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Volume 14
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Plants, Volume 14, Issue 18 (September-2 2025) – 30 articles

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21 pages, 6745 KB  
Article
Characterization and Role of AP2/EREBP Genes with Decreasing Expression During Leaf Development in 84K Poplar
by Sanjiao Wang, Nan Liu, Jingna Si, Sihan Zhang and Xiaomin Liu
Plants 2025, 14(18), 2842; https://doi.org/10.3390/plants14182842 - 11 Sep 2025
Abstract
The 84K poplar (Populus alba × Populus glandulosa) is a fast-growing hybrid poplar that was introduced from South Korea by the Chinese Academy of Forestry in 1984. To gain deeper insight into the regulatory mechanisms of leaf development in 84K poplar, [...] Read more.
The 84K poplar (Populus alba × Populus glandulosa) is a fast-growing hybrid poplar that was introduced from South Korea by the Chinese Academy of Forestry in 1984. To gain deeper insight into the regulatory mechanisms of leaf development in 84K poplar, we performed bulk RNA sequencing and found that numerous members of the AP2/EREBP family exhibited expression changes, suggesting their crucial roles in leaf development. The AP2/EREBP transcription factor family is one of the largest and most conserved gene families in plants. These genes play a crucial role in plant growth, development, and stress responses. In this study, we identified and analyzed 400 AP2/EREBP genes through transcriptome analysis, excluding genes with missing values (NAs) or FPKM < 1, and selected 76 genes based on their expression patterns at different stages of leaf development. The 76 genes were classified into three subfamilies based on phylogenetic analysis and structural domain characteristics: the RAV subfamily, the ERF subfamily, and the AP2 subfamily. Each subfamily shares similar gene structures and motifs while also exhibiting distinct differences. Segmental duplication events may have contributed to the evolution of this gene family. Most of the promoter cis-acting elements are related to light responses, with fewer elements associated with palisade tissues and hormones. Eight genes, selected for their gradually decreasing expression during leaf development, were validated through RT-PCR experiments. Among them, five genes—Pop_G10G022861, Pop_A01G003858, Pop_A01G081120, Pop_A01G074798, and Pop_A07G010900—exhibited a decreasing trend in expression across the three stages of leaf development. Subcellular localization analysis indicated that Pop_A01G003858 and Pop_G11G077730, two randomly selected genes from the eight AP2/EREBP members validated by RT-PCR, are localized in the nucleus. In conclusion, these findings provide valuable insights into the evolutionary relationships of the 73 AP2/EREBP family members in 84K poplar leaves and lay a foundation for future studies on leaf development. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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26 pages, 1078 KB  
Review
Recent Trends in Machine Learning, Deep Learning, Ensemble Learning, and Explainable Artificial Intelligence Techniques for Evaluating Crop Yields Under Abnormal Climate Conditions
by Ji Won Choi, Mohamad Soleh Hidayat, Soo Been Cho, Woon-Ha Hwang, Hoonsoo Lee, Byoung-Kwan Cho, Moon S. Kim, Insuck Baek and Geonwoo Kim
Plants 2025, 14(18), 2841; https://doi.org/10.3390/plants14182841 - 11 Sep 2025
Abstract
Crop yield prediction (CYP) has become increasingly critical in addressing the adverse effects of abnormal climate and enhancing agricultural productivity. This review investigates the application of advanced Artificial Intelligence (AI) techniques including Machine Learning (ML), Deep Learning (DL), Ensemble Learning, and Explainable AI [...] Read more.
Crop yield prediction (CYP) has become increasingly critical in addressing the adverse effects of abnormal climate and enhancing agricultural productivity. This review investigates the application of advanced Artificial Intelligence (AI) techniques including Machine Learning (ML), Deep Learning (DL), Ensemble Learning, and Explainable AI (XAI) to CYP. It also explores the use of remote sensing and imaging technologies, identifies key environmental factors, and analyzes the primary causes of yield reduction. A wide diversity of input features was observed across studies, largely influenced by data availability and specific research goals. Stepwise feature selection was found to be more effective than increasing feature volume in improving model accuracy. Frequently used algorithms include Random Forest (RF) and Support Vector Machines (SVM) for ML, Artificial Neural Networks (ANNs) and Convolutional Neural Networks (CNNs) for DL, as well as stacking-based ensemble methods. Although XAI remains in the early stages of adoption, it shows strong potential for interpreting complex, multi-dimensional CYP models. Hyperspectral imaging (HSI) and multispectral imaging (MSI), often collected via drones, were the most commonly used sensing techniques. Major factors contributing to yield reduction included atmospheric and soil-related conditions under abnormal climate, as well as pest outbreaks, declining soil fertility, and economic constraints. Providing a comprehensive overview of AI-driven CYP frameworks, this review offers insights that support the advancement of precision agriculture and the development of data-informed agricultural policies. Full article
(This article belongs to the Section Plant Modeling)
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22 pages, 4181 KB  
Article
Lemna gibba Clones Show Differences in Phenotypic Responses to the Light Environment
by Pham Thi Hong Xuan, Raja Amri, Nguyen Phuong Bach, Muhammad Irfan, Manuela Bog, Klaus J. Appenroth, K. Sowjanya Sree, Marcel A. K. Jansen, Sándor Szabó, Ilona Mészáros and Viktor Oláh
Plants 2025, 14(18), 2840; https://doi.org/10.3390/plants14182840 - 11 Sep 2025
Abstract
Duckweeds are aquatic plants with a worldwide distribution that can thrive under very contrasting ambient conditions due to their diversity and high phenotypic plasticity. In this study, we analyzed and compared the responses of four clones (i.e., distinct accessions) of Lemna gibba to [...] Read more.
Duckweeds are aquatic plants with a worldwide distribution that can thrive under very contrasting ambient conditions due to their diversity and high phenotypic plasticity. In this study, we analyzed and compared the responses of four clones (i.e., distinct accessions) of Lemna gibba to two different light intensities. The clones represented different geographical origins and, in addition to two diploid cytotypes, included one tetraploid mutant and a triploid interspecific hybrid. We hypothesized that clonal origin had an effect on light acclimation. We studied growth, morphological (frond size and shape, mass-to-area ratio), and photosynthetic (pigment composition, chlorophyll fluorescence induction) traits of these clones to test whether light acclimation was a conserved process or whether clone-specific strategies could be found. We also analyzed frond-level photosynthetic adjustment during ontogenesis to track how light acclimation evolved in developing fronds. Our results confirmed that even clones of the same duckweed species and a hybrid of closely related species followed partially different strategies in acclimation to ambient conditions. This acclimation involved various morphological, physiological, and biochemical adjustments but happened in a very short time window at the early life stage when young, still-developing fronds could flexibly achieve an optimized phenotype. In addition to explaining the worldwide success of duckweeds in colonizing very contrasting habitats, our results also highlight the importance of approaching duckweed responses at the frond level, where the actual acclimation takes place. Full article
(This article belongs to the Special Issue Duckweed: Research Meets Applications—2nd Edition)
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28 pages, 4004 KB  
Article
Influencing Factors and Adaptation Strategies of Stoichiometric Characteristics of Main Shrubs and Herbs in Karst Area at Microhabitat Scale
by Peng Wu, Hua Zhou, Wenjun Zhao, Guangneng Yang, Yingchun Cui, Yiju Hou, Chengjiang Tan, Ting Zhou, Run Liu and Fangjun Ding
Plants 2025, 14(18), 2839; https://doi.org/10.3390/plants14182839 - 11 Sep 2025
Abstract
In order to reveal the adaptation strategies of karst forest plants to “high-calcium (Ca)–low-phosphorus (P) heterogeneous” habitats, the dominant shrubs and herbs in the Maolan karst area were taken as the research objects. The carbon (C), nitrogen (N), P, potassium (K), Ca, and [...] Read more.
