Plants

18 pages, 4206 KiB

Open AccessArticle

Multi-Omics and Functional Insights into Triterpenoid Biosynthesis Pathways in Neopicrorhiza scrophulariiflora (Pennell) D.Y.Hong

by Pinhan Zhou, Juan Wang, Chaohui Li, Lesong Li, Luyuan Duan, Weihao Wang, Xirui Liu, Khadija Tehseen Arshad, Yanli Liang and Yan Zhao

Plants 2025, 14(10), 1562; https://doi.org/10.3390/plants14101562 - 21 May 2025

Viewed by 392

Abstract

Neopicrorhiza scrophulariiflora (Pennell) D.Y.Hong, an endangered perennial herb, is rich in triterpenes, iridoids, and phenolic compounds, which exhibit significant pharmacological effects. However, the molecular mechanisms of triterpenoid biosynthesis in N. scrophulariiflora remain unclear. Here, transcriptomic and metabolomic analyses were performed to investigate the [...] Read more.

Neopicrorhiza scrophulariiflora (Pennell) D.Y.Hong, an endangered perennial herb, is rich in triterpenes, iridoids, and phenolic compounds, which exhibit significant pharmacological effects. However, the molecular mechanisms of triterpenoid biosynthesis in N. scrophulariiflora remain unclear. Here, transcriptomic and metabolomic analyses were performed to investigate the triterpene content in different tissues and the expression patterns of key enzyme-encoding genes related to triterpenoid biosynthesis. We functionally characterized eight upstream oxidosqualene cyclases (OSCs) involved in triterpenoid biosynthesis, among which NsOSC2 is a bifunctional enzyme capable of catalyzing the conversion of 2,3-oxidosqualene to β-amyrin and α-amyrin. Additionally, an efficient regeneration system and a stable genetic transformation system were established for N. scrophulariiflora. These findings reveal key genes in triterpenoid biosynthesis, providing a theoretical foundation for the future production of key triterpenoids in N. scrophulariiflora through synthetic biology approaches. Full article

(This article belongs to the Section Phytochemistry)

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20 pages, 2415 KiB

Open AccessArticle

Integrated Transcriptomic and Targeted Metabolomic Analyses Elucidate the Molecular Mechanism Underlying Dihydromyricetin Synthesis in Nekemias grossedentata

by Fuwen Wu, Zhi Feng, Zhi Yao, Peiling Zhang, Yiqiang Wang and Meng Li

Plants 2025, 14(10), 1561; https://doi.org/10.3390/plants14101561 - 21 May 2025

Viewed by 385

Abstract

Nekemias grossedentata (Hand.-Mazz.) J. Wen & Z. L. Nie is a medicinal and edible plant with a high dihydromyricetin (DHM) content in its bud tips. Vine tea made from its bud tips has served as a health tea and Chinese herbal medicine for [...] Read more.

Nekemias grossedentata (Hand.-Mazz.) J. Wen & Z. L. Nie is a medicinal and edible plant with a high dihydromyricetin (DHM) content in its bud tips. Vine tea made from its bud tips has served as a health tea and Chinese herbal medicine for nearly 700 years. However, the molecular mechanisms underlying the high DHM content in N. grossedentata bud tips remain inadequately elucidated. This study conducted qualitative and quantitative analyses of bud tip flavonoids utilizing HPLC and targeted metabolomics. Core genes influencing the substantial synthesis of DHM in N. grossedentata were identified through integrated transcriptome and metabolome analyses. The results revealed that 65 flavonoid metabolites were detected in bud tips, with DHM as the predominant flavonoid (37.5%), followed by myricetin (0.144%) and taxifolin (0.141%). Correlation analysis revealed a significant positive correlation between NgF3′5′H3 expression and DHM content. Co-expression analysis and qRT-PCR validation demonstrated a significant positive correlation between NgMYB71 and NgF3′5′H3, with consistent expression trends across three periods and four tissues. Consequently, NgF3′5′H3 and NgMYB71 were identified as core genes influencing the substantial synthesis of DHM in N. grossedentata. Elevated NgMYB71 expression in bud tips induced high NgF3′5′H3 expression, facilitating extensive DHM synthesis in bud tips. Molecular docking analysis revealed that NgF3′5′H3 had a strong binding affinity for taxifolin. NgF3′5′H3 was the pivotal core node gene in the dihydromyricetin biosynthesis pathway in N. grossedentata and was highly expressed in bud tips. The strong specific binding of NgF3′5′H3 to dihydromyricetin precursor metabolites catalyzed their conversion into DHM, resulting in higher DHM contents in bud tips than in other tissues or plants. This study aimed to elucidate the molecular mechanisms underlying the substantial synthesis of DHM in N. grossedentata, providing a theoretical foundation for enhancing DHM production and developing N. grossedentata resources. Full article

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

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17 pages, 2536 KiB

Open AccessArticle

Drought-Induced Zinc Finger Transcription Factor OsDi19-3 Positively Regulates Drought Stress Acclimatization in Rice (Oryza sativa L.)

by Yanjie Li, Tianjiao Mu, Tianying Ren and Pan Li

Plants 2025, 14(10), 1560; https://doi.org/10.3390/plants14101560 - 21 May 2025

Viewed by 287

Abstract

The plant Di19 (drought-induced 19) protein belongs to zinc finger transcription factors, which play crucial roles in drought stress acclimatization. OsDi19-3, a drought-induced transcription factor in rice, has not been fully characterized for its biological role in stress acclimatization. In this study, transgenic [...] Read more.

The plant Di19 (drought-induced 19) protein belongs to zinc finger transcription factors, which play crucial roles in drought stress acclimatization. OsDi19-3, a drought-induced transcription factor in rice, has not been fully characterized for its biological role in stress acclimatization. In this study, transgenic rice overexpressing OsDi19-3 was generated. Water deprivation experiments showed that transgenic plants exhibited higher drought tolerance than wild-type (WT) plants, indicating that OsDi19-3 positively regulates drought stress acclimatization. Consistent with this, stomata in overexpression lines closed more significantly than those in WT under drought stress. To explore the molecular mechanism, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments identified two interacting proteins of OsDi19-3: OsCAMK1 and OsNEK6. Notably, these two proteins also interacted with each other. A transcriptome analysis of OsDi19-3 transgenic plants revealed 224 upregulated and 167 downregulated genes (log₂(OE/WT) > 1, p-value < 0.05), including multiple stress-responsive genes. Furthermore, a ChIP-PCR analysis confirmed that OsDi19-3 directly binds to three target genes. This study provides insights into the role of OsDi19-3 in drought acclimatization and its regulatory network in rice. Full article

(This article belongs to the Special Issue Physiological and Molecular Responses for Stress Tolerance in Rice)

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23 pages, 8092 KiB

Open AccessArticle

Freshwater Algae Biostimulant in Mitigating Impacts of Saline Irrigation on Onions

by Jean Carlos Nogueira, Jefferson dos Santos Gomes Calaça, Carla Veronica Barbosa de Souza Gomes, Luiz Emanuel Callou Menezes, José Raliuson Inácio Silva, Alexandre Maniçoba da Rosa Ferraz Jardim, Luiz Guilherme Medeiros Pessoa, João Henrique Barbosa da Silva, Ramon Freire da Silva, Thiago Jardelino Dias and Genival Barros Júnior

Plants 2025, 14(10), 1559; https://doi.org/10.3390/plants14101559 - 21 May 2025

Viewed by 400

Abstract

Salinity poses a significant challenge in modern agriculture, often inhibiting growth and yield, especially in sensitive crops like onions (Allium cepa L.). This study evaluated the effectiveness of a freshwater-algae-based biostimulant on two onion cultivars, Franciscana IPA-10 and Vale Ouro IPA-11, to [...] Read more.

