain of rice OsGPDH1 with the feedback-resistant C-terminal catalytic domain of Escherichia coli gpsA. Overexpression of OEGD in rice enhanced tolerance to drought, phosphorus deficiency, high temperature, and cadmium (Cd²⁺) stresses, while also improving plant growth and yield under drought stress at the adult stage. Notably, the accumulation of glycerol-3-phosphate (G3P) and activities of antioxidant enzymes (SOD, POD, CAT) were significantly elevated in the transgenic plants following osmotic stimuli, and fatty acid profiles were altered, favoring stress adaptation. Transcriptomic analyses revealed that OEGD modulates cell wall biogenesis, reactive oxygen species (ROS) scavenging, and lipid metabolism pathways, with minimal disruption to core G3P metabolic genes. These findings highlight the potential of OEGD as a valuable genetic resource for improving stress resistance in rice. Full article

(This article belongs to the Special Issue Plants for Extreme and Changing Environments: Domestication, Evolution, Crop Breeding and Genetics, 2nd Edition)

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24 pages, 2378 KiB

Open AccessReview

Deciphering Seed Deterioration: Molecular Insights and Priming Strategies for Revitalizing Aged Seeds

by Weigeng Xing, Yi Li, Linyan Zhou, Hao Hong, Yuan Liu, Shuailong Luo, Jialong Zou, Yan Zhao, Yanfei Yang, Zhenjiang Xu and Bin Tan

Plants 2025, 14(11), 1730; https://doi.org/10.3390/plants14111730 - 5 Jun 2025

Viewed by 357

Abstract

Seed deterioration is an inevitable process during storage, characterized by a gradual loss of germination capacity and eventual seed death, which poses challenges to seed longevity and the preservation of genetic resources. Understanding the molecular mechanisms driving seed aging and inherent resistance pathways, [...] Read more.

Seed deterioration is an inevitable process during storage, characterized by a gradual loss of germination capacity and eventual seed death, which poses challenges to seed longevity and the preservation of genetic resources. Understanding the molecular mechanisms driving seed aging and inherent resistance pathways, alongside developing innovative rejuvenation strategies for deteriorated seeds, is crucial for agricultural sustainability and germplasm banking. This review systematically examines (1) redox-regulated deterioration pathways involving reactive oxygen species (ROS) and macromolecular damage cascades, (2) anti-deterioration mechanisms mediated by the antioxidant system and macromolecular repair mechanisms, (3) genetic–epigenetic networks governing seed aging resistance, particularly ABA- and IAA-mediated signaling through ABI3/ABI5/LEC1 regulons, and (4) technological advances in seed priming that restore aged seeds via metabolic resetting and repair potentiation. By integrating multi-omics insights with physiological evidence, we propose a hierarchical model of seed deterioration and establish mechanistic links between priming interventions and longevity enhancement. These insights offer a theoretical framework for cultivating anti-deterioration crop varieties and developing seed longevity-enhancement technologies. Full article

(This article belongs to the Section Crop Physiology and Crop Production)

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21 pages, 5449 KiB

Open AccessArticle

ELD-YOLO: A Lightweight Framework for Detecting Occluded Mandarin Fruits in Plant Research

by Xianyao Wang, Yutong Huang, Siyu Wei, Weize Xu, Xiangsen Zhu, Jiong Mu and Xiaoyan Chen

Plants 2025, 14(11), 1729; https://doi.org/10.3390/plants14111729 - 5 Jun 2025

Viewed by 198

Abstract

Mandarin fruit detection provides crucial technical support for yield prediction and the precise identification and harvesting of mandarin fruits. However, challenges such as occlusion from leaves or branches, the presence of small or partially visible fruits, and limitations in model efficiency pose significant [...] Read more.

Mandarin fruit detection provides crucial technical support for yield prediction and the precise identification and harvesting of mandarin fruits. However, challenges such as occlusion from leaves or branches, the presence of small or partially visible fruits, and limitations in model efficiency pose significant obstacles in a complex orchard environment. To tackle these issues, we propose ELD-YOLO, a lightweight detection framework designed to enhance edge detail preservation and improve the detection of small and occluded fruits. Our method incorporates edge-aware processing to strengthen feature representation, introduces a streamlined detection head that balances accuracy with computational cost, and employs an adaptive upsampling strategy to minimize information loss during feature scaling. Experiments on a mandarin fruit dataset show that ELD-YOLO achieves a precision of 89.7%, a recall of 83.7%, an mAP@50 of 92.1%, and an mAP@50:95 of 68.6% while reducing the parameter count by 15.4% compared with the baseline. These results demonstrate that ELD-YOLO provides an effective and efficient solution for fruit detection in complex orchard scenarios. Full article

(This article belongs to the Special Issue Advances in Artificial Intelligence for Plant Research)

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18 pages, 2180 KiB

Open AccessArticle

Identification of Quantitative Trait Loci for Grain Quality Traits in a Pamyati Azieva × Paragon Bread Wheat Mapping Population Grown in Kazakhstan

by Akerke Amalova, Simon Griffiths, Aigul Abugalieva, Saule Abugalieva and Yerlan Turuspekov

Plants 2025, 14(11), 1728; https://doi.org/10.3390/plants14111728 - 5 Jun 2025

Viewed by 225

Abstract

High grain quality is a key target in wheat breeding and is influenced by genetic and environmental factors. This study evaluated 94 recombinant inbred lines (RILs) from a Pamyati Azieva × Paragon (PA × P) mapping population grown in two regions in Kazakhstan [...] Read more.

High grain quality is a key target in wheat breeding and is influenced by genetic and environmental factors. This study evaluated 94 recombinant inbred lines (RILs) from a Pamyati Azieva × Paragon (PA × P) mapping population grown in two regions in Kazakhstan to assess the genetic basis of six grain quality traits: the test weight per liter (TWL, g/L), grain protein content (GPC, %), gluten content (GC, %), gluten deformation index in flour (GDI, unit), sedimentation value in a 2% acetic acid solution (SV, mL), and grain starch content (GSC, %). A correlation analysis revealed a trade-off between protein and starch accumulation and an inverse relationship between grain quality and yield components. Additionally, GPC exhibited a negative correlation with yield per square meter (YM2), underscoring the challenge of simultaneously improving grain quality and yield. With the use of the QTL Cartographer statistical package, 71 quantitative trait loci (QTLs) were identified for the six grain quality traits, including 20 QTLs showing stability across multiple environments. Notable stable QTLs were detected for GPC on chromosomes 4A, 5B, 6A, and 7B and for GC on chromosomes 1D and 6A, highlighting their potential for marker-assisted selection (MAS). A major QTL found on chromosome 1D (QGDI-PA × P.ipbb-1D.1, LOD 19.4) showed a strong association with gluten deformation index, emphasizing its importance in improving flour quality. A survey of published studies on QTL identification in common wheat suggested the likely novelty of 12 QTLs identified for GDI (five QTLs), TWL (three QTLs), SV, and GSC (two QTLs each). These findings underscore the need for balanced breeding strategies that optimize grain composition while maintaining high productivity. With the use of SNP markers associated with the identified QTLs for grain quality traits, the MAS approach can be implemented in wheat breeding programs. Full article

