Plants

21 pages, 6929 KB

Open AccessArticle

Augmenting pH Confers to Citrus grandis the Ability to Combat Oxidative Stress Triggered by Manganese Excess

by Rong-Yu Rao, Fei Lu, Bin-Bin Lan, Xian Zhu, Wei-Lin Huang, Xu-Feng Chen, Ning-Wei Lai, Lin-Tong Yang, Jiuxin Guo and Li-Song Chen

Plants 2026, 15(1), 172; https://doi.org/10.3390/plants15010172 - 5 Jan 2026

Viewed by 402

Abstract

Citrus trees are mainly cultivated in acidic soils. Excessive manganese (Mn) is the second most limiting factor for crop productivity in acidic soils after aluminum toxicity. The roles of reactive oxygen species (ROS) and methylglyoxal (MG) detoxification systems in augmented pH-mediated amelioration of [...] Read more.

Citrus trees are mainly cultivated in acidic soils. Excessive manganese (Mn) is the second most limiting factor for crop productivity in acidic soils after aluminum toxicity. The roles of reactive oxygen species (ROS) and methylglyoxal (MG) detoxification systems in augmented pH-mediated amelioration of excessive Mn are poorly understood. ‘Sour pummelo’ (Citrus grandis (L.) Osbeck) seedlings were exposed to nutrient solution at a Mn concentration of 500 (Mn500) or 2 (Mn2) μM and a pH of 3 (P3) or 5 (P5). The increase in pH attenuated Mn500-induced increases in ROS production and MG and malondialdehyde accumulation in roots and leaves. Additionally, the increase in pH enhanced the coordinated detoxification capability of both ROS and methylglyoxal scavenging systems in these tissues under Mn500. These findings corroborated the hypothesis that augmenting pH enhances the capability of these tissues to detoxify ROS and methylglyoxal under Mn excess. Therefore, this study provided new evidence on the roles of ROS and MG detoxification systems in the augmented pH-mediated amelioration of oxidative damage in ‘Sour pummelo’ leaves and roots caused by Mn excess, as well as a basis for correcting Mn toxicity by augmenting soil pH. Full article

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

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32 pages, 4171 KB

Open AccessReview

Flavonoids in Plant Salt Stress Responses: Biosynthesis, Regulation, Functions, and Signaling Networks

by Muhammad Tanveer Akhtar, Maryam Noor, Xinyi Lin, Zhaogeng Lu and Biao Jin

Plants 2026, 15(1), 171; https://doi.org/10.3390/plants15010171 - 5 Jan 2026

Viewed by 605

Abstract

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, [...] Read more.

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, and developmental plasticity. This review summarizes current evidence on how salinity remodels flavonoid biosynthesis, regulation, and function from cellular to whole-plant scales. We first outline the phenylpropanoid–flavonoid pathway, with emphasis on transcriptional control by MYB, bHLH, and NAC factors and their integration with ABA, JA, and auxin signaling. We then discussed how post-synthetic modifications such as glycosylation and methylation adjust flavonoid stability, compartmentation, and activity under salt stress. Functional sections highlight roles of flavonoids in ROS scavenging, Na⁺/K⁺ homeostasis, membrane integrity, and the modulation of ABA/MAPK/Ca²⁺ cascades and noncoding RNA networks. Spatial aspects, including root–shoot communication and rhizosphere microbiota recruitment, are also considered. Based on this synthesis, we propose a flavonoid-centered stress network (FCSN), in which specific flavonoids function as key nodes that connect metabolic flux with hormonal crosstalk and stress signaling pathways. We argue that reconceptualizing flavonoids as central stress network regulators, rather than generic antioxidants, provides a basis for metabolic engineering, bio-stimulant design, and breeding strategies aimed at improving crop performance on saline soils. Full article

(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)

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17 pages, 1552 KB

Open AccessArticle

Selenium Biofortification and an Ecklonia maxima-Based Seaweed Extract Jointly Compose Curly Endive Drought Stress Tolerance in a Soilless System

by Beppe Benedetto Consentino, Fabiana Mancuso, Lorena Vultaggio, Pietro Bellitto, Georgia Ntatsi, Claudio Cannata, Gaetano Giuseppe La Placa, Rosario Paolo Mauro, Salvatore La Bella and Leo Sabatino

Plants 2026, 15(1), 170; https://doi.org/10.3390/plants15010170 - 5 Jan 2026

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Abstract

Vegetable cultivation is currently facing complex challenges related to climate change, with negative repercussions on plant performance. In this scenario, the employment of eco-friendly agronomic tools capable of boosting plant tolerance to abiotic stresses is fundamental. Among them, the use of non-microbial biostimulants, [...] Read more.