Salinity poses a significant challenge in modern agriculture, often inhibiting growth and yield, especially in sensitive crops like onions (Allium cepa L.). This study evaluated the effectiveness of a freshwater-algae-based biostimulant on two onion cultivars, Franciscana IPA-10 and Vale Ouro IPA-11, to mitigate saline irrigation’s adverse effects. Five biostimulant concentrations (0, 1, 2, 3, and 4 mL L⁻¹, applied to the soil) were tested, along with two foliar treatments at 2 mL L⁻¹ as controls. Our findings showed that applying 4 mL L⁻¹ to the soil boosted growth rates to 1.0 cm per day (1), increased the potassium-to-sodium ratio in bulbs, and improved both average bulb weight by 25.11% and overall productivity by 24.28%, relative to untreated conditions. These results suggest that the biostimulant at 4 mL L⁻¹ is an effective method to enhance resilience to saline stress and increase productivity in the IPA-10 and IPA-11 cultivars. However, while the biostimulant improved plant performance, it did not counteract the accumulation of salts in the soil. Therefore, additional management practices such as leaching and drainage are recommended to ensure sustainable onion production under saline water irrigation. Full article

(This article belongs to the Special Issue Innovative Fertilizers and Nutrient Chemistry for Sustainable Agriculture)

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26 pages, 1143 KiB

Open AccessReview

Alleviation of Plant Abiotic Stress: Mechanistic Insights into Emerging Applications of Phosphate-Solubilizing Microorganisms in Agriculture

by Xiujie Wang, Zhe Li, Qi Li and Zhenqi Hu

Plants 2025, 14(10), 1558; https://doi.org/10.3390/plants14101558 - 21 May 2025

Viewed by 382

Abstract

Global agricultural productivity and ecosystem sustainability face escalating threats from multiple abiotic stresses, particularly heavy metal contamination, drought, and soil salinization. In this context, developing effective strategies to enhance plant stress tolerance has emerged as a critical research frontier. Phosphate-solubilizing microorganisms (PSMs) have [...] Read more.

Global agricultural productivity and ecosystem sustainability face escalating threats from multiple abiotic stresses, particularly heavy metal contamination, drought, and soil salinization. In this context, developing effective strategies to enhance plant stress tolerance has emerged as a critical research frontier. Phosphate-solubilizing microorganisms (PSMs) have garnered significant scientific attention due to their capacity to convert insoluble soil phosphorus into plant-available forms through metabolite production, and concurrently exhibiting multifaceted plant growth-promoting traits. Notably, PSMs demonstrate remarkable potential in enhancing plant resilience and productivity under multiple stress conditions. This review article systematically examines current applications of PSMs in typical abiotic stress environments, including heavy metal-polluted soils, arid ecosystems, and saline–alkaline lands. We comprehensively analyze the stress-alleviation effects of PSMs and elucidate their underlying mechanisms. Furthermore, we identify key knowledge gaps and propose future research directions in microbial-assisted phytoremediation and stress-mitigation strategies, offering novel insights for developing next-generation bioinoculants and advancing sustainable agricultural practices in challenging environments. Full article

(This article belongs to the Special Issue Integrative Approaches to Understanding and Improving Plant Stress Tolerance)

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17 pages, 5196 KiB

Open AccessArticle

Upregulation of an IAA-Glucosyltransferase OsIAGLU in Rice (Oryza sativa L.) Impairs Root Gravitropism by Disrupting Starch Granule Homeostasis

by Guo Chen, Xiaoyu Fu, Xinya Ruan, Xiaolu Yu, Dianyun Hou and Huawei Xu

Plants 2025, 14(10), 1557; https://doi.org/10.3390/plants14101557 - 21 May 2025

Viewed by 257

Abstract

Indole-3-acetic acid (IAA) glycosyltransferase (IAGLU) plays vital roles in modulating plant development and responses to environmental cues. Here, we elucidate the regulatory mechanism of OsIAGLU in modulating root gravitropism using OsIAGLU-overexpressing (OE) rice (Oryza sativa L.). OsIAGLU upregulation substantially decreases IAA [...] Read more.

Indole-3-acetic acid (IAA) glycosyltransferase (IAGLU) plays vital roles in modulating plant development and responses to environmental cues. Here, we elucidate the regulatory mechanism of OsIAGLU in modulating root gravitropism using OsIAGLU-overexpressing (OE) rice (Oryza sativa L.). OsIAGLU upregulation substantially decreases IAA levels, resulting in the impairment of multiple agronomic traits and root gravitropism, as well as nearly complete suppression of starch granule accumulation in rice root tips. Exogenous application of the auxin analog 1-naphthaleneacetic acid (NAA) effectively rescued both starch granule accumulation and root gravitropism. Starch synthesis genes exhibited relatively stable or slightly decreased expression following NAA treatments, whereas all starch degradation genes displayed a consistent downward trend in expression after NAA treatment. This suggests that starch degradation genes may play a more prominent role in regulating starch granule accumulation in rice roots, contrasting sharply with their roles in Arabidopsis. Moreover, decreased auxin levels perturbed the accumulation and distribution of hydrogen peroxide (H₂O₂) in rice root tips, while NAA treatment restored normal H₂O₂ distribution and accumulation in OE roots. This study clearly demonstrates that auxin not only functions in regulating agronomic traits but also plays an essential role in gravity perception by modulating starch granule accumulation in rice root tips. Full article

(This article belongs to the Special Issue New Gene Mining, New Technology Development, and New Variety Creation for Crop Improvement)

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14 pages, 2975 KiB

Open AccessArticle

The Alkaloid Gelsemine Reduces Aβ Peptide Toxicity by Targeting Transglutaminase Type 2 Enzyme

by Jessica Panes-Fernández, Ana M. Marileo, Nicole Espinoza-Rubilar, Macarena E. Meza, Bernardita A. Salgado-Martínez, Krishna Gaete-Riquelme, Gustavo Moraga-Cid, Patricio A. Castro, Carlos F. Burgos, Jorge Fuentealba and Gonzalo E. Yévenes

Plants 2025, 14(10), 1556; https://doi.org/10.3390/plants14101556 - 21 May 2025

Viewed by 333

Abstract

Gelsemine, a naturally occurring indole alkaloid derived from plants of the Gelsemium species of the Gelsemiaceae family, has been extensively investigated for its neuroprotective and anti-inflammatory properties. Recent studies have demonstrated that gelsemine exerts neuroprotective effects against beta-amyloid (Aβ) oligomers, a key neurotoxic [...] Read more.

Gelsemine, a naturally occurring indole alkaloid derived from plants of the Gelsemium species of the Gelsemiaceae family, has been extensively investigated for its neuroprotective and anti-inflammatory properties. Recent studies have demonstrated that gelsemine exerts neuroprotective effects against beta-amyloid (Aβ) oligomers, a key neurotoxic peptide implicated in the pathogenesis of Alzheimer’s disease (AD). However, despite these beneficial effects, the precise molecular targets underlying gelsemine’s neuroprotective actions in AD remain unidentified. Here, we employed a combination of bioinformatic, biochemical, and functional assays in neuronal models to investigate the mechanism of gelsemine’s action in AD cellular models. Our findings indicate that gelsemine inhibits the activity of transglutaminase 2 (TG2), an enzyme involved in protein cross-linking with emerging roles in Aβ aggregation and neurotoxicity. Molecular modeling and biochemical analyses reveal that gelsemine interacts with the TG2 catalytic site, leading to its inhibition. Furthermore, gelsemine modulates the TG2-mediated Aβ aggregation process, thereby attenuating Aβ-induced neurotoxicity and preserving neuronal function. These findings establish TG2 as a previously unrecognized molecular target of gelsemine and underscore the potential of Gelsemium-derived alkaloids as neuroprotective agents. The modulation of TG2 activity by natural alkaloids may provide a novel therapeutic approach for mitigating Aβ toxicity and preserving neuronal function in AD. Full article

(This article belongs to the Special Issue Alkaloids: Chemical Structures with Pharmaceutical Potential)

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27 pages, 4117 KiB

Open AccessArticle

Integrated Analyses Reveal the Physiological and Molecular Mechanisms of Brassinolide in Modulating Salt Tolerance in Rice

by Jia-Shuang Wu, De-Wei Mu, Nai-Jie Feng, Dian-Feng Zheng, Zhi-Yuan Sun, Aaqil Khan, Hang Zhou, Yi-Wen Song, Jia-Xin Liu and Jia-Qi Luo

Plants 2025, 14(10), 1555; https://doi.org/10.3390/plants14101555 - 21 May 2025

Viewed by 443

Abstract

Salt stress poses a significant threat to crop growth. While brassinolide (BR) has been shown to alleviate its adverse effects and modulate plant development, the precise mechanism underlying BR-induced salt tolerance in rice remains unclear. In this study, the Chaoyouqianhao and Huanghuazhan rice [...] Read more.