In order to reveal the adaptation strategies of karst forest plants to “high-calcium (Ca)–low-phosphorus (P) heterogeneous” habitats, the dominant shrubs and herbs in the Maolan karst area were taken as the research objects. The carbon (C), nitrogen (N), P, potassium (K), Ca, and magnesium (Mg) contents of plant components and their stoichiometric ratios in different microhabitats were systematically measured, and the environmental driving factors were analyzed by redundancy analysis (RDA) and variance partitioning analysis (VPA). The results showed that there were no significant differences in the plant nutrient contents and stoichiometric ratios in different microhabitats, but there were significant differences with respect to the components. The contents of N, P, K, and Mg in shrub leaves were significantly higher than those in branches and roots, while the contents of C/N, C/P, and C/K in branches and roots were significantly higher than those in leaves. The K content of herb leaves was significantly higher than that of roots. This reflects the functional differentiation of plant components and the different trade-off strategies for resource acquisition and storage. The stoichiometric characteristics of shrub leaves are dominated by species characteristics, while herb leaves are controlled by leaf tissue density (LTD), and soil-exchangeable Ca has a significant regulatory effect on the roots of both plant forms. Shrubs directly obtain bedrock slow-release nutrients through deep roots penetrating rock crevices and combine high C/N and C/P to improve nutrient utilization efficiency, forming a “mechanical resistance priority–metabolic cost optimization” adaptation strategy. Herbs respond to environmental fluctuations through functional trait plasticity and achieve rapid growth with high specific leaf area (SLA) and low LTD. Full article
(This article belongs to the Special Issue Advances in Plant Nutrition Responses and Stress)
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16 pages, 3526 KB  
Article
Non-CG DNA Methylation Regulates Root Stem Cell Niche Maintenance, Auxin Signaling, and ROS Homeostasis in Arabidopsis Under Cadmium Stress
by Emanuela Talarico, Eleonora Greco, Fabrizio Araniti, Adriana Chiappetta and Leonardo Bruno
Plants 2025, 14(18), 2838; https://doi.org/10.3390/plants14182838 - 11 Sep 2025
Abstract
Non-CG DNA methylation plays a critical role in regulating root development and stress responses in Arabidopsis thaliana under cadmium (Cd2+) exposure. We compared wild type (WT) plants with the ddc triple mutant (deficient in DRM1, DRM2, and CMT3) [...] Read more.
Non-CG DNA methylation plays a critical role in regulating root development and stress responses in Arabidopsis thaliana under cadmium (Cd2+) exposure. We compared wild type (WT) plants with the ddc triple mutant (deficient in DRM1, DRM2, and CMT3) to assess how epigenetic modifications affect the root apical meristem (RAM) under 100 µM and 150 µM CdCl2 treatments. Cd2+ exposure led to RAM disorganization, reduced cortical cell number, and quiescent center (QC) cell loss in WT roots, while ddc mutants maintained meristem integrity and exhibited QC cell expansion. Auxin signaling, assessed via pDR5::GFP, was disrupted in WT roots at high Cd2+ levels but remained stable in ddc mutants. Similarly, WT roots showed elevated reactive oxygen species accumulation under stress, whereas ddc mutants displayed a reduced oxidative response. These results suggest that non-CG DNA methylation suppresses key regulators of stem cell maintenance, hormonal balance, and redox homeostasis during heavy metal stress. Loss of this methylation in the ddc mutant confers enhanced resilience to Cd2+ toxicity, highlighting an epigenetic mechanism underlying root stress adaptation. Full article
(This article belongs to the Special Issue Molecular Mechanisms Associated with Plant Tolerance upon Abiotic Stress—2nd Edition)
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15 pages, 3131 KB  
Article
Evaluating the Effectiveness of Water-Saving Irrigation on Wheat (Triticum aestivum L.) Production in China: A Meta-Analytical Approach
by Jiayu Ma, Baozhong Yin, Cuijiao Jing, Wanyi Li, Yilan Qiao, Luyao Zhang, Haotian Fan, Limin Gu and Wenchao Zhen
Plants 2025, 14(18), 2837; https://doi.org/10.3390/plants14182837 - 11 Sep 2025
Abstract
Optimized water-saving irrigation (WSI) practices are critical for enhancing resource use efficiency and ensuring sustainable wheat production in water-scarce regions. This meta-analysis quantitatively assessed the effects of various WSI methods on wheat yield, water use efficiency (WUE), and partial factor productivity of nitrogen [...] Read more.
Optimized water-saving irrigation (WSI) practices are critical for enhancing resource use efficiency and ensuring sustainable wheat production in water-scarce regions. This meta-analysis quantitatively assessed the effects of various WSI methods on wheat yield, water use efficiency (WUE), and partial factor productivity of nitrogen (PFPN) across China’s wheat regions. The results showed that optimized irrigation, particularly drip and micro-sprinkler systems, significantly reduced irrigation water and nitrogen inputs by 35.1% and 7.2%, respectively, without yield penalties. Drip and micro-sprinkler irrigation, which together accounted for over 97% of observations, improved WUE by 18.7% and 10.1%, respectively, and increased PFPN by 6.8% and 5.5%, highlighting their dominant role in current WSI practices. Moderate deficit irrigation (60–100% of full irrigation) optimized WUE and PFPN while maintaining stable yields, whereas severe deficit irrigation (<40%) caused substantial yield losses. Soil texture and bulk density strongly modulated WSI effectiveness. Climatic factors, particularly growing season precipitation, negatively correlated with WSI benefits, highlighting enhanced efficiency gains under drier conditions. These findings emphasize the need to prioritize drip and micro-sprinkler irrigation in national water-saving strategies and advocate for integrated approaches combining WSI with soil health management and site-specific irrigation scheduling to promote sustainable wheat intensification under variable agroecological conditions. Full article
(This article belongs to the Special Issue Water and Nitrogen Management in the Soil–Crop System (3rd Edition))
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24 pages, 7843 KB  
Article
Identification of Candidate Genes for Low Phosphorus Tolerance in Maize Seedling Stage Based on GWAS and Transcriptome
by Xiaojia Hao, Gonxin Lei, Zhiming Zhong, Zelong Zhuang, Jianwen Bian, Lei Zhang, Wanling Ta, Zhenping Ren and Yunling Peng
Plants 2025, 14(18), 2836; https://doi.org/10.3390/plants14182836 - 11 Sep 2025
Abstract
Phosphorus is an essential nutrient for maize growth and development, and its deficiency can significantly inhibit plant growth, leading to reduced yield and quality. To elucidate the genetic mechanisms underlying low phosphorus tolerance in maize, this study utilized a panel of 257 maize [...] Read more.
Phosphorus is an essential nutrient for maize growth and development, and its deficiency can significantly inhibit plant growth, leading to reduced yield and quality. To elucidate the genetic mechanisms underlying low phosphorus tolerance in maize, this study utilized a panel of 257 maize inbred lines and conducted controlled experiments under low phosphorus (LP) and normal phosphorus (CK) conditions in artificial climate chambers. Through genome-wide association study (GWAS), a total of 46 SNP loci significantly associated with low phosphorus tolerance were detected, and 74 candidate genes were predicted. To further investigate, the low-phosphorus tolerant material CML422 and the phosphorus-sensitive material CIMBL90 were selected for transcriptome sequencing, which identified a total of 7232 differentially expressed genes (DEGs). KEGG enrichment analysis revealed that these genes were significantly enriched in key pathways such as plant hormone signal transduction, MAPK signaling pathway, and starch and sucrose metabolism, suggesting that maize responds to low phosphorus stress through the coordinated regulation of multiple pathways. By integrating GWAS and transcriptome data, 18 co-localized genes were screened, ultimately identifying 10 candidate genes closely associated with low phosphorus tolerance during the maize seedling stage, which are potentially involved in regulating growth and development under phosphorus stress. This study preliminarily elucidates the molecular mechanisms underlying low phosphorus tolerance in maize through multi-omics analysis, providing both a theoretical basis and genetic resources for breeding new maize varieties with high phosphorus use efficiency. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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16 pages, 11893 KB  
Article
Stoichiometric Homeostasis and Functional Group Divergence Jointly Enhance Alpine Plant Adaptation to Environmental Stress
by Aihui Ma, Zhe Chen, Xin Jing, Yu Chen, Jinhong Guan, Shixiong Wang, Wenying Wang, Huakun Zhou, Jian Sun, Xufeng Mao and Yanxia Jin
Plants 2025, 14(18), 2835; https://doi.org/10.3390/plants14182835 - 11 Sep 2025
Abstract
Climate warming promotes alpine plant migration to higher elevations, yet how they adapt via stoichiometric homeostasis remains unclear. We measured plant C, N, and P traits and homeostasis across community and functional group levels in three alpine vegetation types—meadow (3200–3400 m), shrubland (3400–3700 [...] Read more.