(This article belongs to the Special Issue QTL Mapping of Seed Quality Traits in Crops, 2nd Edition)

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17 pages, 563 KiB

Open AccessReview

Harnessing Artificial Intelligence and Machine Learning for Identifying Quantitative Trait Loci (QTL) Associated with Seed Quality Traits in Crops

by My Abdelmajid Kassem

Plants 2025, 14(11), 1727; https://doi.org/10.3390/plants14111727 - 5 Jun 2025

Viewed by 229

Abstract

Seed quality traits, such as seed size, oil and protein content, mineral accumulation, and morphological characteristics, are crucial for enhancing crop productivity, nutritional value, and marketability. Traditional quantitative trait loci (QTL) mapping methods, such as linkage analysis and genome-wide association studies (GWAS), have [...] Read more.

Seed quality traits, such as seed size, oil and protein content, mineral accumulation, and morphological characteristics, are crucial for enhancing crop productivity, nutritional value, and marketability. Traditional quantitative trait loci (QTL) mapping methods, such as linkage analysis and genome-wide association studies (GWAS), have played fundamental role in identifying loci associated with these complex traits. However, these approaches often struggle with high-dimensional genomic data, polygenic inheritance, and genotype-by-environment (GXE) interactions. Recent advances in artificial intelligence (AI) and machine learning (ML) provide powerful alternatives that enable more accurate trait prediction, robust marker-trait associations, and efficient feature selection. This review presents an integrated overview of AI/ML applications in QTL mapping and seed trait prediction, highlighting key methodologies such as LASSO regression, Random Forest, Gradient Boosting, ElasticNet, and deep learning techniques including convolutional neural networks (CNNs) and graph neural networks (GNNs). A case study on soybean seed mineral nutrients accumulation illustrates the effectiveness of ML models in identifying significant SNPs on chromosomes 8, 9, and 14. LASSO and ElasticNet consistently achieved superior predictive accuracy compared to tree-based models. Beyond soybean, AI/ML methods have enhanced QTL detection in wheat, lettuce, rice, and cotton, supporting trait dissection across diverse crop species. I also explored AI-driven integration of multi-omics data—genomics, transcriptomics, metabolomics, and phenomics—to improve resolution in QTL mapping. While challenges remain in terms of model interpretability, biological validation, and computational scalability, ongoing developments in explainable AI, multi-view learning, and high-throughput phenotyping offer promising avenues. This review underscores the transformative potential of AI in accelerating genomic-assisted breeding and developing high-quality, climate-resilient crop varieties. Full article

(This article belongs to the Special Issue QTL Mapping of Seed Quality Traits in Crops, 2nd Edition)

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24 pages, 13679 KiB

Open AccessArticle

Seed Nanopriming with ZnO and SiO₂ Enhances Germination, Seedling Vigor, and Antioxidant Defense Under Drought Stress

by Erick H. Ochoa-Chaparro, Juan J. Patiño-Cruz, Julio C. Anchondo-Páez, Sandra Pérez-Álvarez, Celia Chávez-Mendoza, Luis U. Castruita-Esparza, Ezequiel Muñoz Márquez and Esteban Sánchez

Plants 2025, 14(11), 1726; https://doi.org/10.3390/plants14111726 - 5 Jun 2025

Viewed by 267

Abstract

Drought stress is one of the main factors limiting seed germination and seedling establishment in field crops such as jalapeño peppers (Capsicum annuum L.). Nanopriming, a seed improvement technique using nanoparticle suspensions, has emerged as a sustainable approach to improving water use [...] Read more.

Drought stress is one of the main factors limiting seed germination and seedling establishment in field crops such as jalapeño peppers (Capsicum annuum L.). Nanopriming, a seed improvement technique using nanoparticle suspensions, has emerged as a sustainable approach to improving water use efficiency during the early stages of development. This study evaluated the effects of zinc oxide (ZnO, 100 mg·L⁻¹), silicon dioxide (SiO₂, 10 mg·L⁻¹), and their combination (ZnO + SiO₂), stabilized with chitosan, on the germination yield and drought tolerance of jalapeño seeds under mannitol-induced water stress (0%, 15%, and 30%). Compared to the hydroprimed control (T1), nanoparticle treatments consistently improved seed yield. Priming with ZnO (T2) increased the germination percentage by up to 25%, priming with SiO₂ (T3) improved the germination rate by 34%, and the combined treatment (T4: ZnO + SiO₂) improved the fresh weight of the seedlings by 40%. Proline accumulation increased 7.5 times, antioxidant capacity (DPPH) increased 6.5 times, and total phenol content increased 4.8 times in the combined treatment. Flavonoid levels also showed notable increases, suggesting enhanced antioxidant defense. These results clearly demonstrate the superior efficacy of nanoparticle pretreatment compared to conventional hydraulic pretreatment, especially under drought conditions. Multivariate analysis further highlighted the synergistic role of ZnO and SiO₂ in improving osmolite accumulation, antioxidant activity, and water use efficiency. Nanopriming with ZnO and SiO₂ offers a promising, economical, and scalable strategy to improve germination, early growth, and drought resistance in jalapeño pepper cultivation under semi-arid conditions. Full article

(This article belongs to the Special Issue Management and Efficient Utilization of Water and Fertilizer in Field Crops—3rd Edition)

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24 pages, 7431 KiB

Open AccessArticle

Phytochemical Characterization, Antioxidant Activity, and Anti-Melanoma Mechanism of Flower Buds of Magnolia biondii Pamp.

by Shanshan Li, Gege Jiao, Penghui Ou, Xiaona Zhang, Yang Yu, Yihui Wang, Qingping Yao and Wei Wang

Plants 2025, 14(11), 1725; https://doi.org/10.3390/plants14111725 - 5 Jun 2025

Viewed by 229

Abstract

The flower buds of Magnolia biondii Pamp. (MBP), one of the botanical sources of Xinyi (Flos Magnoliae), are widely used in traditional medicine; however, their potential role in melanoma treatment remains unexplored. In this study, the phytochemical composition, antioxidant activity, and [...] Read more.