Salt stress poses a significant threat to crop growth. While brassinolide (BR) has been shown to alleviate its adverse effects and modulate plant development, the precise mechanism underlying BR-induced salt tolerance in rice remains unclear. In this study, the Chaoyouqianhao and Huanghuazhan rice varieties were employed to investigate the effects of BR seed soaking on the seedling phenotype, physiology, transcriptome, and metabolome under salt stress. The results demonstrated that BR treatment significantly enhanced rice plant height, root length, biomass, and antioxidant enzyme activities, while reducing leaf membrane damage, promoting ion homeostasis, and improving the photosynthetic capacity and salt tolerance. The transcriptome analysis revealed that BR regulated the expression of 1042 and 826 genes linked to antioxidant activity, ion homeostasis, photosynthesis, and lipid metabolism under salt stress. These included genes involved in Na⁺ efflux (OsNCED2, OsHKT2;1, and OsHKT1;1), photosynthetic electron transport (OsFd5 and OsFdC1), photosystem II (OsPsbR1, OsPsbR2, and OsPsbP), and CO₂ fixation. The metabolomic analysis identified 91 and 57 metabolite alterations induced by BR, primarily linked to amino acid, flavonoid, and lipid metabolism, with notable increases in antioxidant metabolites such as lignanoside, isorhamnetin, and L-glutamic acid. The integrated analysis highlighted the pivotal roles of 12-OPDA in α-linolenic acid metabolism and genes related to lipid metabolism, JA metabolism, and JA signal transduction in BR-mediated salt tolerance. Full article

(This article belongs to the Section Plant Physiology and Metabolism)

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18 pages, 2801 KiB

Open AccessReview

Understanding the Brassinosteroid-Dependent Environmental Adaption in Brassicaceae Plants

by Zhenni Lu, Changrui Ma, Yuzhen Xie, Yuqing Zeng, Jiashi Peng, Dinggang Zhou and Jinfeng Wu

Plants 2025, 14(10), 1554; https://doi.org/10.3390/plants14101554 - 21 May 2025

Viewed by 489

Abstract

Plant adaptation to various stresses depends on transmitting the external stress signals into internal signals. Brassinosteroids (BRs) play pivotal roles in connecting the external and internal signals in Brassicaceae plants, particularly under abiotic stresses such as drought, cold, heat and salinity. They modulate [...] Read more.

Plant adaptation to various stresses depends on transmitting the external stress signals into internal signals. Brassinosteroids (BRs) play pivotal roles in connecting the external and internal signals in Brassicaceae plants, particularly under abiotic stresses such as drought, cold, heat and salinity. They modulate plant growth and stress responses through receptor kinase-mediated signaling pathways, which integrate with redox homeostasis, antioxidant systems and crosstalk with other phytohormones, including auxin, abscisic acid, ethylene, cytokinins, gibberellines, jasmonates and salicylic acid. BR-dependent pathways are critical for balancing stress resilience and productivity in Brassicaceae plants. In this review, we introduce BR metabolism, signaling transduction and discuss their functions in regulating growth and development processes under adverse environment in Brassicaceae plants. We also emphasize recent advances in the crosstalk among BR and other phytohormones in stresses response. Understanding the mechanisms of BR-dependent pathways offers new approaches for enhancing the adaptation under adverse conditions in Brassicaceae crops. Full article

(This article belongs to the Special Issue Physiological and Genetic Mechanisms of Abiotic Stress Tolerance in Crops, Third Edition)

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28 pages, 1724 KiB

Open AccessReview

Managing Arsenic Pollution from Soil–Plant Systems: Insights into the Role of Biochar

by Qitao Su, Zhixuan Du, Xinyi Huang, Muhammad Umair Hassan and Faizah Amer Altihani

Plants 2025, 14(10), 1553; https://doi.org/10.3390/plants14101553 - 21 May 2025

Viewed by 490

Abstract

Soil contamination with arsenic (As) is becoming a serious concern for living organisms. Arsenic is a nonessential metalloid for plants, humans, and other living organisms. Biochar (BC) is a very effective amendment to remediate polluted soils and it received great attention owing to [...] Read more.

Soil contamination with arsenic (As) is becoming a serious concern for living organisms. Arsenic is a nonessential metalloid for plants, humans, and other living organisms. Biochar (BC) is a very effective amendment to remediate polluted soils and it received great attention owing to its appreciable results. Arsenic toxicity negatively affects plant morph-physiological and biochemical functioning and upsurges the generation of reactive oxygen species (ROS), which negatively affect cellular structures. Arsenic toxicity also reduces seed germination and impedes plant growth by decreasing nutrient uptake, causing oxidative damage and disrupting the photosynthetic efficiency. Plants use different strategies like antioxidant defense and increased osmolyte synthesis to counteract As toxicity; nevertheless, this is not enough to counter the toxic impacts of As. Thus, applying BC has shown tremendous potential to counteract the As toxicity. Biochar application to As-polluted soils improves water uptake, maintains membrane stability and nutrient homeostasis, and increases osmolyte synthesis, gene expression, and antioxidant activities, leading to better plant performance. Additionally, BC modulates soil pH, increases nutrient availability, causes As immobilization, decreases its uptake and accumulation in plant tissues, and ensures safer production. The present review describes the sources, toxic impacts of As, and ways to lower As in the environment to decrease its toxic impacts on humans, the ecosystem, and the food chain. It concentrates on different mechanisms mediated by BC to alleviate As toxicity and remediate As-polluted soils and different research gaps that must be fulfilled in the future. Therefore, the current review will help to develop innovative strategies to minimize As uptake and accumulation and remediate As-polluted soils to reduce their impacts on humans and the environment. Full article

(This article belongs to the Special Issue Advances in Phytoremediation Strategies to Address Global Environmental Challenges)

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33 pages, 2956 KiB

Open AccessReview

Integrating Genetic Diversity and Agronomic Innovations for Climate-Resilient Maize Systems

by Xin Li, Yunlong Li, Yan Sun, Sinan Li, Quan Cai, Shujun Li, Minghao Sun, Tao Yu, Xianglong Meng and Jianguo Zhang

Plants 2025, 14(10), 1552; https://doi.org/10.3390/plants14101552 - 21 May 2025

Viewed by 367

Abstract

Maize is a vital staple crop significantly affected by climate change, necessitating urgent efforts to enhance its resilience. This review analyzes advanced methodologies for maize improvement, focusing on the identification of genetic determinants through QTL mapping, candidate gene mining, and GWAS. We highlight [...] Read more.