Climate warming promotes alpine plant migration to higher elevations, yet how they adapt via stoichiometric homeostasis remains unclear. We measured plant C, N, and P traits and homeostasis across community and functional group levels in three alpine vegetation types—meadow (3200–3400 m), shrubland (3400–3700 m), and cushion vegetation (3700–4400 m)—along an altitudinal gradient in the northern Qilian Mountains, Tibetan Plateau. Shrubland, as ecotones, had higher soil C and N, with plant communities showing the highest N and N:P but lowest C:N. At the functional group level, Poaceae (Gramineae) and forbs had the highest N and N:P, while Cyperaceae had the highest P in shrubland. Notably, Cyperaceae in shrubland exhibited weak P and C:P homeostasis. Poaceae (Gramineae) were mainly influenced by soil, Cyperaceae by climate, and forbs by elevation. Structural equation modeling showed elevation indirectly affected stoichiometry via climate and soil; climate influenced nutrient contents, while soil controlled C:N:P ratios. These results reveal diverse nutrient regulation and survival strategies in alpine plants, enhancing understanding of adaptation and community assembly under climate change. Full article
(This article belongs to the Special Issue Physiological and Ecological Responses of Arctic and Alpine Plants to Climate Change)
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18 pages, 2446 KB  
Article
Ionomic Signatures of Olive Trees Affected by Quick Decline Syndrome
by Giorgio Mariano Balestra, Mauro Giordani, Eleonora Coppa, Daniele Schiavi and Stefania Astolfi
Plants 2025, 14(18), 2834; https://doi.org/10.3390/plants14182834 - 11 Sep 2025
Abstract
Olive Quick Decline Syndrome (OQDS), caused by the bacterium Xylella fastidiosa, subsp. pauca, has devastated olive groves in Italy’s Apulia region since 2013. Despite significant scientific progress, the solution remains elusive. This study investigated the link between olive tree nutritional status [...] Read more.
Olive Quick Decline Syndrome (OQDS), caused by the bacterium Xylella fastidiosa, subsp. pauca, has devastated olive groves in Italy’s Apulia region since 2013. Despite significant scientific progress, the solution remains elusive. This study investigated the link between olive tree nutritional status and OQDS severity, aiming to uncover potential mitigation strategies. We analyzed leaf nutrient profiles from olive trees in naturally infected areas, categorizing them as asymptomatic (AS), mildly symptomatic (MS), or severely symptomatic (SS). Distinct nutritional differences were observed across these groups. The integration of univariate statistical analysis, hierarchical clustering, and Principal Component Analysis (PCA) revealed a complex relationship between plant nutritional status and disease progression. Notably, the PCA results highlighted the importance of sulfur metabolism, suggesting its role in olive trees’ defense mechanisms and metabolic responses to OQDS. These results provide promising evidence with potential application for dealing with OQDS, and the question of whether plant nutritional status plays a role in the development of OQDS symptoms deserves to be further examined in depth. Full article
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26 pages, 5820 KB  
Article
The Impact of Elevated Soil pH Levels on Cranberry Growth, Physiology, and Metabolites
by Mura Jyostna Devi, Jinyoung Barnaby, Jessica Rohde, Yi Wang, Lorraine Rodriguez-Bonilla, Juan Zalapa, Amaya Atucha and Giverson Mupambi
Plants 2025, 14(18), 2833; https://doi.org/10.3390/plants14182833 - 11 Sep 2025
Abstract
pH plays a critical role in regulating nutrient availability and uptake, directly influencing plant growth and productivity. Cranberries grow optimally within a soil pH range of 4.2 to 5.5, but achieving this range remains challenging, even with amendments. This study evaluated the effects [...] Read more.
pH plays a critical role in regulating nutrient availability and uptake, directly influencing plant growth and productivity. Cranberries grow optimally within a soil pH range of 4.2 to 5.5, but achieving this range remains challenging, even with amendments. This study evaluated the effects of elevated soil pH (7.0 to 7.2) on cranberry cultivation and identified factors contributing to adverse outcomes. Stems, leaves, and fruits were sampled from plants grown in soil with a pH ranging from 4.8 to 7.0. Nutrient composition, fruit size, yield, and anthocyanin content were analyzed. High soil pH levels resulted in significant reductions in fruit size (25–35%) and yield (29–56%). Cranberry plants grown in elevated pH conditions showed a significant (p < 0.001) decline in nitrogen, phosphorus, and potassium, and increased calcium and magnesium in soil, stems, leaves, and fruits. Additionally, photosynthesis and chlorophyll fluorescence were significantly reduced (p < 0.05 to 0.001). Certain amino acids, carbohydrates, and organic acids increased significantly (p < 0.05 to 0.0001) in high pH soils, suggesting a role in stress adaptation. Calcium levels in fruits and shoots were inversely correlated with fruit size and some metabolites. These findings demonstrate that soil pH levels above the optimal range (4.2–5.5) substantially impair cranberry growth and quality by disrupting nutrient balance and photosynthesis. The results highlight the urgent need for improved water and soil management strategies to mitigate high soil pH stress in commercial cranberry production. Full article
(This article belongs to the Special Issue Biochemical Responses of Horticultural Crops to Abiotic Stresses)
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16 pages, 1438 KB  
Article
Cytotoxic Activity of Chemical Constituents of Clerodendrum glabrum and Combretum nelsonii Root Extracts Against Selected Cancer Cell Lines
by Kopelo V. Mabunda, Douglas Kemboi, Ibukun M. Famuyide, Lyndy J. McGaw, Ntebogeng S. Mokgalaka-Fleischmann and Vuyelwa Jacqueline Tembu
Plants 2025, 14(18), 2832; https://doi.org/10.3390/plants14182832 - 11 Sep 2025
Abstract
Breast and colon cancers are leading causes of death worldwide. There is a need for improved treatment strategies. South African medicinal plants, including Clerodendrum glabrum (C. glabrum) and Combretum nelsonii (C. nelsonii), are known for their cytotoxic properties. This [...] Read more.
Breast and colon cancers are leading causes of death worldwide. There is a need for improved treatment strategies. South African medicinal plants, including Clerodendrum glabrum (C. glabrum) and Combretum nelsonii (C. nelsonii), are known for their cytotoxic properties. This study aimed to isolate and characterize terpenoids and stilbenes from the roots of C. glabrum and C. nelsonii and evaluate their anticancer potential against colorectal adenocarcinoma (Caco-2) and hormone receptor-positive breast cancer (MCF-7) cell lines. Spectroscopic techniques including nuclear magnetic resonance spectroscopy (NMR) were used to characterize the isolated compounds. Repeated column chromatography of C. glabrum extract led to the isolation of ferruginol (1), royleanone (2), and β-amyrin palmitate (3). C. nelsonii extract afforded combretastatin A-1 (4), a mixture of combretastatin A-1-2′-O-β-D-glucopyranoside (5a) and combretastatin B-1-2′-O-β-D-glucopyranoside (5b). Compounds 1, 2, 4, 5a, and 5b were isolated for the first time from the plant species. C. glabrum extract showed good anticancer properties with LC50 of 1.30 × 103 µg/mL (CaCo-2) and 2790 µg/mL (MCF-7). Compound (1) exhibited high toxicity against the Caco-2 at LC50 of 24.3 µg/mL and moderate activity against MCF-7 at 48.4 µg/mL. Compound (4) and the mixture (5a and 5b) showed moderate activity against the MCF-7 at LC50 72.0 and 44.1 µg/mL, respectively. These findings highlight C. glabrum and C. nelsonii as promising sources of anticancer lead compounds. Full article
(This article belongs to the Special Issue Advanced Research in the Chemical and Biological Characterization of Plants)
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15 pages, 1547 KB  
Review
Advances in Cell Wall Dynamics and Gene Expression in Postharvest Fruit Softening
by Xumin Wang, Da Zhang, Tiantian Liu, Zhuo Yan, Xinmei Ji, Yusheng Li, Yaqin Wu, Hehe Cheng, Yingjie Wang, Jianchao Cui, Yongjie Wu and Long Chen
Plants 2025, 14(18), 2831; https://doi.org/10.3390/plants14182831 - 10 Sep 2025
Abstract
Postharvest fruit softening is a critical determinant of fruit shelf life, significantly influencing mechanical damage susceptibility, pathogen invasion, and consumer preference. Collectively, these factors lead to substantial losses in the fruit industry. The structural modifications of cell wall and cuticle during ripening primarily [...] Read more.