Vegetable cultivation is currently facing complex challenges related to climate change, with negative repercussions on plant performance. In this scenario, the employment of eco-friendly agronomic tools capable of boosting plant tolerance to abiotic stresses is fundamental. Among them, the use of non-microbial biostimulants, such as seaweed extracts (SwEs), and microelements, like selenium (Se), is considered an efficient approach to overcome abiotic stresses. In this experiment, the performance of chicory plants cultivated under three different irrigation levels (100%, 75% or 50% of substrate water holding capacity) and treated with SwE, Se or their combination (SwE + Se) was evaluated. The results revealed that drought stress significantly decreased growth, productivity and relative water content but increased soluble solid content, dry matter percentage, and proline and malondialdehyde concentrations. The application of Swe, Se or Swe + Se enhanced growth, productive features and soluble solid content and reduced dry matter percentage, proline and malondialdehyde compared to the control. Based on our results, Se and SwE combined application could be a valuable approach to face moderate drought stress on curly endive plants and improve productive and quality traits. Full article

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

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21 pages, 1898 KB

Open AccessReview

MeJA-Induced Plant Disease Resistance: A Review

by Lifeng Xiao, Yuting Li, Lingyan Cui, Jie Deng, Qiuyue Zhao, Qin Yang and Sifeng Zhao

Plants 2026, 15(1), 169; https://doi.org/10.3390/plants15010169 - 5 Jan 2026

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Abstract

This review offers a comprehensive analysis of the extensive research on methyl jasmonate (MeJA)-induced plant disease resistance. It aims to elucidate the signal transduction pathways, interactions with other phytohormones, regulation of related gene expression, and the fundamental mechanisms contributing to plant disease resistance. [...] Read more.

This review offers a comprehensive analysis of the extensive research on methyl jasmonate (MeJA)-induced plant disease resistance. It aims to elucidate the signal transduction pathways, interactions with other phytohormones, regulation of related gene expression, and the fundamental mechanisms contributing to plant disease resistance. The review provides a detailed examination of MeJA-induced defense responses and the sustainability of the induced resistance. Furthermore, it assesses the practical applications and current status of MeJA across various plant species and explores potential research directions in disease management. It serves as a systematic reference for a deeper understanding of MeJA-induced plant disease resistance and holds significant importance for advancing further developments in the field. Full article

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

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17 pages, 2482 KB

Open AccessArticle

Reactive Oxygen Species Homeostasis Regulates Pistil Development and Pollination in Salix linearistipularis

by Xueting Guan, Chaoning Zhao, Junjie Song, Jiaqi Shi, Bello Hassan Jakada, Gege Dou, Xingguo Lan and Shurong Ma

Plants 2026, 15(1), 168; https://doi.org/10.3390/plants15010168 - 5 Jan 2026

Viewed by 472

Abstract

During the development of the gametophyte in angiosperms, a series of processes occurs, including pollination, pollen recognition, adhesion, hydration, germination, pollen tube growth, and the guidance of the pollen tube toward the ovule for the delivery of sperm cells to the female gametophyte. [...] Read more.

During the development of the gametophyte in angiosperms, a series of processes occurs, including pollination, pollen recognition, adhesion, hydration, germination, pollen tube growth, and the guidance of the pollen tube toward the ovule for the delivery of sperm cells to the female gametophyte. These processes require a substantial energy supply, which is provided by cellular respiration in the plant. Throughout this sequence, the generation of reactive oxygen species (ROS) is concomitantly observed. At present, the mechanisms underlying ROS production remain incompletely understood, especially in plant trees such as Salix linearistipularis. In this study, pistils of S. linearistipularis were used as experimental materials, and pistils were divided according to their development into three stages—S1, S2, and S3. Transcriptome sequencing (RNA-Seq) was performed for the three developmental stages, and the results indicated that metabolic pathways associated with oxidoreductase activity were highly significant during pistil development in S. linearistipularis. During pistil development, the levels of ROS accumulated rapidly. After pollination, with the adhesion and germination of pollen, the levels of ROS decreased significantly. Moreover, bidirectional regulation of ROS levels revealed that treatment with ROS inducers and scavengers led to increased and decreased ROS accumulation, which were accompanied by the inhibition and promotion of pollen tube number and length. These two opposite results indicate that ROS are the key factor regulating pistil development and pollen tube germination in S. linearistipularis. Full article