Maize is a vital staple crop significantly affected by climate change, necessitating urgent efforts to enhance its resilience. This review analyzes advanced methodologies for maize improvement, focusing on the identification of genetic determinants through QTL mapping, candidate gene mining, and GWAS. We highlight the transformative potential of CRISPR gene editing for identifying key regulators in maize development and the utility of virus-induced gene silencing (VIGS) for functional genomics. Additionally, we discuss breeding strategies leveraging the genetic diversity of maize wild relatives and innovations such as speed breeding and genomic selection (GS), which accelerate breeding cycles. Marker-assisted selection (MAS) plays a critical role in developing superior maize varieties. The review also encompasses agronomic practices and technological innovations, including GS, aimed at climate mitigation. High-throughput phenotyping and omics-based approaches, including transcriptomics and metabolomics, are essential tools for developing climate-resilient maize. Climate changes have a significant impact on maize production and pose unprecedented challenges to its cultivation. Full article

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

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34 pages, 1492 KiB

Open AccessReview

Toward Low-Emission Agriculture: Synergistic Contribution of Inorganic Nitrogen and Organic Fertilizers to GHG Emissions and Strategies for Mitigation

by Shahzad Haider, Jiajie Song, Jinze Bai, Xing Wang, Guangxin Ren, Yuxin Bai, Yuming Huang, Tahir Shah and Yongzhong Feng

Plants 2025, 14(10), 1551; https://doi.org/10.3390/plants14101551 - 21 May 2025

Viewed by 637

Abstract

Nitrogen (N) and organic-source fertilizers in agriculture are important to sustain crop production for feeding the growing global population. However, their use can result in significant greenhouse gas (GHG) emissions, particularly carbon dioxide (CO₂), methane (CH₄), and nitrous oxide [...] Read more.

Nitrogen (N) and organic-source fertilizers in agriculture are important to sustain crop production for feeding the growing global population. However, their use can result in significant greenhouse gas (GHG) emissions, particularly carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O), which are important climate drivers. This review discusses the interactive effects, uncovering both additive and suppressive outcomes of emissions under various soil and climatic conditions. In addition to examining the effects of nitrogen and the nitrogen use efficiency (NUE), it is crucial to comprehend the mechanisms and contributions of organic fertilizers to GHG emissions. This understanding is vital for developing mitigation strategies that effectively reduce emissions while maintaining agricultural productivity. In this review, the current knowledge is utilized for the management of nitrogen practices, such as the optimization of fertilization rates, timing, and methods of application, in terms of the nitrogen use efficiency and the related GHG emissions. Moreover, we discuss the role of organic fertilizers, including straw, manure, and biochar, as a mitigation strategy in relation to GHG emissions through soil carbon sequestration and enhanced nutrient cycling. Important strategies such as crop rotation, tillage, irrigation, organic fertilizers, and legume crops are considered as suitable approaches for minimizing emissions. Even with the progress made in mitigating fertilizer-related emissions, research gaps remain, specifically concerning the long-term effect of organic fertilizers and the interactions between microbial communities in the soil and fertilization practices. Furthermore, the differences in application practices and environmental conditions present considerable obstacles to accurate emission quantification. This review underlines the importance of conducting more thorough research on the combined application of N and organic fertilizers in multiple cropping systems to evolve region-specific mitigation strategies. Full article

(This article belongs to the Special Issue Fertilizer and Abiotic Stress)

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27 pages, 8811 KiB

Open AccessArticle

Participation of Wild Species Genus Avena L. (Poaceae) of Different Ploidy in the Origin of Cultivated Species According to Data on Intragenomic Polymorphism of the ITS1-5.8S rRNA Region

by Alexander A. Gnutikov, Nikolai N. Nosov, Igor G. Loskutov, Alexander V. Rodionov and Victoria S. Shneyer

Plants 2025, 14(10), 1550; https://doi.org/10.3390/plants14101550 - 21 May 2025

Viewed by 339

Abstract

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal [...] Read more.

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal transcribed spacer ITS1 and the 5.8S rRNA gene in the cultivated species was studied with next-generation sequencing (NGS), and the patterns of occurrence and distribution of the ribotypes were compared among them and with those of the wild species. According to these data diploid, A. strigosa is more closely related to the diploid A. hirtula than to polyploid oats, and it could have evolved independently of polyploid cultivated species. The tetraploid Avena abyssinica could be a cultivated derivative of A. vaviloviana. Two hexaploid cultivated species, A. byzantina and A. sativa, could have a different origin; A. sativa could be the cultivated form of A. fatua, whereas A. byzantina could originate independently. It was found that the oat species with the A and C subgenomes, even with strong morphological and karyological differences, could intercross and pass the further stages of introgression producing a new stable combination of genomes. Our data show that almost all species of Avena could form an introgressive interspecies complex. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

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20 pages, 3728 KiB

Open AccessArticle

Effect of Vegetation Degradation on Soil Nitrogen Components and N-Cycling Enzyme Activities in a Wet Meadow on the Qinghai–Tibetan Plateau

by Wanpeng He, Weiwei Ma, Jianan Du, Wenhua Chang and Guang Li

Plants 2025, 14(10), 1549; https://doi.org/10.3390/plants14101549 - 21 May 2025

Viewed by 308

Abstract

The responses of soil nitrogen component dynamics and enzyme activities to vegetation degradation in wet meadows ecosystems remain unclear. This study employed a combination of field surveys and laboratory experiments to investigate soil nitrogen components and nitrogen cycling enzyme activities under different intensities [...] Read more.

The responses of soil nitrogen component dynamics and enzyme activities to vegetation degradation in wet meadows ecosystems remain unclear. This study employed a combination of field surveys and laboratory experiments to investigate soil nitrogen components and nitrogen cycling enzyme activities under different intensities of vegetation degradation and during the vegetation growth season in a wet meadow on the Qinghai–Tibetan Plateau. The aim was to explore the responses of soil nitrogen components and nitrogen cycling enzyme activities to vegetation degradation and their interrelationships. The results showed that vegetation degradation significantly reduced TN, NH₄⁺-N, MBN, PRO, and NiR, and increased NO₃⁻-N, URE, and NR. Soil nitrogen components and enzyme activities exhibited seasonal fluctuations across different degradation levels during the growing season. The Pearson correlation analysis revealed a significant positive correlation between temperature, moisture, nitrogen fractions, and nitrogen cycle-related enzyme activities, as well as between the nitrogen fractions and the enzyme activities themselves. Partial Least Squares Path Modeling (PLS-PM) elucidated the relationships between soil properties and nitrogen components under different degradation levels, explaining 78% of the variance in nitrogen components. Degradation level, growth season, and soil physical properties had indirect associations with nitrogen components, whereas soil enzyme activities exerted a direct positive influence on nitrogen components. Our research revealed the universal impact mechanism of environmental factors, soil characteristics, and vegetation degradation on nitrogen cycling in a wet meadow, thereby making a significant contribution to the restoration and maintenance of functional integrity in alpine wetland ecosystems. Full article

(This article belongs to the Section Plant Ecology)

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12 pages, 1686 KiB

Open AccessArticle

Development of Single Nucleotide Polymorphism and Phylogenetic Analysis of Rhododendron Species in Zhejiang Province, China, Using ddRAD-Seq Technology

by Hong Zhu, Dongbin Li, Chunlei Yue and Hepeng Li

Plants 2025, 14(10), 1548; https://doi.org/10.3390/plants14101548 - 21 May 2025

Viewed by 395

Abstract

The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a [...] Read more.