Postharvest fruit softening is a critical determinant of fruit shelf life, significantly influencing mechanical damage susceptibility, pathogen invasion, and consumer preference. Collectively, these factors lead to substantial losses in the fruit industry. The structural modifications of cell wall and cuticle during ripening primarily govern fruit softening. The objective of this review is to synthesize recent advances and provide a comprehensive analysis of the molecular mechanisms underlying this process. In this review, we provide a comprehensive analysis of cell wall composition and softening-associated cell wall remodeling proteins. We examine recent advances in manipulating single or multiple genes encoding cell wall-modifying proteins that influence fruit softening, and identify key transcription factors regulating the expression of these gene networks. This review synthesizes current understanding of the molecular mechanisms governing fruit ripening, providing a foundation for future research in postharvest biology. Full article
(This article belongs to the Special Issue Postharvest and Storage of Horticultural Plants)
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21 pages, 2717 KB  
Article
Soil Disturbance of Plateau Zokor (Eospalax baileyi) Promotes the Stability of Alpine Plant Communities
by Xidong Zhu, Feiyang Xue, Zhiying Zhang, Rui Dong, Limin Hua and Guohui Ye
Plants 2025, 14(18), 2830; https://doi.org/10.3390/plants14182830 - 10 Sep 2025
Abstract
Alpine meadows on the Tibetan Plateau experience chronic, fine-scale disturbances from the plateau zokor (Eospalax baileyi), a subterranean rodent that alters soil and vegetation structure through persistent burrowing and mounding. While classical theory predicts that plant community stability peaks at intermediate [...] Read more.
Alpine meadows on the Tibetan Plateau experience chronic, fine-scale disturbances from the plateau zokor (Eospalax baileyi), a subterranean rodent that alters soil and vegetation structure through persistent burrowing and mounding. While classical theory predicts that plant community stability peaks at intermediate disturbance levels, this may not apply under spatially heterogeneous disturbance regimes. We assessed community stability across a five-level zokor disturbance gradient using a multi-indicator framework integrating compositional variability (average variation degree, AVD), co-occurrence-based cohesion, indicator species analysis, and boosted regression tree (BRT) modeling. Stability (1−AVD) peaked under extreme disturbance, alongside reduced indicator species richness and the dominance of disturbance-tolerant taxa. Increased cohesion suggested stronger species associations. Drivers of stability shifted from plant attributes under low disturbance to soil constraints (bulk density and moisture) under high disturbance. These results challenge the intermediate disturbance–stability paradigm and suggest that abiotic filtering can promote compositional convergence and structural stability. Our findings highlight the importance of spatial disturbance patterns in shaping community resilience and provide early warning indicators and targeted guidance for managing alpine grasslands under subterranean disturbance. Full article
(This article belongs to the Section Plant Ecology)
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34 pages, 4551 KB  
Review
Multi-Scale Remote-Sensing Phenomics Integrated with Multi-Omics: Advances in Crop Drought–Heat Stress Tolerance Mechanisms and Perspectives for Climate-Smart Agriculture
by Xiongwei Liang, Shaopeng Yu, Yongfu Ju, Yingning Wang and Dawei Yin
Plants 2025, 14(18), 2829; https://doi.org/10.3390/plants14182829 - 10 Sep 2025
Abstract
Climate change is intensifying the co-occurrence of drought and heat stresses, which substantially constrain global crop yields and threaten food security. Developing climate–resilient crop varieties requires a comprehensive understanding of the physiological and molecular mechanisms underlying combined drought–heat stress tolerance. This review systematically [...] Read more.
Climate change is intensifying the co-occurrence of drought and heat stresses, which substantially constrain global crop yields and threaten food security. Developing climate–resilient crop varieties requires a comprehensive understanding of the physiological and molecular mechanisms underlying combined drought–heat stress tolerance. This review systematically summarizes recent advances in integrating multi-scale remote-sensing phenomics with multi-omics approaches—genomics, transcriptomics, proteomics, and metabolomics—to elucidate stress response pathways and identify adaptive traits. High-throughput phenotyping platforms, including satellites, UAVs, and ground-based sensors, enable non-invasive assessment of key stress indicators such as canopy temperature, vegetation indices, and chlorophyll fluorescence. Concurrently, omics studies have revealed central regulatory networks, including the ABA–SnRK2 signaling cascade, HSF–HSP chaperone systems, and ROS-scavenging pathways. Emerging frameworks integrating genotype × environment × phenotype (G × E × P) interactions, powered by machine learning and deep learning algorithms, are facilitating the discovery of functional genes and predictive phenotypes. This “pixels-to-proteins” paradigm bridges field-scale phenotypes with molecular responses, offering actionable insights for breeding, precision management, and the development of digital twin systems for climate-smart agriculture. We highlight current challenges, including data standardization and cross-platform integration, and propose future research directions to accelerate the deployment of resilient crop varieties. Full article
(This article belongs to the Special Issue Physiological and Molecular Mechanisms of Plant Resistance to Abiotic Stress)
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38 pages, 5546 KB  
Article
Network Pharmacology, Molecular Docking and Molecular Dynamics Studies to Predict the Molecular Targets and Mechanisms of Action of Melissa officinalis Phytoconstituents in Type-2 Diabetes Mellitus
by Chimaobi J. Ononamadu, Ziyad Ben Ahmed and Veronique Seidel
Plants 2025, 14(18), 2828; https://doi.org/10.3390/plants14182828 - 10 Sep 2025
Abstract
Network pharmacology, molecular docking, and molecular dynamics (MD) studies were used to investigate the molecular targets and mechanisms of action of Melissa officinalis phytoconstituents in type-2 diabetes mellitus (T2DM). SciFinder was used to retrieve previously known phytoconstituents from M. officinalis aerial parts. Targets [...] Read more.
Network pharmacology, molecular docking, and molecular dynamics (MD) studies were used to investigate the molecular targets and mechanisms of action of Melissa officinalis phytoconstituents in type-2 diabetes mellitus (T2DM). SciFinder was used to retrieve previously known phytoconstituents from M. officinalis aerial parts. Targets related to these compounds were predicted using the Swiss TargetPrediction, SEA (similarity ensemble approach) and BindingDB databases, and were intersected with T2DM-relevant targets from public databases. Networks were constructed using the STRING online tool and Cytoscape (v.3.9.1) software. Gene ontology/KEGG pathway analysis was performed using DAVID and SHINEGO 0.77. Molecular docking used the MOE suite. MD simulations were conducted for 100 ns using GROMACS 2023 with a CHARMM36 force field. A total of 17 phytoconstituents and 154 targets associated with T2DM were identified. The protein–protein interaction (PPI) and target–pathway (TP) network analysis identified key hub genes, including EGFR, SRC, AKT1, TNF, PPARG, PIK3R1, RELA, INSR, GSK3B, PIK3CG, FYN, PTBIN, and PPARA, with critical roles in insulin resistance and T2DM-relevant pathways. The pathway enrichment analysis highlighted notable involvement in insulin signaling, inflammation, and diabetic complications. The compound–target (CT) network predicted quercetin, luteolin, ursolic acid, isoquercitrin, 2α-hydroxy-ursolic acid, and oleanolic acid to be key bioactive compounds. Molecular docking, followed by MD studies, identified that isoquercitrin showed most energetically favorable and stable complexes with three targets, namely EGFR, PPARα, and AKT1. These findings enhance our understanding of the antidiabetic potential of M. officinalis and underscore the need for further studies on its phytoconstituents, such as isoquercitrin, in search for new antidiabetic agents. Full article
(This article belongs to the Section Phytochemistry)
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20 pages, 29237 KB  
Article
Predicting Potential Habitats of the Endangered Mangrove Species Acanthus ebracteatus Under Current and Future Climatic Scenarios Based on MaxEnt and OPGD Models
by Jiaqi Chen, Liuping Wu, Chongcheng Yang, Qiongzhen Qiu, Yi Wang, Zhixin Li and Chunhua Xia
Plants 2025, 14(18), 2827; https://doi.org/10.3390/plants14182827 - 10 Sep 2025
Abstract
Climate change threatens coastal biodiversity, necessitating proactive conservation for endangered species like the mangrove Acanthus ebracteatus. This study integrated the MaxEnt and OPGD models to simulate its potential suitable habitats under current and three future SSP scenarios (SSP126, SSP245, and SSP585). Based on [...] Read more.