The flower buds of Magnolia biondii Pamp. (MBP), one of the botanical sources of Xinyi (Flos Magnoliae), are widely used in traditional medicine; however, their potential role in melanoma treatment remains unexplored. In this study, the phytochemical composition, antioxidant activity, and anti-melanoma mechanisms of MBP extracts were systematically investigated. Phytochemical profiling using UHPLC-Q-Exactive Orbitrap MS identified 26 bioactive compounds. The ethanol extract exhibited high total flavonoid and polyphenol contents, correlating with enhanced antioxidant capacity as demonstrated by DPPH and ABTS assays. Network pharmacology analysis highlighted the JAK/STAT signaling pathway, identifying STAT3 and STAT1 as core targets. Western blot analysis confirmed MBP significantly inhibited the phosphorylation of JAK1 and STAT1 in melanoma cells. Connectivity Map (CMap) and network analyses further pinpointed naringenin as a primary active constituent. In vitro assays demonstrated that MBP and naringenin inhibited the proliferation and migration of A375 and B16F10 melanoma cells, while exhibiting relatively low cytotoxicity toward normal keratinocytes. Molecular docking and dynamics simulations revealed strong and stable binding interactions between naringenin and JAK1/STAT1 proteins. These findings collectively support MBP and naringenin as promising candidates for melanoma treatment, providing mechanistic evidence for their targeted activity and laying a foundation for future research and clinical applications. Full article

(This article belongs to the Special Issue Biological Activity of Plant Extracts: Applications in Modern Pharmacology)

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14 pages, 1107 KiB

Open AccessArticle

PlantDeepMeth: A Deep Learning Model for Predicting DNA Methylation States in Plants

by Zhongwei Guo, Wenyuan Fan, Chengcheng Cai, Kang Zhang, Xilin Hou, Ying Li and Feng Cheng

Plants 2025, 14(11), 1724; https://doi.org/10.3390/plants14111724 - 5 Jun 2025

Viewed by 197

Abstract

Cytosine DNA methylation (5mCs) is an important epigenetic modification in genomic research. However, the methylation states of some cytosine sites are not available due to the limitations of different studies, and there are few tools developed to deal with this problem, especially in [...] Read more.

Cytosine DNA methylation (5mCs) is an important epigenetic modification in genomic research. However, the methylation states of some cytosine sites are not available due to the limitations of different studies, and there are few tools developed to deal with this problem, especially in plants, which have more methylation types than animals. Here, we report PlantDeepMeth, a novel deep learning model that utilizes deep learning to predict DNA methylation states in plants. The evaluation of PlantDeepMeth on known cytosine sites in both the Brassica rapa and Arabidopsis thaliana genomes shows good performance in predicting methylation states, indicating that the tool is good at learning patterns for methylation imputation. Motif analysis of the model’s predictions identified specific motifs associated with hypo- or hyper-methylation states in B. rapa and A. thaliana, further revealing key regulatory patterns captured by the model. Moreover, cross-species validation between B. rapa and A. thaliana demonstrated the generalizability of PlantDeepMeth, with the model maintaining high performance across different plant species. These results highlight the effectiveness of PlantDeepMeth and demonstrate the potential of deep learning to advance plant genomics research. Full article

(This article belongs to the Special Issue Bioinformatics and Functional Genomics in Modern Plant Science)

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30 pages, 1209 KiB

Open AccessReview

Complexity Meets Risk—The Next Generation of Genome-Edited Plants Challenges Established Concepts for Environmental Risk Assessment in the EU

by Marion Dolezel, Marianne Miklau, Andreas Heissenberger, Iris Kroeger and Mathias Otto

Plants 2025, 14(11), 1723; https://doi.org/10.3390/plants14111723 - 5 Jun 2025

Viewed by 273

Abstract

For 20 years, the environmental risk assessment (ERA) of genetically modified plants (GMPs) has used a comparative assessment approach, comparing the GMP to presumably safe and familiar non-modified plant varieties. With new genomic techniques, it is now possible to design complex GMP applications [...] Read more.

For 20 years, the environmental risk assessment (ERA) of genetically modified plants (GMPs) has used a comparative assessment approach, comparing the GMP to presumably safe and familiar non-modified plant varieties. With new genomic techniques, it is now possible to design complex GMP applications with systemic metabolic changes, resulting in novel plant phenotypes. These plant phenotypes can exhibit profoundly altered morphological, physiological, or compositional characteristics, intentionally lacking equivalence with parental plants and non-modified comparators. Through the analysis of case studies involving GMPs with modifications of complex metabolic pathways, we evaluate the current practice of the comparative safety assessment approach applied in ERA in the European Union and its ability to inform ERA, particularly regarding environmental risks. Our findings show that the existing approach has notable weaknesses when applied to complex GMP applications. We suggest complementing ERA with a hypothesis-driven assessment approach that considers various protection goals and relies on whole-plant experimental assessments to draw risk conclusions. As plant modifications become increasingly complex, such as the development of synthetic biology plants, conducting ecologically realistic assessments will be crucial for future ERA. Full article

(This article belongs to the Special Issue Biosafety and Ecological Assessment of Genetically Engineered and Edited Crops—2nd Edition)

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25 pages, 12268 KiB

Open AccessArticle

Modeling Growth Dynamics of Lemna minor: Process Optimization Considering the Influence of Plant Density and Light Intensity

by Jannis von Salzen, Finn Petersen, Andreas Ulbrich and Stefan Streif

Plants 2025, 14(11), 1722; https://doi.org/10.3390/plants14111722 - 5 Jun 2025

Viewed by 260

Abstract

The production of duckweed (Lemnaceae) as a novel protein source could make a valuable contribution to human nutrition. The greatly reduced habitus of duckweed enables simple cultivation with extremely low space requirements, making this free-floating freshwater plant ideal for substrate-free and vertical cultivation [...] Read more.