The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a biodiversity hotspot for this genus. Using R. simsii as the reference genome, we generated 39.40 Gb of high-quality sequencing data with a Q30 score of 96.65% and a GC content of 39.63%, achieving an average alignment rate of 92.79%. Through stringent filtering (QD ≥ 2, MQ ≥ 40), we identified 14,048,702 genome-wide single nucleotide polymorphism (SNP), predominantly characterized by the mutation types T:A>C:G and C:G>T:A. The widespread R. simsii and R. simsii var. putuoense exhibited significant genetic diversity, whereas the low-altitude widespread R. molle and the endemic R. simiarum exhibited lower genetic diversity. Moderate genetic differentiation (F_st = 0.097) was observed between R. simsii and R. simsii var. putuoense, while substantial genetic differentiation was detected among the other Rhododendron species. Principal component analysis (PCA), combined with phylogenomic reconstruction, demonstrated that the Rhododendron genus can be stratified into six well-supported genetic clades. Furthermore, this study provides the first genomic validation of the sibling relationship between R. simsii and its variety, R. simsii var. putuoense, and clarifies the systematic position of R. huadingense, suggesting that it should be classified as a new subgenus. This study establishes ddRAD-seq as a cost-effective tool, providing both a theoretical framework for SNP-based phylogenetics and critical insights for conserving China’s azalea biodiversity. Full article

(This article belongs to the Special Issue Recent Advancements in Taxonomy and Phylogeny of Plants)

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17 pages, 3335 KiB

Open AccessArticle

Efficient Virus-Induced Gene Silencing (VIGS) Method for Discovery of Resistance Genes in Soybean

by Kelin Deng, Zihua Lu, Hongli Yang, Shuilian Chen, Chao Li, Dong Cao, Hongwei Wang, Qingnan Hao, Haifeng Chen and Zhihui Shan

Plants 2025, 14(10), 1547; https://doi.org/10.3390/plants14101547 - 21 May 2025

Viewed by 421

Abstract

Soybean (Glycine max L.) is a vital grain and oil crop, serving as a primary source of edible oil, plant-based protein, and livestock feed. Its production is crucial for ensuring global food security. However, soybean yields are severely impacted by various diseases, [...] Read more.

Soybean (Glycine max L.) is a vital grain and oil crop, serving as a primary source of edible oil, plant-based protein, and livestock feed. Its production is crucial for ensuring global food security. However, soybean yields are severely impacted by various diseases, and the development of disease-resistant cultivars remains the most sustainable strategy for mitigating these losses. While stable genetic transformation is a common approach for studying gene function, virus-induced gene silencing (VIGS) offers a rapid and powerful alternative for functional genomics, enabling efficient screening of candidate genes. Nevertheless, the application of VIGS in soybean has been relatively limited. In this study, we established a tobacco rattle virus (TRV)-based VIGS system for soybean, utilizing Agrobacterium tumefaciens-mediated infection. The TRV vector was delivered through cotyledon nodes, facilitating systemic spread and effective silencing of endogenous genes. Our results demonstrate that this TRV–VIGS system efficiently silences target genes in soybean, inducing significant phenotypic changes with a silencing efficiency ranging from 65% to 95%. Key genes, including phytoene desaturase (GmPDS), the rust resistance gene GmRpp6907, and the defense-related gene GmRPT4, were successfully silenced, confirming the system’s robustness. This work establishes a highly efficient TRV–VIGS platform for rapid gene function validation in soybean, providing a valuable tool for future genetic and disease resistance research. Full article

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

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15 pages, 2437 KiB

Open AccessArticle

Invasion Status, Mechanisms, and Future Distribution Prediction of Solidago canadensis in the Trade Port Region: A Case Study of Ningbo Port, China

by Xu Luo, Sixiao Shen, Ke Liao, Saiqiang Li, Qinqin Pan, Jiahao Ma, Weiqiang Li and Xiaodong Yang

Plants 2025, 14(10), 1546; https://doi.org/10.3390/plants14101546 - 21 May 2025

Viewed by 325

Abstract

Trade ports are the first places where alien species invade and the source of their spread to other areas. Controlling invasions in these regions can effectively reduce invasion pressure and disrupt the spread pathways of invasive species, thereby significantly reducing their threat to [...] Read more.

Trade ports are the first places where alien species invade and the source of their spread to other areas. Controlling invasions in these regions can effectively reduce invasion pressure and disrupt the spread pathways of invasive species, thereby significantly reducing their threat to local ecosystems and biodiversity loss. Based on 595 field survey plots, the Generalized Linear Model (GLM) and Species Distribution Model (MaxEnt) were employed to analyze and predict the invasion mechanisms and future possible distribution of Solidago canadensis in the Ningbo Port, China. The results indicate that the invasion of S. canadensis in the Ningbo Port was particularly severe, with a 67.7% occurrence rate of all sampling plots in the field survey, and a risk level classified as Grade 1. Biodiversity (p < 0.001) and the minimum temperature of the coldest month (p < 0.01) significantly affect the invasiveness. Highly diverse communities could resist the invasion of alien species, which support Elton’s diversity–invasibility hypothesis. Low temperatures had a restrictive effect on the invasion of S. canadensis. The total suitable area continued to expand under three different climate change scenarios compared to current conditions (increased by 3.73%, 5.67%, and 3.74% by the 2070s). The total potential habitat area of S. canadensis reached its maximum extent (89.77%) under the medium greenhouse gas emission scenario in the 2050s. Meanwhile, the medium suitable area exhibited the greatest fluctuation among the three climate scenarios. Under the low emission condition, the medium suitable area of S. canadensis diminished by 63.10 km², but in the medium and high emission condition, its area expanded by 91.13 km² and 16.20 km², respectively. Under future climate warming scenarios, the invasion risk of S. canadensis in Ningbo Port will continue to increase. The results of our study reveal the diffusion mechanisms of invasive plants at the colonization source, providing important theoretical support for invasive alien species’ initial prevention and control. Full article

(This article belongs to the Topic Plant Invasion)

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16 pages, 2015 KiB

Open AccessArticle

Somatic Embryogenesis and Genetic Transformation of Caragana intermedia

by Ju Tian, Jialei Zhu, Xiaohan Deng, Xu Zhu, Ruigang Wang and Guojing Li

Plants 2025, 14(10), 1545; https://doi.org/10.3390/plants14101545 - 21 May 2025

Viewed by 392

Abstract

Caragana intermedia is a perennial shrub species in the genus Caragana (Fabaceae), demonstrating remarkable stress resistance and adaptability. However, research on its somatic embryogenesis (SE) and genetic transformation techniques remains limited. In this study, we established an SE system by utilizing immature cotyledons [...] Read more.

Caragana intermedia is a perennial shrub species in the genus Caragana (Fabaceae), demonstrating remarkable stress resistance and adaptability. However, research on its somatic embryogenesis (SE) and genetic transformation techniques remains limited. In this study, we established an SE system by utilizing immature cotyledons isolated from young C. intermedia seeds. Our findings demonstrated that the immature cotyledons at 6–7 weeks after flowering (WAF) were the best explants for SE. The optimal embryo induction medium consisted of an MS basal medium supplemented with 5 mg/L α-naphthaleneacetic acid (NAA), 3 mg/L 6-benzylaminopurine (6-BA), 30 g/L sucrose, 7 g/L agar, and 500 mg/L hydrolyzed casein. Cotyledon-stage embryos germinated on a half-strength MS medium, exhibiting a 34.36% germination rate. Based on the SE system, we developed a preliminary genetic transformation system using the RUBY reporter gene, which successfully generated transgenic calli and cotyledon-stage embryos. The establishment of the SE system is expected to shorten breeding cycles, facilitate propagation of superior cultivars, and support large-scale industrial applications in C. intermedia. Furthermore, the stable transformation system provides a platform for molecular breeding and gene function verification. Full article

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

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17 pages, 5446 KiB

Open AccessArticle

Transcriptome Profiling Identifies Key Regulators of Tuber Skin Color in Potato

by Boshu Li, Shuo Wang, Jun Hu, Liping Jin and Jianfei Xu

Plants 2025, 14(10), 1544; https://doi.org/10.3390/plants14101544 - 20 May 2025

Viewed by 360

Abstract

The color of tuber skin exhibits remarkable diversity in potato (Solanum tuberosum L.) and is intricately associated with variance in anthocyanin accumulation across different varieties. The regulatory mechanisms governing this phenomenon are poorly understood. In this study, we identified a natural, yellow-skinned [...] Read more.