Climate change threatens coastal biodiversity, necessitating proactive conservation for endangered species like the mangrove Acanthus ebracteatus. This study integrated the MaxEnt and OPGD models to simulate its potential suitable habitats under current and three future SSP scenarios (SSP126, SSP245, and SSP585). Based on the MaxEnt model, sea surface salinity (SSS_range), sea surface temperature (SST_max), soil texture (T_silt, T_sand), and annual precipitation (Bio12) were identified as the dominant factors influencing its distribution, with SSS_range emerging as the key constraint. Furthermore, interaction analysis using the OPGD model revealed significant synergistic effects, particularly between salinity and soil properties (q > 0.8), underscoring the importance of multi-factor interactions in ecological niche modeling. Under the three SSP scenarios, the suitable habitat is projected to expand northeastward, accompanied by a poleward shift in the distribution centroid, driven predominantly by warming temperatures and altered rainfall patterns. KDE analysis revealed that existing protected areas do not fully cover regions with high habitat suitability. We propose a stratified conservation strategy that enhances in situ protection in core zones, initiates assisted restoration in potential habitats, and promotes experimental outplanting in future climatically suitable areas. This study provides scientific insights for the conservation and management of Acanthus ebracteatus under global climate change. Full article
(This article belongs to the Topic Responses of Trees and Forests to Climate Change)
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21 pages, 5363 KB  
Article
Organic Fertilizers Promote Accumulation of Mineral Nutrients in Citrus Leaves by Affecting Soil Biochemical Properties and Bacteria
by Lei Yang, Min Wang, Jianjun Yu, Shuang Li and Lin Hong
Plants 2025, 14(18), 2826; https://doi.org/10.3390/plants14182826 - 10 Sep 2025
Abstract
This study aimed to investigate the influence of different organic fertilizers and their concentrations on the growth of ‘Orah’ (Citrus reticulata Blanco) seedlings, as well as on the mineral nutrient contents, chemical and biological properties, and microbial community of the [...] Read more.
This study aimed to investigate the influence of different organic fertilizers and their concentrations on the growth of ‘Orah’ (Citrus reticulata Blanco) seedlings, as well as on the mineral nutrient contents, chemical and biological properties, and microbial community of the soil. Five types of organic fertilizers and three concentrations were studied. The seedling growth indexes, leaf mineral elements, soil mineral elements, soil enzyme activity, and soil microorganisms were measured. The results showed that organic fertilization significantly increased the contents of eight mineral elements in leaves, depending on the types and concentrations used. Specifically, rapeseed cake fertilizer was found to significantly increase the content of iron (Fe), manganese (Mn), and zinc (Zn) in the leaves. Furthermore, compared with applying only chemical fertilizers or no fertilizers at all, the application of organic fertilizer significantly increased the content of soil organic matter (SOM) and several mineral elements in the soil. The bacterial species composition of soil treated with common organic fertilizer and bio-organic fertilizer, and sheep manure were similar; however, the bacterial composition was significantly different in the soil which been treated with rapeseed cake compared to these other three fertilizers. Additionally, PICRUSt function predicting indicates that the core microbial community in the rapeseed cake group could promote synthesis and the transport of sugar, iron and other substances. Organic fertilizer can change soil chemical and biological properties by affecting the core microbial community structure, and further promote accumulation of mineral elements in the leaves of citrus seedlings. Full article
(This article belongs to the Special Issue Nutrient Requirements and Fertilizer Management Strategies in Plant Cultivation, Second Edition)
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21 pages, 8044 KB  
Article
Synergistic Interactions Between Leaf Traits and Photosynthetic Performance in Young Pinus tabuliformis and Robinia pseudoacacia Trees Under Drought and Shade
by Xinbing Yang, Chang Liu, Shaoning Li, Xiaotian Xu, Bin Li, Meng Tian, Shaowei Lu and Na Zhao
Plants 2025, 14(18), 2825; https://doi.org/10.3390/plants14182825 - 10 Sep 2025
Abstract
Spring droughts, increasingly coinciding with canopy shade, interactively stress the growth of urban tree species and are poorly understood in Beijing. Three-year-old saplings of Pinus tabuliformis and Robinia pseudoacacia were subjected to comparative analysis under four drought–shade sequences, with a full-light, well-watered treatment [...] Read more.
Spring droughts, increasingly coinciding with canopy shade, interactively stress the growth of urban tree species and are poorly understood in Beijing. Three-year-old saplings of Pinus tabuliformis and Robinia pseudoacacia were subjected to comparative analysis under four drought–shade sequences, with a full-light, well-watered treatment serving as the control. During two periods encompassing the drought to wilting point and subsequent rewatering, we assessed leaf morphology, water status, photosynthetic gas exchange, and chlorophyll fluorescence. Both species exhibited losses in leaf water and carbon assimilation under drought, yet their adaptive strategies substantially differed. P. tabuliformis conserved water through the stable leaf anatomy and conservative stomatal control. In particular, P. tabuliformis under full-light and drought conditions decreased their specific leaf area (SLA) by 23%, as well as showing reductions in stomatal conductance (Gs) and transpiration rate (Tr) along with the drought duration (p < 0.01). As the duration of post-drought rewatering increased, the reductions in the net photosynthetic rates (Pn) of P. tabulaeformis showed that the shade condition intensified its photosynthetic limitation and slowed recovery after drought. Under low-light drought, R. pseudoacacia exhibited a 52% increase in SLA and a 77% decline in Gs; the latter was markedly smaller than the reduction observed under full-light drought. After rewatering, Gs displayed an overcompensation response. The rise in specific leaf area and the greater flexibility of stomatal regulation partly offset the adverse effects of drought. Nevertheless, post-drought Pn recovered to only 40%, significantly lower than the 61% recovery under full-light drought. Moreover, the negative correlation between SLA and Pn became significantly stronger, indicating that the “after-effects” of shade–drought hindered photosynthetic recovery once the stress was relieved. Drought duration eroded the phenotypic performance in both species, while the light environment during drought and subsequent rehydration determined the time trajectory and completeness of recovery. These results validate a trade-off between shade mitigation and drought legacy, and guide species selection: plant shade-tolerant R. pseudoacacia in light-limited urban pockets and reserve sun-dependent P. tabuliformis for open, high-light sites to enhance drought resilience of Beijing’s urban forests. Full article
(This article belongs to the Special Issue Plant Stress Physiology and Molecular Biology (3rd Edition))
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23 pages, 2284 KB  
Review
Old-Growth Forests and Bryophyte Communities in Italy and the Broader Mediterranean Region: A Literature Review
by Mattia Letizia Marino, Patrizia Campisi and Fortunato Cirlincione
Plants 2025, 14(18), 2824; https://doi.org/10.3390/plants14182824 - 10 Sep 2025
Abstract
Beginning with general references to old-growth forests and the numerous benefits that they provide at multiple levels, this review mentions the main surveys conducted in Italy to identify and characterise Italian old-growth forests and offers an overview of the state of knowledge on [...] Read more.