The production of duckweed (Lemnaceae) as a novel protein source could make a valuable contribution to human nutrition. The greatly reduced habitus of duckweed enables simple cultivation with extremely low space requirements, making this free-floating freshwater plant ideal for substrate-free and vertical cultivation in controlled environment agriculture. Of particular importance in the design of a plant-producing Indoor Vertical Farming process is the determination of light intensity, as artificial lighting is generally the most energy-intensive feature of daylight-independent cultivation systems. In order to make the production process both cost-effective and low emission in the future, it is, therefore, crucial to understand and mathematically describe the primary metabolism, in particular the light utilization efficiency. To achieve this, a growth model was developed that mathematically describes the combined effects of plant density and light intensity on the growth rate of Lemna minor L. and physiologically explains the intraspecific competition of plants for light through mutual shading. Furthermore, the growth model can be utilized to derive environmental and process parameters, including optimum harvest quantities and efficiency-optimized light intensities to improve the production process. Full article

(This article belongs to the Special Issue Duckweed: Research Meets Applications—2nd Edition)

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14 pages, 866 KiB

Open AccessArticle

“Secreted in Xylem” Genes (SIX Genes): Relationship to the Aggressiveness of Fusarium oxysporum f. sp. albedinis

by Abdelhi Dihazi, Youness Jouihri, Ahmed Tadlaoui-Ouafi, Mohamed Najib Alfeddy, Cherkaoui El Modafar, Hassan Dihazi, Abdellatif El Meziane, Mohammad Sayari and Fouad Daayf

Plants 2025, 14(11), 1721; https://doi.org/10.3390/plants14111721 - 5 Jun 2025

Viewed by 203

Abstract

Fusarium oxysporum f. sp. Albedinis (Foa) is the causal agent of Bayoud disease, responsible for the loss of 75% of date palm trees in Morocco and posing a threat to its cultivation across North Africa. This study examined ten Foa isolated [...] Read more.

Fusarium oxysporum f. sp. Albedinis (Foa) is the causal agent of Bayoud disease, responsible for the loss of 75% of date palm trees in Morocco and posing a threat to its cultivation across North Africa. This study examined ten Foa isolated from various Moroccan locations for the presence of the transposable element Fot1 and the distribution of “Secreted in Xylem” (SIX) genes. Pathogenicity assays on date palm seedlings revealed varying levels of aggressiveness among isolates, with a positive correlation between aggressiveness and SIX gene count. Highly aggressive isolates harbored 9–12 SIX genes, while hypo-aggressive and moderately aggressive isolates carried 0–6. SIX2, SIX6, SIX7, SIX11, SIX12, and SIX13 were differently dispersed among aggressive isolates, whereas SIX12 and SIX13 were present in all aggressive isolates, suggesting their potential role in virulence. This study is the first to highlight a correlation between Foa aggressiveness and SIX gene distribution, providing a foundation for future functional analyses to elucidate their role in pathogenicity. Full article

(This article belongs to the Section Plant Protection and Biotic Interactions)

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11 pages, 5443 KiB

Open AccessArticle

Effective Bud Induction of Acacia mangium and A. auriculiformis Without KNO₃ and NH₄NO₃ in Media

by Lin Sun, Yanping Lu and Liejian Huang

Plants 2025, 14(11), 1720; https://doi.org/10.3390/plants14111720 - 5 Jun 2025

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Abstract

Stem segments of Acacia mangium and A. auriculiformis containing full axillary buds were used to study the effects of reduced amounts of the main nitrogen source in the growth media. This condition, referred to as nitrogen deficiency in this article and denoted as [...] Read more.

Stem segments of Acacia mangium and A. auriculiformis containing full axillary buds were used to study the effects of reduced amounts of the main nitrogen source in the growth media. This condition, referred to as nitrogen deficiency in this article and denoted as -N, involved the omission of ammonium nitrate and potassium nitrate from MS media, and its impact on bud induction was assessed. The results show that in media lacking nitrogen, the bud induction rate, contamination rate, browning rate, stem length, and leaf number of induced buds of A. mangium and A. auriculiformis varied depending on the different culture media used. The optimal bud induction medium for A. mangium and A. auriculiformis was as follows: 1/4MS (-N) + 1.0 mg·L⁻¹ 6-BA + 0.2 g·L⁻¹ chlorothalonil + 5 g·L⁻¹ AGAR. The bud induction rates were 72.6% and 100.0%, respectively. There were no significant differences in the rooting rates of the induced buds between the -N treatment and the complete nutrient treatment. We found that the buds induced in the -N media did not show obvious symptoms of nitrogen deficiency, and their growth status was not significantly different from those induced in the complete nutrient media, which indicates that nitrogen is not essential for the bud induction of A. mangium and A. auriculiformis. The results of this study provide an important reference for conducting related research on other plants and have are greatly significant for the sustainable development of tissue culture technology in the future. Full article

(This article belongs to the Special Issue Sexual and Asexual Reproduction in Forest Plants)

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17 pages, 2876 KiB

Open AccessArticle

Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (Brassica napus L.)

by Mengfan Qin, Xiang Liu, Jia Song, Feixue Zhao, Yiji Shi, Yu Xu, Zhiting Guo, Tianye Zhang, Jiapeng Wu, Jinxiong Wang, Wu Li, Keqi Li, Shimeng Li, Zhen Huang and Aixia Xu

Plants 2025, 14(11), 1719; https://doi.org/10.3390/plants14111719 - 5 Jun 2025

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Abstract

The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid [...] Read more.

The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F₂ populations (r ranging from 0.395 to 0.635, p < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04–9.48 Mb and 13.52–13.66 Mb) and A04 (19.84–20.14 Mb) of ZS11 and Darmor-bzh reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including FLOWERING LOCUS T, RGL1, MYB-like, CYP96A8, BLH3, NIT2, ASK6, and three CLAVATA3/ESR (CLE)-related genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed. Full article

(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)

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19 pages, 3346 KiB

Open AccessArticle

Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of SWEET and CWIV Genes in Five Dandelion Species Through RNA Sequencing

by Sivagami-Jean Claude, Sunmi Park, Seong-Jun Park and SeonJoo Park

Plants 2025, 14(11), 1718; https://doi.org/10.3390/plants14111718 - 5 Jun 2025

Viewed by 279

Abstract

Taraxacum, a genus in the Asteraceae family, is widely distributed across temperate regions and plays a vital ecological role by providing nectar and pollen to pollinators during the early flowering season. Floral nectar is a key reward that plants use to attract [...] Read more.