The color of tuber skin exhibits remarkable diversity in potato (Solanum tuberosum L.) and is intricately associated with variance in anthocyanin accumulation across different varieties. The regulatory mechanisms governing this phenomenon are poorly understood. In this study, we identified a natural, yellow-skinned variant (Z28M) from the red-skinned tetraploid variety, Zhongshu 28 (Z28W), using simple sequence repeat (SSR) molecular marker amplification and trait observation. The transcriptional regulatory mechanisms underlying tuber skin color variation were investigated by analyzing anthocyanin profiles and transcriptomic data at the developmental and maturation stages. Ultra-performance liquid chromatography (UPLC-QTOF-MS) analysis indicated markedly reduced levels of pelargonidin and peonidin in Z28M compared with those in Z28W. Transcriptome profiling identified 1858 differentially expressed genes between Z28W and Z28M, with significant enrichment in the flavonoid and phenylpropanoid biosynthetic pathways. Weighted gene co-expression network analysis indicated a red-skinned associated module, MEred, encompassing key anthocyanin biosynthetic genes co-expressed with the transcription factor, StMYB3, which exhibited substantially higher expression in Z28W than in Z28M. K-means clustering indicated coordinated expression patterns among StCHS, StDFR, and StMYB3, suggesting transcriptional co-regulation. Collectively, these results highlight StMYB3 as a pivotal regulator of anthocyanin biosynthesis and a contributor to the tuber skin color divergence observed between Z28W and Z28M. Full article

(This article belongs to the Special Issue Genetics and Physiology of Tuber and Root Crops)

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19 pages, 1416 KiB

Open AccessArticle

Screening of Germplasm Resources with Low-Phosphorus Tolerance During the Seedling Stage of Rice

by Mengru Zhang, Ye Wang, Zexin Qi, Qiang Zhang, Huan Wang, Chenglong Guan, Wenzheng Sun, Fenglou Ling, Zhian Zhang and Chen Xu

Plants 2025, 14(10), 1543; https://doi.org/10.3390/plants14101543 - 20 May 2025

Viewed by 376

Abstract

Rice is a globally important food crop, and phosphorus is an essential nutrient element for rice growth. In many of China’s arable lands, there is a deficiency in available phosphorus content. Therefore, screening and breeding rice germplasm resources that are tolerant to low [...] Read more.

Rice is a globally important food crop, and phosphorus is an essential nutrient element for rice growth. In many of China’s arable lands, there is a deficiency in available phosphorus content. Therefore, screening and breeding rice germplasm resources that are tolerant to low phosphorus can enhance the growth capability of rice in low-phosphorus soils. This study set up treatments with two phosphorus concentrations: H₂PO₄⁻ at 0.18 mmol/L, referred to as normal phosphorus (NP), and H₂PO₄⁻ at 0.009 mmol/L, referred to as low phosphorus (LP). Using hydroponic methods, 156 different genotype rice germplasms were treated for 35 days, after which the morpho-physiological traits of the rice seedling shoots, root morphology, and material content were measured. An analysis of the coefficient of variation (CV) for low phosphorus tolerance coefficients across different rice germplasm resources revealed that 16 indicators had CVs greater than 10%, which can be used as criteria for screening rice varieties with low phosphorus tolerance at the seedling stage. The relevant indicators and low-phosphorus resistance characteristics of different rice varieties were comprehensively evaluated using principal component analysis, correlation analysis, membership function, and cluster analysis methods. The results indicate that the principal component analysis transformed 23 indicators into 5 comprehensive indicators, with a cumulative contribution rate of 86.947%. The D value was evaluated in a comprehensive evaluation of low-phosphorus resistance, and 156 rice germplasm resources were divided into four types by cluster analysis. A scatter plot was created using the comprehensive phosphorus efficiency values of different rice germplasms under normal phosphorus and low phosphorus conditions. Through further verification, the germplasms with strong low-phosphorus tolerance finally selected through comprehensive screening were Y3-14, Y3-35, Y3-21, Jinnongda 705, Changjing 625, and Jinnongda 873. The germplasms with poor low-phosphorus tolerance were Jijing 338, Jingu 981, Tong 35, Y3-31, and Longdao 20. Full article

(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice—2nd Edition)

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23 pages, 12391 KiB

Open AccessArticle

Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics

by Fu Shi, Li Li, Mingjie Chen, Junli Chang, Min Tu, Guangyuan He, Yin Li and Guangxiao Yang

Plants 2025, 14(10), 1542; https://doi.org/10.3390/plants14101542 - 20 May 2025

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Abstract

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development [...] Read more.

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement. Full article

(This article belongs to the Special Issue ‘Omics’ and ‘Multi-Omics’ Insights into Plant Responses to Abiotic Stresses)

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15 pages, 6196 KiB

Open AccessArticle

Effects of Early-Stage Treeline Shifts on Soil Microbial Biomass and Catabolic Diversity in Reserved and Grazed Subalpine Meadows

by Kristina Ivashchenko, Anastasiya Romanova, Sofia Sushko, Anna Zhuravleva, Anna Kvitkina, Anna Khodzhaeva and Nadezhda Ananyeva

Plants 2025, 14(10), 1541; https://doi.org/10.3390/plants14101541 - 20 May 2025

Viewed by 329

Abstract

Treelines are advancing upward on mountain slopes due to climate warming and reduced grazing intensity. However, the effects of initial vegetation changes on soil C, N, and P retention, microbial biomass, and catabolic diversity in the subalpine meadows during the early stages of [...] Read more.

Treelines are advancing upward on mountain slopes due to climate warming and reduced grazing intensity. However, the effects of initial vegetation changes on soil C, N, and P retention, microbial biomass, and catabolic diversity in the subalpine meadows during the early stages of treeline shifts remain poorly understood. This research aimed to better understand the direction and drivers of microbial processes related to C, N, and P cycles in the soil of subalpine natural and grazed meadows, with treatments involving meadow grasses alone (GR, control) and as a mixture with forest litter, specifically birch leaves (BLs), in a one-year microcosm experiment. The addition of BLs with GR resulted in a 12–67% decrease in the retention of C, N, and P in soil microbial biomass, but an 8–9% increase in catabolic diversity compared to the control. The most pronounced effect was observed in the N content of the soil microbial biomass (MBN) for both land uses. The increased proportion of recalcitrant plant residue fractions (acid-insoluble and non-polar extractables) contributed to the decrease in soil MBN content. This shift also reduced the microbial metabolic response to carbohydrates in total substrate-induced respiration, leading to a more balanced and catabolically diverse microbial community. These results improve our understanding of the early response of C, N, and P cycling in mountain soils to treeline shifts mediated by climate warming. Full article

(This article belongs to the Topic Plant-Soil Interactions, 2nd Volume)

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16 pages, 5248 KiB

Open AccessArticle

Manganese Nanomaterials: A Green Solution to Suppress Xanthomonas oryzae in Rice

by Yaqi Jiang, Yi Sun, Pingfan Zhou, Meng Tian and Yukui Rui

Plants 2025, 14(10), 1540; https://doi.org/10.3390/plants14101540 - 20 May 2025

Viewed by 310

Abstract

Due to the environmental concerns surrounding widely used antimicrobial agents, the use of nanotechnology to suppress crop diseases has attracted increasing attention in the agricultural field. This paper investigated the inhibitory effects of manganese-based nanomaterials (NMs) on rice leaf blight. In vitro experiments [...] Read more.