Beginning with general references to old-growth forests and the numerous benefits that they provide at multiple levels, this review mentions the main surveys conducted in Italy to identify and characterise Italian old-growth forests and offers an overview of the state of knowledge on bryophytes of these ecosystems in Sicily. Then, it focuses on the relationship between bryophyte diversity and old-growth traits (e.g., structural characteristics, long-term continuity), as well as the potential use of bryophytes as bioindicators of forest continuity and naturalness. In this regard, studies on bryophyte floras and communities in old-growth forests were examined in detail not only for Italy but also for the broader Mediterranean region, also taking into account evidence from investigations conducted in other bioclimatic zones. The analysis shows that old-growth forests often provide refuges for rare and noteworthy taxa and host highly diverse bryophyte communities. However, it appears that in Mediterranean forests, which have been less studied than temperate and boreal forests, the influence of certain factors that are known to be important in other contexts, such as deadwood, may be comparatively less relevant. Also, bryophyte species highly related to old-growth stands or with mature and ancient trees in the Mediterranean area are reported. Full article
(This article belongs to the Section Plant Ecology)
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15 pages, 4944 KB  
Article
Zeatin Regulates Somatic Embryogenesis in Liriodendron sino-americanum via CYCD3
by Yuanming Tang, Nannan Chen, Xiao Sun, Liming Zhu, Jinhui Chen and Ying Chen
Plants 2025, 14(18), 2823; https://doi.org/10.3390/plants14182823 - 9 Sep 2025
Abstract
Somatic embryogenesis (SE) is a crucial strategy for in vitro regeneration in woody plants, yet its efficiency is affected by multiple factors, and the underlying regulatory mechanisms remain insufficiently understood. In this study, callus tissues from two Liriodendron sino-americanum genotypes involving different hybrid [...] Read more.
Somatic embryogenesis (SE) is a crucial strategy for in vitro regeneration in woody plants, yet its efficiency is affected by multiple factors, and the underlying regulatory mechanisms remain insufficiently understood. In this study, callus tissues from two Liriodendron sino-americanum genotypes involving different hybrid combinations, ON-LoS and TN-LoS, were treated with varying concentrations (0, 0.005, 0.01, 0.05 mg/L) of exogenous zeatin (ZT) to evaluate its regulatory effect on SE. Treatment with 0.01 mg/L ZT significantly promoted SE in ON-LoS but suppressed it in TN-LoS, indicating that ZT elicited divergent regulatory effects on SE between the two genotypes. To explore the molecular basis of this divergence, transcriptome analysis was conducted at the early stage of SE. Differentially expressed genes (DEGs) were significantly enriched in hormone signaling, particularly in the cytokinin (CK) and brassinosteroid (BR) signaling pathways, as well as biosynthetic and redox-related pathways. In particular, given the established role of cell cycle-related gene CYCD3 (Lchi20922) in promoting cell division, CYCD3 was markedly upregulated by ZT in ON-LoS but downregulated in TN-LoS. These results indicate that ZT regulates SE efficiency through differential modulation of CYCD3 expression in distinct genotypes. This study enhances our understanding of the molecular basis of SE regulation in Liriodendron sino-americanum and offers a theoretical framework for improving regeneration efficiency in woody plants. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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12 pages, 1322 KB  
Article
Chemical Constituents from Euphorbia esula
by Defeng Yan, Miaomiao Zhang, Yuqing Song, Liu Liu, Nurmirza Begmatov, Orzimat Turdimatovich Turginov, Bo Zhao, Hequn Yang and Guoan Zou
Plants 2025, 14(18), 2822; https://doi.org/10.3390/plants14182822 - 9 Sep 2025
Abstract
Euphorbia esula is widely distributed across China, Central Asia and other regions worldwide. For centuries, it has been applied in folk and traditional medicine as a cure for diverse ailments. Nevertheless, the bioactive components responsible for anti-inflammatory and cytotoxic effects remain incompletely identified. [...] Read more.
Euphorbia esula is widely distributed across China, Central Asia and other regions worldwide. For centuries, it has been applied in folk and traditional medicine as a cure for diverse ailments. Nevertheless, the bioactive components responsible for anti-inflammatory and cytotoxic effects remain incompletely identified. In this study, two undescribed chemical constituents, a pyrrole alkaloid (1) and a loliolide analogue (2), alongside nine known components (3–11) were separated from the aerial parts of Euphorbia esula indigenous to Uzbekistan. Their chemical structures were comprehensively elucidated utilizing HRESIMS, NMR, IR and UV spectroscopy. Corresponding absolute configurations were determined based on comparison of experimental and calculated ECD data. Compounds 3–11 were firstly isolated from Euphorbia esula, among which 4, 5, 7 and 9–11 were yielded from the genus Euphorbia for the first time. Chemically, the discovery of various skeletons covering pyrrole alkaloids (1, 9), norisoprenoids (2–8), furanone (10) and unusual cyclooct-2-enone (11) particularly highlighted the structural diversity. Bioactivity assays revealed that some compounds (1, 3, 5, 6, 7 and 8) exhibited certain anti-inflammatory effects via inhibiting the NO release in LPS-induced RAW 264.7 macrophages. Full article
(This article belongs to the Special Issue Phytochemistry, Pharmacology, and Toxicity of Medicinal Plants)
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25 pages, 1811 KB  
Review
Sustainable Production of Ginsenosides: Advances in Biosynthesis and Metabolic Engineering
by Yang Xue, Ruixiang Zhang, Tie Li, Qindi Deng, Weidong Luo, Ruyue Chang, Dongchang Zeng, Jiantao Tan, Tianhu Sun, Yao-Guang Liu, Yang Xiang, Qinlong Zhu and Nan Chai
Plants 2025, 14(18), 2821; https://doi.org/10.3390/plants14182821 - 9 Sep 2025
Abstract
Ginsenosides, the primary bioactive components of Panax ginseng, exhibit diverse pharmacological properties, ranging from anticancer to neuroprotective effects. However, traditional production by ginseng cultivation faces limitations due to extended growth cycles, insufficient yields, intricate extraction processes, and significant environmental dependencies. Synthetic biology [...] Read more.
Ginsenosides, the primary bioactive components of Panax ginseng, exhibit diverse pharmacological properties, ranging from anticancer to neuroprotective effects. However, traditional production by ginseng cultivation faces limitations due to extended growth cycles, insufficient yields, intricate extraction processes, and significant environmental dependencies. Synthetic biology and synthetic metabolic engineering offer promising alternatives for sustainable manufacturing of essential bioactive compounds, including ginsenosides. First, this review describes the ginsenoside biosynthesis pathways, emphasizing crucial enzymes (e.g., HMG-CoA reductase, squalene epoxidase, dammarenediol-II synthase, amyrin synthase, and various UDP-glycosyltransferases) and their regulatory networks. Understanding these fundamental pathways enables rational engineering of production systems. Second, it examines current synthetic biology approaches, encompassing plant cell, tissue, and hairy root cultures, engineered microbial hosts including Saccharomyces cerevisiae and Escherichia coli, and cell-free enzymatic synthesis. Third, it evaluates the medicinal significance, market prospects, and industrial feasibility of these biomanufactured compounds. Finally, it analyzes the sustainability of production models and explores the emerging potential of engineered plant chassis. These advanced methodologies directly address traditional agricultural constraints and establish a robust framework for future ginsenoside synthesis. Full article
(This article belongs to the Section Phytochemistry)
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26 pages, 5087 KB  
Article
High Basal Expression and Dual Stress Responsiveness of Soybean (Glycine max) Resistance Gene SRC4
by Zikai Zhou, Zhuo Bao, Di Miao, Yuxi Zhou, Niu Niu and Hada Wuriyanghan
Plants 2025, 14(18), 2820; https://doi.org/10.3390/plants14182820 - 9 Sep 2025
Abstract
Genes involved in disease resistance are crucial for plant immune systems, yet their transcriptional regulatory mechanisms remain poorly understood. SRC4, a key member of the soybean mosaic virus resistance cluster (SRC), encodes a Ca2+-binding EF-hand domain and possesses antiviral activity, [...] Read more.