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

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14 pages, 2800 KB

Open AccessReview

MicroRNA-Mediated Hormonal Control of Fruit Morphology

by Kanghua Du, Da Zhang, Weiwu Lv, Guangping Chen, Lingfeng Bao, Xiaomei Li, Wanfu Mu and Zhong Dan

Plants 2026, 15(1), 167; https://doi.org/10.3390/plants15010167 - 5 Jan 2026

Viewed by 397

Abstract

Fruit morphogenesis represents a complex biological process resulting from the interactions among transcriptional regulation, hormone signaling, and environmental factors. MicroRNA (miRNAs) have been recognized recently as key genetic and epigenetic regulators in various plants, and they play critical roles in the regulation of [...] Read more.

Fruit morphogenesis represents a complex biological process resulting from the interactions among transcriptional regulation, hormone signaling, and environmental factors. MicroRNA (miRNAs) have been recognized recently as key genetic and epigenetic regulators in various plants, and they play critical roles in the regulation of diverse processes in response to endogenous developmental signals and external environmental cues, respectively. Recently, miRNA-mediated regulation mechanisms have also been extensively in horticulture plants, many novel mechanisms unveiled. Compared with model plants and field crops, miRNAs exhibit greater complexity and unique regulatory characteristics in governing fruit development in horticultural crops. Integrating the latest research, this review explores the roles of conserved miRNAs across multiple horticulture crops and synthesizes their regulatory networks in conjunction with phytohormones and transcription factors in governing fruit development, morphogenesis, and stress responses. It highlights the dual role of plant miRNAs under temperature stress, coordinating temperature adaptation, and fruit developmental plasticity through hormones and transcription factor networks. This review discusses the challenges and future prospects of utilizing this complex but promising epigenetic mechanism for crop improvement to cope with climate change. Full article

(This article belongs to the Special Issue Omics in Horticultural Crops)

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24 pages, 2289 KB

Open AccessArticle

Inhibition by Nitrogen Addition of Moss-Mediated CH₄ Uptake and CO₂ Emission Under a Well-Drained Temperate Forest, Northeastern China

by Xingkai Xu, Jin Yue, Weiguo Cheng, Yuhua Kong, Shuirong Tang, Dmitriy Khoroshaev and Vladimir Shanin

Plants 2026, 15(1), 166; https://doi.org/10.3390/plants15010166 - 5 Jan 2026

Viewed by 405

Abstract

Nitrogen (N) deposition poses a multi-pronged threat to the carbon (C)-regulating services of moss understories. For forest C-cycle modeling under increasing N deposition, failure to mechanistically incorporate the moss-mediated processes risks severely overestimating the C sink potential of global forests. To explore whether [...] Read more.

Nitrogen (N) deposition poses a multi-pronged threat to the carbon (C)-regulating services of moss understories. For forest C-cycle modeling under increasing N deposition, failure to mechanistically incorporate the moss-mediated processes risks severely overestimating the C sink potential of global forests. To explore whether and how N input affects the moss-mediated CH₄ and carbon dioxide (CO₂) fluxes, a five-year field measurement was performed in the N manipulation experimental plots treated with 22.5 and 45 kg N ha⁻¹ yr⁻¹ as ammonium chloride for nine years under a well-drained temperate forest in northeastern China. In the presence of mosses, the average annual CH₄ uptake and CO₂ emission in all N-treated plots ranged from 0.96 to 1.48 kg C-CH₄ ha⁻¹ yr⁻¹ and from 4.04 to 4.41 Mg C-CO₂ ha⁻¹ yr⁻¹, respectively, with a minimum in the high-N-treated plots, which were smaller than those in the control (1.29–1.83 kg C-CH₄ ha⁻¹ yr⁻¹ and 4.82–6.51 Mg C-CO₂ ha⁻¹ yr⁻¹). However, no significant differences in annual cumulative CO₂ and CH₄ fluxes across all treatments occurred without moss cover. Based on the differences in C fluxes with and without mosses, the average annual moss-mediated CH₄ uptake and CO₂ emission in the control were 0.77 kg C-CH₄ ha⁻¹ yr⁻¹ and 2.40 Mg C-CO₂ ha⁻¹ yr⁻¹, respectively, which were larger than those in the two N treatments. The N effects on annual moss-mediated C fluxes varied with annual meteorological conditions. Soil pH, available N and C contents, and microbial activity inferred from δ¹³C shifts in respired CO₂ were identified as the main driving factors controlling the moss-mediated CH₄ and CO₂ fluxes. The results highlighted that this inhibitory effect of increasing N deposition on moss-mediated C fluxes in the context of climate change should be reasonably taken into account in model studies to accurately predict C fluxes under well-drained forest ecosystems. Full article