Due to the environmental concerns surrounding widely used antimicrobial agents, the use of nanotechnology to suppress crop diseases has attracted increasing attention in the agricultural field. This paper investigated the inhibitory effects of manganese-based nanomaterials (NMs) on rice leaf blight. In vitro experiments showed that manganese oxide (MnO₂) NMs and manganese tetroxide (Mn₃O₄) NMs directly inhibited Xanthomonas oryzae (Xoo) with a maximum OD value of 0.177, which was 11.5% lower than the control. In vivo experiments demonstrated that spraying MnO₂ NMs and Mn₃O₄ NMs reduced the diseased leaf length to 22–28% and 25–26%, respectively. This is due to Mn-based NMs inducing enhanced plant resistance by increasing the activity of phenylalanine ammonia–lyase in rice leaves by 36–61%. Single particle inductively coupled plasma mass spectrometry showed that Mn₃O₄ NMs are more frequently retained as NMs in rice than MnO₂ NMs, resulting in enhanced antimicrobial effects. Mn-based NMs exhibit strong antimicrobial activity and hold significant promise as alternatives for plant protection and agricultural applications; however, careful consideration must be given to their concentrations and application methods. Full article

(This article belongs to the Special Issue Botanical Effects of Nanomaterials and Their Applications in Agriculture)

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27 pages, 530 KiB

Open AccessArticle

Physiological and Agronomic Responses of Maize (Zea mays L.) to Compost and PGPR Under Different Salinity Levels

by Ibrahim El-Akhdar, Nevien Elhawat, Mahmoud M. A. Shabana, Hesham M. Aboelsoud and Tarek Alshaal

Plants 2025, 14(10), 1539; https://doi.org/10.3390/plants14101539 - 20 May 2025

Viewed by 380

Abstract

Salinity stress severely limits maize (Zea mays L.) productivity, necessitating sustainable mitigation strategies to ensure food security in affected regions. This study investigates the efficacy of compost (5 and 10 t/ha) and plant growth-promoting rhizobacteria (PGPR; Azospirillum brasilense) in enhancing maize [...] Read more.

Salinity stress severely limits maize (Zea mays L.) productivity, necessitating sustainable mitigation strategies to ensure food security in affected regions. This study investigates the efficacy of compost (5 and 10 t/ha) and plant growth-promoting rhizobacteria (PGPR; Azospirillum brasilense) in enhancing maize productivity and soil health under salinity stress (EC_e 3.5 and 6.3 dS/m) across three varieties (Single Cross 131, 132, and 178) in field experiments conducted in 2023 and 2024. Combined compost-10 + PGPR treatment significantly increased grain yield by up to 197% and straw yield by nearly 300% in Single Cross 178 under high salinity, surpassing single treatments. Nitrogen content in grains and straw rose by 157%, while proline, peroxidase activity, and chlorophyll content improved, indicating robust stress tolerance. Soil properties, including pH, EC_e, sodium adsorption ratio, and exchangeable sodium percentage, were significantly ameliorated, with bulk density reduced and porosity increased. Soil organic matter and microbial populations (bacteria and fungi) were also enhanced. Single Cross 178 exhibited superior stress tolerance, highlighting varietal differences. These findings, supported by comparisons with the existing literature, underscore the synergistic role of compost and PGPR in improving nutrient uptake, antioxidant defenses, and soil structure. This study offers a sustainable strategy for maize cultivation in saline environments, with implications for global food security. Full article

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

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15 pages, 9259 KiB

Open AccessArticle

Characterization of a New Stripe Rust Resistance Gene on Chromosome 2StS from Thinopyrum intermedium in Wheat

by Chengzhi Jiang, Yujie Luo, Doudou Huang, Meiling Chen, Ennian Yang, Guangrong Li and Zujun Yang

Plants 2025, 14(10), 1538; https://doi.org/10.3390/plants14101538 - 20 May 2025

Viewed by 384

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a highly destructive disease prevalent across most wheat-growing regions globally. The most effective strategy for combating this disease is through the exploitation of durable and robust resistance genes from the relatives of wheat. [...] Read more.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a highly destructive disease prevalent across most wheat-growing regions globally. The most effective strategy for combating this disease is through the exploitation of durable and robust resistance genes from the relatives of wheat. Thinopyrum intermedium (Host) Barkworth and D.R. Dewey has been widely hybridized with common wheat and has been shown to be a valuable source of genes, conferring resistance and tolerance against both the biotic and abiotic stresses affecting wheat. In this study, a novel wheat–Th. intermedium 2StS.2J^SL addition line, named Th93-1-6, which originated from wheat–Th. intermedium partial amphidiploid line, Th24-19-5, was comprehensively characterized using nondenaturing-fluorescence in situ hybridization (ND-FISH) and Oligo-FISH painting techniques. To detect plants with the transfer of resistance genes from Th93-1-6 to wheat chromosomes, 2384 M₁-M₃ plants from the cross between Th93-1-6 and the susceptible wheat cultivar MY11 were studied by ND-FISH using multiple probes. A total of 37 types of 2StS.2J^SL chromosomal aberrations were identified. Subsequently, 12 homozygous lines were developed to construct a cytological bin map. Ten chromosomal bins on the 2StS.2J^SL chromosome were constructed based on 84 specific molecular markers. Among them, eight alien chromosome aberration lines, which all contained the bin 2StS-3, showed enhanced stripe rust resistance. Consequently, the gene(s) for stripe rust resistance was physically mapped to the 92.88-155.32 Mb region of 2StS in Thinopyrum intermedium reference genome sequences v2.1. Moreover, these newly developed wheat–Th. intermedium 2StS.2J^SL translocation lines are expected to serve as valuable genetic resources in the breeding of rust-resistant wheat cultivars. Full article

(This article belongs to the Special Issue Molecular Approaches for Plant Resistance to Rust Diseases)

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16 pages, 2138 KiB

Open AccessArticle

The Divergence History of Two Japanese Torreya Taxa (Taxaceae): Implications for Species Diversification in the Japanese Archipelago

by Qian Ou, Xin Huang, Dingguo Pan, Shulan Wang, Yuting Huang, Sisi Lu, Yujin Wang and Yixuan Kou

Plants 2025, 14(10), 1537; https://doi.org/10.3390/plants14101537 - 20 May 2025

Viewed by 390

Abstract

The Japanese archipelago as a continental island of the Eurasia continent and harboring high levels of plant species diversity provides an ideal geographical setting for investigating vicariant allopatric speciation due to the sea-level fluctuations associated with climatic oscillations during the Quaternary. In this [...] Read more.

The Japanese archipelago as a continental island of the Eurasia continent and harboring high levels of plant species diversity provides an ideal geographical setting for investigating vicariant allopatric speciation due to the sea-level fluctuations associated with climatic oscillations during the Quaternary. In this study, three chloroplast DNA regions and 14 nuclear loci were sequenced for 31 individuals from three populations of Torreya nucifera var. nucifera and 52 individuals from three populations of T. nucifera var. radicans. Population genetic analyses (Network, STRUCTURE and phylogeny) revealed that the genetic boundaries of the two varieties are distinct, with high genetic differentiation (F_ST) of 0.9619 in chloroplast DNA and 0.6543 in nuclear loci. The relatively ancient divergence times between the two varieties were estimated to 3.03 Ma by DIYABC and 1.77 Ma by IMa2 when dated back to the late Pliocene and the early Pleistocene, respectively. The extremely weak gene flow (2Nm = 0.1) between the two varieties was detected by IMa2, which might be caused by their population expansion since the early Pleistocene (~2.0 Ma) inferred in the Bayesian skyline plots and DIYABC. Niche modeling showed that the two varieties had significant ecological differentiation (p < 0.001) since the Last Interglacial even earlier. These results demonstrate that vicariant allopatric speciation due to sea-level fluctuations may be a common mode of speciation in the Japanese archipelago. This finding provides insights into the understanding of species diversification in the Japanese Archipelago and even East Asian flora under climatic oscillations during the Quaternary. Full article

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

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18 pages, 2309 KiB

Open AccessArticle

Effect of Nitrogen and Phosphorus Fertilizers on Dry Matter Accumulation and Translocation of Two Amylose Content Indica Rice on Yield

by Xiaohong Qin, Xinyue Rao, Hongjing Liu, Jiale Hong, Wanlin Tang, Shengmin Yan, Guotao Yang, Hong Chen and Yungao Hu

Plants 2025, 14(10), 1536; https://doi.org/10.3390/plants14101536 - 20 May 2025

Viewed by 353

Abstract

Nitrogen (N) and phosphorus (P) are key factors affecting rice yield. To study the effects of single application of nitrogen, phosphorus and their combined application on dry matter accumulation and yield of rice, two types of indica rice with contenting amylose contents, low [...] Read more.