Genes involved in disease resistance are crucial for plant immune systems, yet their transcriptional regulatory mechanisms remain poorly understood. SRC4, a key member of the soybean mosaic virus resistance cluster (SRC), encodes a Ca2+-binding EF-hand domain and possesses antiviral activity, but its expression regulation is unclear. Here, we systematically analyzed 4085 soybean (Glycine max) transcriptome datasets and conducted SMV inoculation experiments to characterize SRC4 expression patterns. Cis-acting element analysis identified 12 regulatory elements in the SRC4 promoter, including salicylic acid (SA)-responsive elements. Furthermore, a ProSRC4::GUS reporter vector was constructed and functional analysis was performed in tobacco (Nicotiana benthamiana) and transgenic Arabidopsis thaliana. SRC4 exhibited significantly higher basal expression than typical resistance genes (R genes) and was induced by SMV infection, SA treatment, and Ca2+ supplementation, with peak expression at 2–5 h post-treatment (hpi). In transgenic tobacco overexpressing NahG, neither SMV nor Ca2+ could induce ProSRC4::GUS expression, demonstrating that SRC4 transcriptional regulation is mediated through SA signaling pathways. SRC4 showed predominant expression in roots and leaves and responded to temperature stress. Transgenic plants overexpressing SRC4 exhibited enhanced tolerance to both 12 °C and 37 °C temperature stress. This study elucidates the molecular mechanisms underlying SRC4 transcriptional regulation through Ca2+ and SA signaling pathways, revealing its dual role in both biotic and abiotic stress responses, especially in temperature stress. Full article
(This article belongs to the Special Issue Advances in Soybean Research: From Genetics to Climate Resilience and Sustainable Production)
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16 pages, 4560 KB  
Article
Functional Changes of Rhizosphere and Non-Rhizosphere Soils Under the Decline of Pinus sylvestris var. mongolica Plantations
by Tao Kong, Zeyu Zeng, Haotian Cheng, Sinuo Bao, Lin Xiao, Tong Liu and Xiaoliang Zhao
Plants 2025, 14(18), 2819; https://doi.org/10.3390/plants14182819 - 9 Sep 2025
Abstract
The decline of Mongolian Scots pine (Pinus sylvestris var. mongolica) plantations in the “Three-North” shelterbelt region is closely linked to soil degradation. This study compared rhizosphere and non-rhizosphere soils across different stand ages, focusing on nutrient availability, microbial biomass, enzyme activities, [...] Read more.
The decline of Mongolian Scots pine (Pinus sylvestris var. mongolica) plantations in the “Three-North” shelterbelt region is closely linked to soil degradation. This study compared rhizosphere and non-rhizosphere soils across different stand ages, focusing on nutrient availability, microbial biomass, enzyme activities, and soil particle morphology. Results showed that SOC and TN accumulated with age, whereas AP, AK, and pH declined in older stands, indicating progressive acidification. Results demonstrated that SOC and TN increased with stand age, whereas AP, AK, and pH exhibited a marked decline in the older stands (stands aged ≥ 40 years), reflecting progressive acidification and nutrient depletion. Rhizosphere soils consistently displayed higher SOC, TN, microbial biomass, and enzyme activities than non-rhizosphere soils, largely driven by root exudation and enhanced microbial turnover. The increasing Cmic/Nmic ratio with age suggested a fungal-dominated microbial community, which may exacerbate stand decline by fostering pathogenic fungi. Scanning electron microscopy revealed pronounced particle fragmentation and surface roughness with increasing stand age, particularly in rhizosphere soils, indicating root-driven physical and biochemical weathering. These findings highlight the synergistic effects of stand development and rhizosphere processes on soil structure and fertility, providing a theoretical basis for the sustainable management and restoration of declining plantations. Full article
(This article belongs to the Special Issue Soil-Beneficial Microorganisms and Plant Growth: 2nd Edition)
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12 pages, 9775 KB  
Article
5-AzaC Facilitates Somatic Embryogenesis and Germination Across Two Embryogenic Lines in Larix olgensis
by Wenna Zhao, Yu Liu, Chen Wang, Yajing Ning, Chengpeng Cui, Hanguo Zhang, Meng Li and Shujuan Li
Plants 2025, 14(18), 2818; https://doi.org/10.3390/plants14182818 - 9 Sep 2025
Abstract
Long-term subculture of embryogenic callus leads to a decline in somatic embryogenesis and germination capacity, which may be associated with increased methylation levels. 5-Azacytidine (5-AzaC), a methylation inhibitor, modulates DNA methylation and is widely involved in regulating plant growth, development, and metabolism. In [...] Read more.
Long-term subculture of embryogenic callus leads to a decline in somatic embryogenesis and germination capacity, which may be associated with increased methylation levels. 5-Azacytidine (5-AzaC), a methylation inhibitor, modulates DNA methylation and is widely involved in regulating plant growth, development, and metabolism. In order to investigate the effect of 5-AzaC on somatic embryogenesis and germination in Larix olgensis, we supplemented the proliferation medium with different concentrations of 5-AzaC. The results showed that the addition of 5-AzaC inhibited the proliferation of embryogenic callus, with the proliferation of embryogenic line N2 completely inhibited at 100 μM, while that of embryogenic line N4 ceased at 20 μM. In contrast, treatment with 10 μM and 20 μM of 5-AzaC significantly increased the somatic embryo yield in both embryogenic lines, with the peak yield observed at 20 μM for embryogenic line N2 and at 10 μM for embryogenic line N4. Furthermore, the addition of 10 μM 5-AzaC effectively reduced the deformity rate during somatic embryo germination in embryogenic line N2 and N4, by 15.91% and 13.53%, respectively. These findings demonstrate that 5-AzaC can partially restore the somatic embryogenesis potential of embryogenic callus in L. olgensis under long-term subculture. Additionally, these results suggest that its effects may be both concentration-dependent and genotype-specific. The results provide a potential approach to mitigating the decline in embryogenic competence, while also demonstrating significant potential for large-scale propagation. Full article
(This article belongs to the Special Issue Sexual and Asexual Reproduction in Forest Plants—2nd Edition)
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19 pages, 7094 KB  
Article
Group 1 LEA Proteins in Durum Wheat: Evolution, Expression, and Roles in Abiotic Stress Tolerance
by Najeh Soltani, Ikram Zaidi, Mohamed Najib Saidi and Faiçal Brini
Plants 2025, 14(18), 2817; https://doi.org/10.3390/plants14182817 - 9 Sep 2025
Abstract
Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive [...] Read more.
Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive survey of group 1 LEA proteins and their encoding genes in Triticum turgidum ssp. Durum (durum wheat). Eight group 1 LEA (TtEM1 to TtEM8) genes were identified in the durum wheat genome, which were named according to their chromosomal location. Analyses of the physiochemical characteristics and subcellular location revealed that all TtEM proteins exhibited a highly disordered structure (more than 90% of tendency of disorder) and were located in the nucleus. Evolutionary analysis between the durum wheat family and all other known group 1 LEA proteins from Arabidopsis thaliana, rice (Oryza sativa), barley (Hordeum vulgare), and barrel medic (Medicago truncatula) showed four phylogenetic groups; each group shares the same conserved motifs and gene structure. Interestingly, almost TtEM genes harbor cis-elements related to hormone regulation, stress response, and growth regulation, indicating their function in stress tolerance and developmental control. Subsequently, Expression analysis of two homoeologous genes, TtEM1 and TtEM4, demonstrated that the two genes exhibited distinct expression profiles across different tissues and in response to various stress treatments, suggesting that these genes may be involved in regulating growth, development, and stress adaptation in durum wheat. TtEM1 and TtEM4 purified proteins act as molecular chaperones and protect LDH activity against desiccation, cold, and heat treatments. Moreover, TtEM1 and TtEM4 genes were proved to enhance heat, cold, oxidative, and drought tolerance in yeast. These results clearly described the characteristics and the evolutionary dynamics of the EM gene family in wheat, and unveiled their role in wheat development and response to abiotic stress. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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13 pages, 1796 KB  
Article
Changes in Cell Aggregation in Arabidopsis thaliana Suspension Culture Following Knockout of GAUT Gene Family Members
by Tatyana A. Frankevich, Natalya V. Permyakova, Yury V. Sidorchuk and Elena V. Deineko
Plants 2025, 14(18), 2816; https://doi.org/10.3390/plants14182816 - 9 Sep 2025
Abstract
Plant cells, particularly suspension cell cultures, represent a promising platform for the biosynthesis of biopharmaceutical proteins. However, one of the limitations of this system is the tendency of cells to form aggregates of varying sizes, which can restrict their productivity in terms of [...] Read more.