Taraxacum, a genus in the Asteraceae family, is widely distributed across temperate regions and plays a vital ecological role by providing nectar and pollen to pollinators during the early flowering season. Floral nectar is a key reward that plants use to attract pollinators, and its production is tightly regulated by genes such as SWEET sugar transporters and CELL WALL INVERTASE (CWIN), which govern sugar efflux and hydrolysis. Despite their ecological importance, the molecular mechanisms underlying nectar secretion in Taraxacum remain poorly understood. In this study, we performed RNA sequencing of flower tissues from five Taraxacum species—T. coreanum, T. monogolicum, T. ohwianum, T. hallaisanense, and T. officinale—to investigate the expression of nectar-related genes. De novo transcriptome assembly revealed that T. coreanum had the highest unigene count (74,689), followed by T. monogolicum (69,234), T. ohwianum (64,296), T. hallaisanense (59,599), and T. officinale (58,924). Functional annotation and phylogenetic analyses identified 17 putative SWEET and 18 CWIN genes across the five species. Differential gene expression analysis highlighted tarSWEET9 and tarCWIN4 as consistently up-regulated during the flowering stage. Quantitative PCR in T. officinale further validated that tarSWEET9, tarCWIN4, tarCWIN6, and tarSPAS2 show significant expression during floral development but are down-regulated after pollination. These genes are likely central to the regulation of nectar secretion in response to pollination cues. Our findings suggest that T. officinale may have evolved to have an efficient, pollinator-responsive nectar secretion system, contributing to its global adaptability. This study sheds light on how pollinator interactions influence gene expression patterns and may drive evolutionary divergence among Taraxacum species. Full article

(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)

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24 pages, 4578 KiB

Open AccessArticle

Plant Architectural Structure and Leaf Trait Responses to Environmental Change: A Meta-Analysis

by Runze Li, Xiping Cheng, Pengyue Dai, Mengting Zhang, Minxuan Li, Jing Chen, Wajee ul Hassan and Yanfang Wang

Plants 2025, 14(11), 1717; https://doi.org/10.3390/plants14111717 - 4 Jun 2025

Viewed by 367

Abstract

The relationship between plants and their environment has always been a core issue in ecological research. This study about how plant architecture and leaf traits respond to environmental changes helps to more deeply understand the adaptive mechanisms of plants in diverse environments. Although [...] Read more.

The relationship between plants and their environment has always been a core issue in ecological research. This study about how plant architecture and leaf traits respond to environmental changes helps to more deeply understand the adaptive mechanisms of plants in diverse environments. Although there have been related studies, a systematic analysis on a China-wide scale is still lacking. To address this gap, we conducted a meta-analysis of 115 studies across China examining plant architectural and leaf trait responses to environmental changes. The dataset includes 849 observations across 11 ecological variables, such as the mean annual precipitation, mean annual temperature, soil type, and elevation, and evaluates their effects on seven key plant traits. The results indicated that variations in the plant height, diameter at breast height (DBH), and root-to-shoot ratio are primarily influenced by the soil type and mean annual precipitation. In contrast, the soil type and mean annual sunshine duration mainly affected the specific leaf area (SLA), leaf area, leaf thickness, and leaf dry matter content. Moreover, while the magnitude of trait responses varies across precipitation, temperature, elevation, and soil property gradients, the impacts of environmental change are particularly pronounced under more extreme conditions. This study provides robust scientific evidence for understanding the effects of environmental change on plant growth across China and offers valuable insights into ecological conservation and the sustainable use of plant resources. Full article

(This article belongs to the Special Issue Trait–Environment Relationships in Plants: Acclimation and Adaptation)

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18 pages, 3325 KiB

Open AccessArticle

CtWRKY41 Transcription Factor from Cynanchum thesioides Mediates Salt Stress Resistance and Controls Flowering Time

by Xiaoyao Chang, Xiaoyan Zhang, Xiumei Huang, Fenglan Zhang and Zhongren Yang

Plants 2025, 14(11), 1716; https://doi.org/10.3390/plants14111716 - 4 Jun 2025

Viewed by 289

Abstract

Cynanchum thesioides (Freyn) K. Schum is an ecologically significant species inhabiting the desert and semi-desert regions of northwestern China, distinguished by its remarkable resilience to environmental stressors. Elucidating the functional roles of its stress-responsive genes not only advances the theoretical framework of plant [...] Read more.

Cynanchum thesioides (Freyn) K. Schum is an ecologically significant species inhabiting the desert and semi-desert regions of northwestern China, distinguished by its remarkable resilience to environmental stressors. Elucidating the functional roles of its stress-responsive genes not only advances the theoretical framework of plant stress tolerance but also provides valuable genetic resources for stress-resilient crop breeding. This study identified a WRKY transcription factor, CtWRKY41, which is strongly induced by salt stress and plays a pivotal role in regulating both flowering time and abiotic stress responses. Subcellular localization analysis confirmed that CtWRKY41 resides in the nucleus and exhibits transcriptional activation activity. Arabidopsis plants overexpressing CtWRKY41 exhibited a significant delay in flowering and enhanced tolerance to salt stress. Further investigation revealed that CtWRKY41 enhances stress resilience by markedly increasing antioxidant enzyme activity, promoting proline accumulation, and upregulating multiple stress-responsive genes. These coordinated mechanisms collectively contribute to the improved salt stress tolerance observed in transgenic Arabidopsis. This study underscores the regulatory significance of CtWRKY41 in plant stress adaptation and establishes a theoretical basis for its potential application in crop genetic improvement programs aimed at enhancing stress resistance. Full article

(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)

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16 pages, 30420 KiB

Open AccessArticle

Hormonal and Transcriptomic Insights into Inflorescence Stalk Elongation in Oil Palm

by Peng Shi, Yin Min Htwe, Dapeng Zhang, Zhiying Li, Qun Yu, Xiangman He, Jing Yang and Yong Wang

Plants 2025, 14(11), 1715; https://doi.org/10.3390/plants14111715 - 4 Jun 2025

Viewed by 244

Abstract

Longer inflorescence stalks in oil palm enhance harvesting efficiency and reduce labor costs. However, the research on this topic is limited. This study aimed to investigate the differences in stalk lengths between male and female inflorescences in Tenera oil palm and to elucidate [...] Read more.

Longer inflorescence stalks in oil palm enhance harvesting efficiency and reduce labor costs. However, the research on this topic is limited. This study aimed to investigate the differences in stalk lengths between male and female inflorescences in Tenera oil palm and to elucidate the underlying hormonal and transcriptomic mechanisms. The stalk lengths from inflorescences associated with the fourth to eighteenth leaf positions of Tenera oil palm trees were measured, and hormone profiling and RNA sequencing (RNA-seq) were conducted in immature (F4 and M5) and mature (F14 and M13) stalks from an individual tree. The male stalks were significantly longer than the female stalks since the thirteenth inflorescences and the differences increased with maturation. The elevated levels of indole-3-acetic acid (IAA) in both immature and mature male stalks suggested auxin’s critical role in promoting stalk elongation. In M13, we identified the upregulated auxin influx carrier LAX2, Gibberellic Acid-Stimulated Arabidopsis 6 (GASA6), and SMALL AUXIN UP RNA (SAUR) genes, indicating enhanced auxin accumulation, signaling, and response. Moreover, the auxin response factor (ARF11) was upregulated, linking auxin transport to gene activation for cell elongation. Conversely, in F14, higher levels of abscisic acid (ABA) and the expression of ABA receptor PYL3 and gibberellin 2-beta-dioxygenase 8 GA2ox8, which may inhibit stalk elongation, were identified. The results suggested that LAX2-mediated IAA accumulation activates ARF11 and SAURs, promoting stalk elongation, with GASA6 possibly acting as a downstream modulator. This study provides insights into the hormonal and genetic regulators of stalk elongation in oil palm and may guide breeding strategies for oil palm varieties with longer stalks of female inflorescences, thereby enhancing harvesting efficiency. Full article