(This article belongs to the Section Plant–Soil Interactions)

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18 pages, 2459 KB

Open AccessArticle

Study on the Susceptibility of Some Almond (Prunus dulcis) Cultivars to the Pathogen Diaporthe amygdali

by Pompea Gabriella Lucchese, Naïma Dlalah, Amélie Buisine, Franco Nigro, Stefania Pollastro and Henri Duval

Plants 2026, 15(1), 165; https://doi.org/10.3390/plants15010165 - 5 Jan 2026

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Abstract

Diaporthe amygdali Delacr. is a phytopathogenic fungus of considerable agronomic importance, responsible for branch canker in almond (Prunus dulcis [Mill.] D.A. Webb) and peach (Prunus persica L.) trees. It represents a major phytosanitary threat to almond cultivation in Europe, particularly in [...] Read more.

Diaporthe amygdali Delacr. is a phytopathogenic fungus of considerable agronomic importance, responsible for branch canker in almond (Prunus dulcis [Mill.] D.A. Webb) and peach (Prunus persica L.) trees. It represents a major phytosanitary threat to almond cultivation in Europe, particularly in Mediterranean regions. Almond is currently among the most rapidly expanding perennial crops, with cultivated areas increasing as a result of the introduction of new cultivars and the adoption of improved agronomic practices. The objectives of this study were to isolate and identify fungal pathogens from infected almond samples collected in France through multilocus phylogenetic analyses (ITS, tef1-α, his3, tub2, cal genes) combined with morphological characterization; evaluate the susceptibility of 18 almond genotypes, using ‘Ferragnès’ and ‘Texas’ as reference standards for susceptibility and tolerance, respectively; and compare three field inoculation methods. All isolates were identified as D. amygdali. The varietal screening identified marked differences in resistance among the tested cultivars. In particular, ‘Ferrastar’, ‘R1877’, ‘R1413’, and ‘R1542’ exhibited high levels of resistance, whereas ‘Tuono’, ‘Guara’, and ‘R1568’ showed susceptibility comparable to that of ‘Ferragnès’, which was used as the susceptible control. Among the inoculation methods evaluated, the mycelial plug technique proved to be the most consistent and reliable, outperforming both conidial suspension inoculation and the toothpick method coated with mycelium. These findings further confirm the genetic resistance of the cultivars ‘Ferrastar’ and ‘Ardèchoise’ to branch canker across different growing conditions, supporting their suitability for use in breeding and genetic improvement programs. Full article

(This article belongs to the Special Issue Advances in Plant–Fungal Pathogen Interaction—2nd Edition)

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16 pages, 1592 KB

Open AccessArticle

Multi-Omics Reveals Protected Cultivation Improves Chinese Plum (Prunus salicina L.) Quality via Light-Regulated Sugar Metabolism

by Liangliang Cao, Xi Long, Xiaolou Zhu, Jiangong Wang, Weidong Xu, Qiang Lu, Zanyu Ruan, Jiashun Miao and Zhangliang Yao

Plants 2026, 15(1), 164; https://doi.org/10.3390/plants15010164 - 5 Jan 2026

Viewed by 378

Abstract

The Chinese plum (Prunus salicina L.), ‘Zuili’, is a geographically protected cultivar that is valued for its high polyphenol levels and distinctive flavor. Light availability strongly influences sugar accumulation and secondary metabolism in plum fruit, yet the molecular processes associated with quality [...] Read more.