Plant cells, particularly suspension cell cultures, represent a promising platform for the biosynthesis of biopharmaceutical proteins. However, one of the limitations of this system is the tendency of cells to form aggregates of varying sizes, which can restrict their productivity in terms of recombinant protein accumulation. The primary cause of such aggregation is likely related to intercellular adhesion, which is characteristic of plant cells grown in vitro. To assess the potential for reducing intercellular adhesion in in vitro plant cell cultures, we obtained two Arabidopsis thaliana cell lines carrying mutations in the GAUT7 and GAUT8 genes, which are involved in the biosynthesis of cell wall pectin. The GAUT7 mutant was generated by CRISPR/Cas9-mediated knockout of the target gene in a transgenic A. thaliana line carrying the gfp gene. The GAUT8 mutant cell line was derived from the A. thaliana Quasimodo1-1 mutant. We present a comparative analysis of these two in vitro cultured cell lines in terms of their aggregation behavior. The resulting mutant with a knockout in the GAUT7 gene had an altered cell culture phenotype. The GAUT7 suspension culture was characterized by a darker coloration, an increase in the number of large aggregates by 18%, and a decrease in the level of pectins, and the accumulation of recombinant GFP protein in the GAUT7 culture significantly decreased by 10.4%. The Qua1-1 culture showed the opposite results: a 20% decrease in the number of large aggregates, a high increase in biomass, and an increased level of pectins compared with the control and GAUT7. Thus, we have shown that a violation of pectin synthesis leads to different results depending on which GAUT family gene we knock out; intercellular adhesion decreased in the cell culture with a knockout of the GAUT8 gene. These data can be used to improve the properties of plant cellular expression systems of biopharmaceutically valuable proteins. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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11 pages, 3622 KB  
Communication
Are Furanocoumarins Present in the Cichorieae Tribe of Asteraceae? A Comparative Study of Cicerbita alpina (Asteraceae) and Peucedanum ostruthium (Apiaceae)
by Calisto Moreno Cardenas, Gaia Maria Francesca Grieco, Dimitrina Zheleva-Dimitrova, Giovanni Appendino and Christian Zidorn
Plants 2025, 14(18), 2815; https://doi.org/10.3390/plants14182815 - 9 Sep 2025
Abstract
Cicerbita alpina (L.) Wallroth and Peucedanum ostruthium W.D.J. Koch occur in megaphorb communities in alpine and subalpine areas; both species often share the same habitats. P. ostruthium is used as a spice for spirits, while young shoots of C. alpina are collected in [...] Read more.
Cicerbita alpina (L.) Wallroth and Peucedanum ostruthium W.D.J. Koch occur in megaphorb communities in alpine and subalpine areas; both species often share the same habitats. P. ostruthium is used as a spice for spirits, while young shoots of C. alpina are collected in the northeastern regions of Italy as a local delicacy. In the present study, we isolated eleven known coumarins and one chromone from subaerial parts of P. ostruthium; two furanocoumarins were found for the first time in this species. Using UHPLC-HRMS, we analyzed the furanocoumarin content of two P. ostruthium accessions, one commercially purchased and one collected in the wild. These samples were compared to six rootstock samples of Cicerbita alpina collected in the wild. Though the furanocoumarins imperatorin, isoimperatorin, oxypeucedanin, and ostruthol had been reported from C. alpina before, we were not able to detect any of these compounds in our samples of C. alpina. Therefore, and due to the occurrence of both taxa in the same habitat, we assume that the original report of furanocoumarins in C. alpina was based on a mixed collection of C. alpina and P. ostruthium. This hypothesis seems plausible, because furanocoumarins have not been reported from any other taxon of the Cichorieae tribe of the Asteraceae family. Full article
(This article belongs to the Special Issue Valuable Sources of Bioactive Natural Products from Plants, 2nd Edition)
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14 pages, 735 KB  
Article
Genetic Diversity in Coffea canephora Genotypes via Digital Phenotyping
by Priscila Sousa, Henrique Vieira, Eileen Santos, Alexandre Viana and Fábio Partelli
Plants 2025, 14(18), 2814; https://doi.org/10.3390/plants14182814 - 9 Sep 2025
Abstract
C. canephora exhibits high genetic variability, and to estimate this variability, morphological descriptors associated with coffee quality are used. Bean size is a physical trait of great importance for coffee classification. Manual classification is known to be inaccurate and time-consuming, which is why [...] Read more.
C. canephora exhibits high genetic variability, and to estimate this variability, morphological descriptors associated with coffee quality are used. Bean size is a physical trait of great importance for coffee classification. Manual classification is known to be inaccurate and time-consuming, which is why researchers have adopted digital imaging techniques to improve classification efficiency. The objective of this study was to quantify the genetic diversity in 43 C. canephora clones using the Ward-MLM strategy and to estimate genetic parameters and correlations from digital phenotyping of beans and cherries. The experiment was conducted on a crop consisting of 43 C. canephora genotypes, where the cherries were manually pulped and dried until they reached 12% moisture content. Using GroundEye® equipment, four replicates of 50 beans and cherries were evaluated for each treatment, and the software generated spreadsheets with the results of the geometric traits. To determine the existence of genetic variability among the genotypes, the data obtained were subjected to analysis of variance, estimation of genetic parameters, Ward-MLM analysis, and Pearson correlation. The genotypic variance was higher than the environmental variance for all variables analyzed, both for beans and cherries, indicating that the genotypes evaluated have high genetic variability. The greatest genetic distance was observed between groups I and IV, suggesting favorable conditions for crosses between the genotypes of these groups. Phenotypic correlation analysis revealed significant positive and negative correlations between the variables. Digital seed analysis successfully detected genetic divergence among the 43 C. canephora clones. The variables ‘area’, ‘maximum diameter’, and ‘minimum diameter’ are the most suitable for selecting genotypes with larger beans. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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Article
Effects of Abscisic Acid Induction on the Underground Weed Inhibition Strategies of Allelopathic and Non-Allelopathic Rice Accessions
by Jiayu Li, Ting Wang, Xinyi Ye, Shuyu Chen, Yanping Wang and Changxun Fang
Plants 2025, 14(18), 2813; https://doi.org/10.3390/plants14182813 - 9 Sep 2025
Abstract
Despite our preliminary research about the inductive effect of exogenous abscisic acid (ABA) on the weed-suppressive activity of rice in a hydroponic system, there is a lack of knowledge regarding the induction mechanism for ABA application to enhance the ability for weed control [...] Read more.
Despite our preliminary research about the inductive effect of exogenous abscisic acid (ABA) on the weed-suppressive activity of rice in a hydroponic system, there is a lack of knowledge regarding the induction mechanism for ABA application to enhance the ability for weed control underground. Here, two pot experiments using rice–barnyard grass mixed culture were conducted to investigate the effects of exogenous ABA treatment on weed inhibition strategies in both allelopathic rice PI312777 (PI) and non-allelopathic rice Lemont (Le). The largest observed weed inhibition changes in the two rice accessions both occurred with the 9 μmol/L ABA treatment. ABA induction on PI significantly increases the inhibitory effect on the plant height of barnyard grass with root contact and root segregation by 25.7% and 19.1%, respectively, with 23.5% increases observed in Le rice with root contact and no significant increases in plants with root segregation with nylon mesh. ABA induction also significantly increased the root distribution in the soil of Le. Compared with the uninduced group, ABA treatment significantly elevated the total amounts of reversibly adsorbed phenolic acids in the two soil layers of PI and the irreversibly adsorbed phenolic acids in Le soil layers. Furthermore, exogenous ABA could change the bacterial composition in rhizosphere soil of the two rice accessions, with the change in the species composition in the rhizosphere soil of the allelopathic rice PI being greater. Importantly, the bacterial compositions (Anaerolineales, Bacteroidales, and Myxococcale) in the PI rhizosphere soil of rice induced by ABA were more related to the contents of reversibly adsorbed phenolic acids in the soil. However, the core bacterial compositions that promote plant growth (Sphingomonadales, Cyanobacteriales, and Rhizobiales) in the Le rhizosphere soil were more related to the contents of irreversibly adsorbed phenolic acids in the soil. These findings suggested that the ABA induction mainly changed root distribution and core bacterial compositions in Le to enhance resource competition, whereas it stimulated the release of reversibly adsorbed phenolic acids to modulate the specific bacterial compositions in rhizosphere soil of PI and to strengthen allelopathic effects. Full article
(This article belongs to the Special Issue Weed Management and Control in Paddy Fields)
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