Nitrogen (N) and phosphorus (P) are key factors affecting rice yield. To study the effects of single application of nitrogen, phosphorus and their combined application on dry matter accumulation and yield of rice, two types of indica rice with contenting amylose contents, low amylose content (LAC) and high amylose content (HAC) were used as the test materials. Four different levels of nitrogen and phosphorus were applied (N0: 0, N1: 90, N2: 150, N3: 270 kg/hm²) and (P0: 0, P1: 15, P2: 30, P3: 60 kg/hm²). The application of N fertilizer alone and in combination with P effectively promote dry matter accumulation, translocation and increase yield. Under the N3P0 and N3P1 treatments, LAC and HAC achieved their highest yield of 10.03 t/hm² and 11.24 t/hm², respectively. representing increased of 46.19% and 29.05% compared to N0P0 treatment. Phosphorus application influenced dry matter accumulation at maturity and stem and leaf dry matter translocation to the panicle, translocation rates, and their contribution to the panicle, there by increasing yield. Effective panicles, spikelets per panicle, grain filling, stem and leaf dry matter translocation, stem and leaf dry matter translocation rate were significantly or highly significantly positively correlated with yield, and 1000-grain weight was highly significantly negatively correlated with yield, which were mainly increased by increasing panicle dry matter accumulation at maturity, the increase in the amount of increase in dry matter of panicle, the contribution rate of stem and leaf dry matter translocation to the panicle, the amount of stem and leaf dry matter translocation, and the rate of stem and leaf dry matter translocation to increase spikelets per panicle and the grain filling, and then to improvement of yield. Full article

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16 pages, 1854 KiB

Open AccessArticle

Evaluation of Saponin-Rich Callus from Saponaria officinalis L. as a Novel Scrub Material with Significant Exfoliating and Anti-Inflammatory Effects

by Ga-Ram Yu, Da-Hoon Kim, Hyuck Kim and Dong-Woo Lim

Plants 2025, 14(10), 1535; https://doi.org/10.3390/plants14101535 - 20 May 2025

Viewed by 465

Abstract

Saponaria officinalis L., a plant rich in saponins, has long been used as a natural surfactant. It has traditionally been used for its cleansing and anti-inflammatory properties in the treatment of various skin conditions, including eczema, psoriasis, and acne. In this study, we [...] Read more.

Saponaria officinalis L., a plant rich in saponins, has long been used as a natural surfactant. It has traditionally been used for its cleansing and anti-inflammatory properties in the treatment of various skin conditions, including eczema, psoriasis, and acne. In this study, we investigated the potential of S. officinalis callus (SC), mass-produced via plant tissue culture, as a novel exfoliating cosmetic ingredient. The callus was induced using Murashige and Skoog (MS) medium supplemented with 1 mg/L 2,4-D, and the resulting extract (SCE) was analyzed via high-performance liquid chromatography (HPLC), confirming the presence of saponarin—a bioactive compound with known anti-inflammatory properties. In vitro assays demonstrated that SCE significantly suppressed nitric oxide production and reduced the expression of pro-inflammatory mediators, including iNOS, COX-2, TNF-α, IL-1β, and IL-6, in LPS-stimulated RAW264.7 macrophages. The foaming ability and stability of SC and SCE were also comparable to commercial surfactants. Clinical studies further supported the material’s cosmetic potential: a skin patch test in 30 volunteers revealed no signs of irritation (mean score: 0.28), while a desquamation index assessment in 21 participants showed a significant reduction of 44.07%, confirming its exfoliating efficacy. Taken together, these results suggest that the SC scrub is a safe, eco-friendly, and sustainable alternative to synthetic exfoliating agents, offering functional and industrial advantages for cosmetic applications. Full article

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

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26 pages, 10996 KiB

Open AccessArticle

Altitudinal Variations in Coniferous Vegetation and Soil Carbon Storage in Kalam Temperate Forest, Pakistan

by Bilal Muhammad, Umer Hayat, Lakshmi Gopakumar, Shuangjiang Xiong, Jamshid Ali, Muhammad Tariq Badshah, Saif Ullah, Arif UR Rehman, Qun Yin and Zhongkui Jia

Plants 2025, 14(10), 1534; https://doi.org/10.3390/plants14101534 - 20 May 2025

Viewed by 481

Abstract

Understanding the complex interplay among altitudinal gradients, tree species diversity, structural attributes, and soil carbon (C) is critical for effective coniferous forest management and climate change mitigation. This study addresses a knowledge gap by investigating the effects of altitudinal gradient on coniferous tree [...] Read more.

Understanding the complex interplay among altitudinal gradients, tree species diversity, structural attributes, and soil carbon (C) is critical for effective coniferous forest management and climate change mitigation. This study addresses a knowledge gap by investigating the effects of altitudinal gradient on coniferous tree diversity, biomass, carbon stock, regeneration, and soil organic carbon storage (SOCs) in the understudied temperate forests of the Hindu-Kush Kalam Valley. Using 120 sample plots 20 × 20 m (400 m²) each via a field inventory approach across five altitudinal gradients [E1 (2000–2200 m)–E5 (2801–3000 m)], we comprehensively analyzed tree structure, composition, and SOCs. A total of four coniferous tree species and 2172 individuals were investigated for this study. Our findings reveal that elevation indirectly influences species diversity, SOCs, and forest regeneration. Notably, tree height has a positive relationship with altitudinal gradients, while tree carbon stock exhibits an inverse relationship. Forest disturbance was high in the middle elevation gradients E2–E4, with high deforestation rate at E1 and E2. Cedrus deodara, the dominant species, showed the highest deforestation rate at lower elevations (R² = 0.72; p < 0.05) and regeneration ability (R² = 0.77; p < 0.05), which declined with increasing elevation. Middle elevations had the highest litter carbon stock and SOCs values emphasizing the critical role of elevation gradients in carbon sink and species distribution. The regeneration status and number of trees per ha in Kalam Valley forests showed a significant decline with increasing elevation (p < 0.05), with Cedrus deodara recording the highest regeneration rate at E1 and Abies pindrow the lowest at E5. The PCA revealed that altitudinal gradients factor dominate variability via PCA1, while the Shannon and Simpson Indices drives PCA2, highlighting ecological diversity’s independent role in shaping distinct yet complementary vegetative and ecological perspectives. This study reveals how altitudinal gradients shape forest structure and carbon sequestration, offering critical insights for biodiversity conservation and climate-resilient forest management. Full article

(This article belongs to the Special Issue Plant Functional Diversity and Nutrient Cycling in Forest Ecosystems)

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42 pages, 1199 KiB

Open AccessReview

Complex Signaling Networks Underlying Blue-Light-Mediated Floral Transition in Plants

by Yun Kong and Youbin Zheng

Plants 2025, 14(10), 1533; https://doi.org/10.3390/plants14101533 - 20 May 2025

Viewed by 549

Abstract

Blue light (BL) is important in regulating floral transition. In a controlled environment production system, BL can be manipulated easily and precisely in aspects like peak wavelength, intensity, duration, and co-action with other wavelengths. However, the results of previous studies about BL-mediated floral [...] Read more.

Blue light (BL) is important in regulating floral transition. In a controlled environment production system, BL can be manipulated easily and precisely in aspects like peak wavelength, intensity, duration, and co-action with other wavelengths. However, the results of previous studies about BL-mediated floral transition are inconsistent, which implies that an in-depth critical examination of the relevant physiological mechanisms is necessary. This review consolidates the recent findings on the role of BL in mediating floral transition not only in model plants, such as Arabidopsis thaliana, but also in crops, especially horticultural crops. The photoreceptors, floral integrator proteins, signal pathways, and key network components involved in BL-mediated floral transition are critically reviewed. This review provides possible explanations for the contrasting results of previous studies on BL-mediated flowering; it provides valuable information to explain and develop BL manipulation strategies for mediating flowering, especially in horticultural plants. The review also identifies the knowledge gaps and outlines future directions for research in related fields. Full article

(This article belongs to the Special Issue Advances in Plant Photobiology)

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Plants, Volume 14, Issue 10 (May-2 2025) – 158 articles

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