The Chinese plum (Prunus salicina L.), ‘Zuili’, is a geographically protected cultivar that is valued for its high polyphenol levels and distinctive flavor. Light availability strongly influences sugar accumulation and secondary metabolism in plum fruit, yet the molecular processes associated with quality variation under protected cultivation remain unclear. Here, we compare three cultivation systems—multi-span greenhouse (M), retractable electric rain shelter (R), and conventional open field (CK)—to evaluate their effect on fruit quality using integrated transcriptomic and metabolomic analyses. Field trials showed that M treatment increased fruit sweetness by 28.10% versus CK (14.68 vs. 11.46 °Brix, p < 0.001) without yield loss and significantly improved vertical fruit diameter. RNA-seq analysis identified 7561 and 7962 upregulated genes in the M and R treatments compared to CK, respectively, with significant functional enrichment in pathways related to sucrose metabolism, light-response, and ethylene-mediated signaling. Untargeted metabolomic signaling identified 1373 metabolites, with shading treatments increasing the abundance of several sugar-conjugated compounds (e.g., epicatechin 3-O-(2-trans-cinnamoyl)-β-D-allopyranoside). Multi-omics integration revealed coordinated changes in gene expression and metabolite abundance, suggesting that controlled light environments are associated with the concurrent modulation of sugar metabolism and phenylpropanoid-related pathways. These patterns were supported by the upregulation of GT2-family glycosyltransferase genes and the accumulation of lignin-related flavonoid precursors, such as pinobanksin and pinobanksinol. Collectively, these results highlight statistically robust associations between light-regulated cultivation practices and fruit quality traits, providing a molecular framework for optimizing protected cultivation strategies to enhance both the sensory and nutritional attributes of P. salicina fruit without compromising yield. Full article

(This article belongs to the Special Issue Horticultural Plant Physiology and Molecular Biology—2nd Edition)

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16 pages, 3799 KB

Open AccessArticle

Phylogenetic Divergence and Domestication Jointly Shape the Tomato Root Microbiome

by Grigorios Thomaidis, Georgios Boutzikas, Athanasios Alexopoulos and Christos Zamioudis

Plants 2026, 15(1), 163; https://doi.org/10.3390/plants15010163 - 5 Jan 2026

Viewed by 440

Abstract

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and [...] Read more.

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

(This article belongs to the Special Issue Root Development and Adaptations)

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30 pages, 5205 KB

Open AccessArticle

Ecological Niche Differentiation and Distribution Dynamics Revealing Climate Change Responses in the Chinese Genus Dysosma

by Rui Chen, Fangming Luo, Weihao Yao, Runmei Yang, Lang Huang, He Li and Mao Li

Plants 2026, 15(1), 162; https://doi.org/10.3390/plants15010162 - 5 Jan 2026

Viewed by 449

Abstract

The genus Dysosma, a group of perennial herbaceous plants with significant medicinal value and a relatively narrow ecological niche, is potentially at risk due to the combined pressures of habitat degradation and climate change. As their habitats continue to degrade, all species [...] Read more.