(This article belongs to the Section Plant Molecular Biology)

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12 pages, 1878 KiB

Open AccessArticle

Micropropagation of Philodendron ‘White Knight’ via Shoot Regeneration from Petiole Explants

by Iro Kang and Iyyakkannu Sivanesan

Plants 2025, 14(11), 1714; https://doi.org/10.3390/plants14111714 - 4 Jun 2025

Viewed by 211

Abstract

Philodendron ‘White Knight’ is a popular climbing evergreen plant typically propagated through stem cuttings. However, this method is slow and inefficient, making it challenging to meet the rising market demand. In vitro propagation could enhance the multiplication of this cultivar. However, research on [...] Read more.

Philodendron ‘White Knight’ is a popular climbing evergreen plant typically propagated through stem cuttings. However, this method is slow and inefficient, making it challenging to meet the rising market demand. In vitro propagation could enhance the multiplication of this cultivar. However, research on its in vitro propagation is limited. Therefore, the objective of the present study was to establish an efficient micropropagation technique to mass-produce Philodendron ‘White Knight’ to meet the market demand. We investigate the impact of silver nanoparticles (Ag NPs) on the surface sterilization of Philodendron ‘White Knight’ petioles, the role of plant growth regulators in adventitious shoot regeneration and shoot multiplication, and the effect of auxins on the rooting ability of Philodendron ‘White Knight’ microshoots. There are few stages in plant micropropagation. The establishment of aseptic culture is the first and most important stage. For Philodendron ‘White Knight’, aseptic petiole explants (100%) were obtained after treatment with 40 mg L⁻¹ Ag NPs for 60 min. This was followed by adventitious shoot induction, and the highest rate of adventitious shoot induction (52.6%) and the maximum shoot number (13.9 shoots per petiole) were achieved on Murashige and Skoog shoot multiplication B (MS-B) medium with 20 µM of 2-isopentenyl adenine (2-IP) and 5.0 µM of naphthalene acetic acid (NAA). The shoot multiplication stage was achieved with the highest number of shoots (34 shoots per shoot tip) with a length of 5.1 cm, which was obtained on MS-B medium with 5.0 µM 2-IP and 2.5 µM NAA. All the microshoots produced roots during the root induction stage with the maximum root number (8.2 roots per shoot), and the greatest plantlet height (9.1 cm) was achieved on half-strength Murashige and Skoog medium containing indole-3-butyric acid (10.0 μM). The rooted plantlets of Philodendron ‘White Knight’ were transplanted into a substrate composed of 10% peat moss, 50% orchid stone, and 40% coconut husk chips and acclimatized in a greenhouse environment, achieving a survival rate of 100%. This micropropagation protocol can be used for the commercial production of Philodendron ‘White Knight’. Full article

(This article belongs to the Special Issue Plant Tissue Culture V)

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21 pages, 14751 KiB

Open AccessArticle

Identification and Expression Analysis of the bHLH Gene Family in Rhododendron × pulchrum Sweet with Different Flower Colors

by Jiaran Sheng, Jianshang Shen, Yingying Shan, Xia Chen, Xueqin Li, Huasen Wang and Songheng Jin

Plants 2025, 14(11), 1713; https://doi.org/10.3390/plants14111713 - 4 Jun 2025

Viewed by 221

Abstract

Basic helix–loop–helix (bHLH) transcription factors play significant roles in plant growth and organ development and diverse biochemical processes. However, the function of bHLH transcription factors in woody plants is not fully understood. In this study, the bHLH gene family in Rhododendron [...] Read more.

Basic helix–loop–helix (bHLH) transcription factors play significant roles in plant growth and organ development and diverse biochemical processes. However, the function of bHLH transcription factors in woody plants is not fully understood. In this study, the bHLH gene family in Rhododendron × pulchrum Sweet was identified and characterized using whole-genome data. A total of 109 bHLH family genes (RpbHLHs) were identified in R. pulchrum, and their expression levels were analyzed in flowers of different colors and developmental stages. The results showed that the RpbHLH family is divided into 24 subfamilies. Chromosomal localization and collinearity analyses revealed numerous duplication events during evolution, which is one of the main reasons for the diversification of gene functions. The bHLH domains showed relative conservation of RpbHLH proteins. In the promoter regions of the RpbHLHs, various cis-regulatory elements involved in light response, gibberellic acid (GA) response, and abscisic acid (ABA) response were identified. These elements may regulate flower development and pigment synthesis. A Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of the target RpbHLHs revealed that 25 genes are enriched in the flavonoid biosynthetic pathway. Potential RpbHLHs related to flower development and pigment synthesis were identified through a transcriptome analysis and validated through quantitative reverse transcription PCR (qRT-PCR). This study will enhance our understanding of RpbHLH functions and provide a reference for the study of flower development and coloration in R. pulchrum. Full article

(This article belongs to the Special Issue Horticultural Plant Physiology and Molecular Biology)

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17 pages, 2242 KiB

Open AccessArticle

Ginsenoside-Enriched Panax ginseng Sprouts Cultivated from Aquaponic System with a Novel Nutrient Solution Regulate LPS-Induced Inflammatory Cytokines and UVB-Induced Photoaging Responses via MAPK/AP-1 Signaling Pathways

by Jeong-Ho Kim, Kyung-Wuk Park, Beom-Gyun Jeong, Jun-Ki Park, Ho-Yeol Jang, Yun-Seo Oh, Jin-Yeong Choi and Kyung-Yun Kang

Plants 2025, 14(11), 1712; https://doi.org/10.3390/plants14111712 - 4 Jun 2025

Viewed by 208

Abstract

Panax ginseng sprouts (GSs) have attracted attention as functional resources due to their short cultivation time and enriched ginsenoside content. This study aimed to evaluate the bioactivities of GSs cultivated using kelp fermentates (KF) as a nutrient solution under a smart-farming system. Ginsenoside-enriched [...] Read more.

Panax ginseng sprouts (GSs) have attracted attention as functional resources due to their short cultivation time and enriched ginsenoside content. This study aimed to evaluate the bioactivities of GSs cultivated using kelp fermentates (KF) as a nutrient solution under a smart-farming system. Ginsenoside-enriched extract (FGE), its water-soluble saponin fraction (WFGE), and 70% ethanol-soluble saponin fraction (EFGE) were analyzed for phytochemical contents and biological activities. The EFGE exhibited the highest levels of eight major ginsenosides, including Rg1, Rb1, Rc, Rg2, Rb2, Rd, Rf, and F2. Total phenolic and flavonoid contents were significantly higher in KF-treated ginseng and their crude saponin fractions, with EFGE showing the highest values. WFGE and EFGE indicated strong antioxidant activity through ABTS radical scavenging assays. In LPS-stimulated RAW264.7 macrophages, all extracts significantly inhibited nitric oxide production and downregulated IL-1β, IL-6, iNOS, and COX-2 expression. Moreover, UVB-irradiated human fibroblasts (Hs68) treated with KF-derived fractions showed increased cell viability, enhanced procollagen synthesis, and reduced MMP-1 and MMP-3 expression. These effects were associated with suppression of MAPK/AP-1 signaling. In conclusion, GSs cultivated with KF exhibit notable antioxidant, anti-inflammatory, and anti-photoaging activities, suggesting their potential as natural ingredients for skin health applications. Full article

(This article belongs to the Special Issue Plant Extracts for Health Benefits and Nutrition)

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16 pages, 4849 KiB

Open AccessArticle

Plant Origin Regulates the Response of Solidago canadensis Reproductive Traits to Long-Term Warming and Nitrogen Addition

by Xiaohui Zhou, Xin Chen, Xin Luo, Yanling Wu, Juanjuan Li, Jianxin Ren and Jingji Li

Plants 2025, 14(11), 1711; https://doi.org/10.3390/plants14111711 - 4 Jun 2025

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Abstract

Climate warming and nitrogen (N) deposition have already occurred and will continue to occur, profoundly affecting exotic plant invasion. Most studies on the effects of climate change focus on plant growth, biomass, and leaf traits, with limited reports on reproductive responses. We selected [...] Read more.

Climate warming and nitrogen (N) deposition have already occurred and will continue to occur, profoundly affecting exotic plant invasion. Most studies on the effects of climate change focus on plant growth, biomass, and leaf traits, with limited reports on reproductive responses. We selected Solidago canadensis from North America and China as focal species and conducted a long-term common garden experiment simulating climate warming and N deposition to examine how climate warming, N addition, and plant origin influence its reproductive traits. Chinese Solidago canadensis exhibited significantly greater ramet height, more robust ramet diameters, longer and wider inflorescences, and higher seed mass compared to North American Solidago canadensis. Long-term warming and plant origin alone or in combination significantly influenced reproductive traits, while N addition did not influence these traits. The vegetative propagation of a native population was sensitive to warming and N addition, while the generative propagation of an invasive population was sensitive to their combined effects. These findings suggest that the reproductive strategies of Solidago canadensis varied with their origin, and plant origin might be important in mediating climate change effects on their reproduction under plant invasion. Full article

(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)

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12 pages, 4382 KiB

Open AccessArticle

Impact of Overhead Irrigation Timing on Ornamental Plant Phytotoxicity Following Preemergence Herbicide Applications

by Chengyao Yin, Christopher Marble, Jianjun Chen and Adam Dale

Plants 2025, 14(11), 1710; https://doi.org/10.3390/plants14111710 - 4 Jun 2025

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Abstract

The use of preemergence herbicides is the primary method of controlling weeds in container-grown ornamental plants, but it may cause injury to common popular ornamentals. The objective of this research was to evaluate the use of overhead irrigation to reduce phytotoxicity in ornamental [...] Read more.

The use of preemergence herbicides is the primary method of controlling weeds in container-grown ornamental plants, but it may cause injury to common popular ornamentals. The objective of this research was to evaluate the use of overhead irrigation to reduce phytotoxicity in ornamental plants. Dimethenamid-P and flumioxazin were applied at standard label rates to container-grown coneflower (Echinacea purpurea), lady fern (Anthyrium filix-femina), and blue plumbago (Plumbago auriculata). Plants were subjected to one of four irrigation regimes at the time of herbicide treatment, including receiving 1.3 cm of overhead irrigation before treatment, immediately after treatment, both immediately before and after treatment, and no irrigation until the next irrigation cycle resumed at 4 h after treatment. For all three species, irrigation timing had minimal effect on visual injury ratings following treatment with dimethenamid-P, as injury was minimal overall. Severe injury was observed following treatment with flumioxazin, but significant recovery was noted in both lady ferns and echinacea when irrigation was applied immediately after treatment. The results indicate that irrigating plants immediately after treatment could improve crop tolerance to preemergence herbicide applications and should be further investigated as an injury management strategy for container-grown ornamental plants. Full article

(This article belongs to the Section Horticultural Science and Ornamental Plants)

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16 pages, 3846 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Wild Ancient Camellia tetracocca in Pu’an, Guizhou, China

by Deqin Li, Lushan Li, Shukui Chang, Shunrong Zhang, Jian Feng, Lifei Wang, Xiaoxia Huang, Huizhen Hu, Feng Zu and Xiaomao Cheng

Plants 2025, 14(11), 1709; https://doi.org/10.3390/plants14111709 - 4 Jun 2025

Viewed by 292

Abstract

Pu’an County, located in southwestern Guizhou Province, China, is one of the original habitats for wild tea plants. It is renowned not only as the “Home of Ancient Tea Trees in China” but also as the “Core Production Area for High-Quality Early Tea [...] Read more.

Pu’an County, located in southwestern Guizhou Province, China, is one of the original habitats for wild tea plants. It is renowned not only as the “Home of Ancient Tea Trees in China” but also as the “Core Production Area for High-Quality Early Tea in China”. The wild ancient Camellia tetracocca tea trees are considered “living fossil”. Understanding the genetic diversity of wild ancient C. tetracocca in Pu’an, Guizhou, is of great significance for addressing conservation concerns and mitigating genetic erosion in this endemic species. This study investigates the genetic diversity and population structure of wild ancient C. tetracocca tea plants in Pu’an County to support the development of conservation strategies. We genotyped 138 ancient wild C. tetracocca specimens using 40 intron-length polymorphism markers. A total of 180 alleles were detected, with the allele numbers per locus ranging from 2 to 10 and an average of 4.50. The number of effective alleles varied from 1.36 to 8.01, with an average of 2.86. The Shannon information index ranged from 0.28 to 2.19, with an average of 1.10. Nei’s gene diversity index ranged from 0.14 to 0.88, with an average of 0.58. The polymorphic information content (PIC) varied from 0.14 to 0.85, with an average of 0.58. Our findings indicate that the genetic diversity of wild ancient C. tetracocca tea plants in Pu’an is high. Specifically, the genetic diversity in Qingshan Township surpassed that in Xindian Township. Analysis of molecular variance indicated that 91.59% of the genetic variation occurred within the subpopulations, suggesting limited differentiation. Despite their geographical separation, populations from Qingshan and Xindian showed a complex genetic relationship (F_ST = 0.04). STRUCTURE analysis identified three distinct genetic clusters, indicating a complex demographic history. These findings underscore the conservation significance of wild C. tetracocca populations in Pu’an and highlight the need for conservation strategies that prioritize the protection of genetically diverse subpopulations, especially in the Qingshan region. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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18 pages, 2286 KiB

Open AccessArticle

Transcriptomic Profiling of Quinoa Reveals Distinct Defense Responses to Exogenous Methyl Jasmonate and Salicylic Acid

by Oscar M. Rollano-Peñaloza, Sara Neyrot, Jose A. Bravo Barrera, Patricia Mollinedo and Allan G. Rasmusson

Plants 2025, 14(11), 1708; https://doi.org/10.3390/plants14111708 - 3 Jun 2025

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Abstract

Plant defense responses are mediated by hormones such as jasmonic acid (JA) and salicylic acid (SA). JA and SA are known to trigger a range of different defense responses in model plants but little is described in crops like quinoa. Here, we present [...] Read more.

Plant defense responses are mediated by hormones such as jasmonic acid (JA) and salicylic acid (SA). JA and SA are known to trigger a range of different defense responses in model plants but little is described in crops like quinoa. Here, we present the first molecular description of JA and SA signaling at the transcriptomic level in quinoa. The transcriptomes of quinoa cv. Kurmi seedlings treated with 100 µM methyl JA or 1 mM SA for 4 h were analyzed, using on average 4.1 million paired-end reads per sample. Quinoa plants treated with JA showed 1246 differentially expressed (DE) genes and plants treated with SA showed 590 DE genes. The response to JA included the induction of genes for the biosynthesis of JA (8/8 genes) and lignin (10/11 genes), and displayed a strong association with treatments with Trichoderma biocontrol agents. The SA treatment triggered the upregulation of genes for the biosynthesis of monoterpenoids and glucosinolates, both having defense properties. Overall, this suggest that JA and SA promotes the biosynthesis of lignin polymers and chemical defense compounds, respectively. Overall, the DE genes identified can be used as molecular markers in quinoa for tracking plant-hormone pathway involvements in defense responses. Full article

(This article belongs to the Section Plant Protection and Biotic Interactions)

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24 pages, 5633 KiB

Open AccessArticle

Architectural Analysis for Novel Olive Crop Management

by Khouloud Annabi, Faouzi Haouala, AbdelKarim Hamrita, Rania Kouki, Foued Laabidi, Mokhtar Rejili, Samra Akef Bziouech and Mouna Mezghani Aïachi

Plants 2025, 14(11), 1707; https://doi.org/10.3390/plants14111707 - 3 Jun 2025

Viewed by 290

Abstract

Efficient fruit production, quality improvement, and timely harvesting are essential in olive cultivation, which requires optimised distribution and management of fruiting sites. This study aimed to support sustainable olive crop management by analysing the morphological characteristics of five cultivars (Chemlali, Chetoui [...] Read more.

Efficient fruit production, quality improvement, and timely harvesting are essential in olive cultivation, which requires optimised distribution and management of fruiting sites. This study aimed to support sustainable olive crop management by analysing the morphological characteristics of five cultivars (Chemlali, Chetoui, Koroneiki, Meski, and Picholine) under semi-arid Tunisian conditions. Through a detailed architectural analysis, we investigated the relationships between branching patterns, density, distribution of inflorescence and fruit sites, biometric traits (shoot length, internode number, and shoot dimensions), and geometric variability within each cultivar. Three trees per cultivar were analysed across three architectural units. The results showed marked architectural differences, highlighting the need for cultivar-specific strategies in planting, pruning, and orchard management. The distribution of shoots across botanical orders revealed unique branching patterns: Chemlali and Koroneiki showed thinner shoots and higher shoot density, reflecting strong apical dominance and their suitability for hyper-intensive systems. In addition, nonsignificant differences in long shoots’ insertion angles between Meski, Chetoui, and Koroneiki suggest compatibility for co-cultivation, facilitating mechanised maintenance and harvesting. Emphasis on inter-cultivar compatibility and architectural coherence is crucial for orchard design. These findings provide important insights for optimising orchard management practices to improve productivity, fruit quality, and operational efficiency. Full article

(This article belongs to the Special Issue Development of Woody Plants)

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21 pages, 7485 KiB

Open AccessArticle

Endocarp Morphology of Premna (Lamiaceae) in Thailand and Its Taxonomic Significance

by Jiratthi Satthaphorn, Alan J. Paton, Pornsawan Sutthinon and Charan Leeratiwong

Plants 2025, 14(11), 1706; https://doi.org/10.3390/plants14111706 - 3 Jun 2025

Viewed by 627

Abstract

Fruits and endocarps of 21 species within the genus Premna (Lamiaceae) in Thailand were examined using light (LM) and scanning electron microscopy (SEM) to evaluate taxonomic relevance. Overall, mature fruits were classified into two types: fully developed mericarp (fruit type I) and partly [...] Read more.

Fruits and endocarps of 21 species within the genus Premna (Lamiaceae) in Thailand were examined using light (LM) and scanning electron microscopy (SEM) to evaluate taxonomic relevance. Overall, mature fruits were classified into two types: fully developed mericarp (fruit type I) and partly developed mericarp (fruit type II), with three shape patterns: broadly obovoid, narrowly obovoid, and clavoid. Fruit size ranged from 1.52 to 7.48 mm in length and 0.98 to 7.71 mm in width. In LM investigations, the endocarps were classified into three types based on the presence and shape of the protruding structure: saccate-like (protrusion type I), thorn-like (protrusion type II), and no protrusion (protrusion type III). The examination of endocarps under SEM showed that they consist of multilayers of sclerenchyma cells. The shape of the sculpturing cells on the endocarp surface can be divided into two patterns: irregular tetragonal and polygonal, with distinct or obscure straight cell faces. The morphological comparison and phenetic analyses using factor analysis of mixed data (FAMD) show that fruit and endocarp characteristics of Premna hold significant taxonomic value for distinguishing certain related species and classifying within the genus in Thailand. From the first two FAMD dimensions, fruit shape, shape of sculptured cells on the endocarp, and protrusion type of the endocarp are considered as the most significant contributing variables. The findings also support the reinstatement of species previously synonymized with P. serratifolia, namely P. cordifolia, P. paniculata, and P. punctulata. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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Plants, Volume 14, Issue 11 (June-1 2025) – 173 articles

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