The genus Dysosma, a group of perennial herbaceous plants with significant medicinal value and a relatively narrow ecological niche, is potentially at risk due to the combined pressures of habitat degradation and climate change. As their habitats continue to degrade, all species of this genus have been included in the National Key Protected Wild Plants List (Category II). Investigating the impacts of climate change on the distribution of Dysosma resources is vital for their sustainable utilization. In this study, the potential distribution dynamics of seven Dysosma species under current and three future climate scenarios (SSP126, SSP245, SSP585) were quantified using 534 occurrence points and 25 environmental variables in a MaxEnt model, accompanied by the ecological niche overlap index (Schoener’s D), dynamic metrics (relative change rate [RCR], change intensity [CI], stability index [SI], spatial displacement rate [SDR]), and centroid migration analysis. The results indicated that (1) areas of high habitat suitability were consistently concentrated in the mountainous and hilly regions of southwestern Guizhou, Chongqing, and Hubei, with the minimum temperature of the coldest month (Bio6) and the mean diurnal temperature range (Bio2) being identified as the primary driving factors. (2) The future suitable habitat areas remained highly stable overall (SI > 97.89%), though dynamic changes varied across scenarios. Under SSP126, only slight fluctuations were observed, with an average CI of approximately 3.78% and RCR ranging from −0.46% to 1.97%. Under the SSP245 scenario, suitable habitat areas showed a continuous, slight expansion (RCR = 0.45% to 1.54%), whereas under the high-emission SSP585 scenario, a typical “mid-term expansion–late-term contraction” pattern was observed, with RCR shifting from positive (1.32%, 1.44%) to negative (−0.92%). The SI reached its lowest value of 97.89% in the late term, and the spatial displacement rate increased, signaling a reorganization of the distribution pattern. (3) High ecological niche differentiation was observed within the genus, with the highest overlap index being only 0.562, and approximately one-third of species pairs exhibiting completely non-overlapping niches. (4) Dysosma tsayuensis, a niche-specialist species, exhibited a distribution that was highly dependent on the annual mean ultraviolet-B radiation (UVB, contribution rate 52.9%), displaying an adaptation strategy markedly different from that of conservative species. (5) Centroid analysis indicated that, although the overall centroid remained stable in Guizhou, the presence of niche-specialist species under the high-emission SSP585 scenario resulted in migration paths opposite to those observed under other scenarios. The findings reveal the potential vulnerability and differential response patterns of Dysosma species under rapid climate warming, thereby providing a scientific basis for targeted conservation, in situ and ex situ conservation strategies, and population restoration. Full article

(This article belongs to the Section Plant Ecology)

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13 pages, 4666 KB

Open AccessArticle

Transcriptomics Reveals Cold Tolerance Maize Lines Involved in the Phenylpropanoid and Flavonoid Pathways

by Shuna Zhou, Xinling Yu, Jian Tan, Haixiao Sun, Wei Yang, Liangyu Jiang, Zhenyuan Zang, Jiabin Ci and Xuejiao Ren

Plants 2026, 15(1), 161; https://doi.org/10.3390/plants15010161 - 5 Jan 2026

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Abstract

Low temperature during early spring severely impairs maize germination, leading to significant yield losses. To elucidate the mechanisms underlying cold tolerance at the germination stage, we compared two cold-tolerant maize inbred lines (AM and CM) with a cold-sensitive line (BM) under control (25 [...] Read more.

Low temperature during early spring severely impairs maize germination, leading to significant yield losses. To elucidate the mechanisms underlying cold tolerance at the germination stage, we compared two cold-tolerant maize inbred lines (AM and CM) with a cold-sensitive line (BM) under control (25 °C) and chilling (6 °C) conditions. Phenotypic observations showed that AM and CM maintained high germination rates and exhibited enhanced coleoptile elongation under cold stress, whereas BM displayed substantial growth inhibition. Cold-tolerant lines accumulated less malondialdehyde and showed markedly higher SOD and POD activities, indicating a stronger antioxidant defense. Transcriptome profiling revealed that cold tolerance is associated with a more robust transcriptional response in AM and CM, characterized by significant activation of the phenylpropanoid and flavonoid biosynthesis pathways. Among the differentially expressed genes, the class III peroxidase gene ZmPER5 was strongly upregulated in AM and CM but only weakly induced in BM, suggesting its central role in reinforcing the cell wall structure and enhancing ROS-scavenging capacity under chilling conditions. Other lignin- and flavonoid-related genes, including ZmHCT4 and ZmCYP75, also exhibited genotype-specific induction patterns consistent with cold tolerance. qRT-PCR validation confirmed the RNA-seq expression trends. These results demonstrate that maize cold tolerance during germination relies on the coordinated enhancement of antioxidant enzyme activity, activation of phenylpropanoid-derived lignin biosynthesis, and accumulation of protective flavonoids. The identified candidate genes, especially ZmPER5, provide valuable targets for improving cold tolerance in maize breeding. Full article

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

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16 pages, 4940 KB

Open AccessArticle

Comprehensive Investigation of GRF Transcription Factors and Associated Responses to Drought Stress in Oat (Avena sativa)

by Shirui Xu, Xiajie Ji, Fumeng Sai, Mingchuan Ma, Zhang Liu, Lijun Zhang and Longlong Liu

Plants 2026, 15(1), 160; https://doi.org/10.3390/plants15010160 - 5 Jan 2026

Viewed by 395

Abstract

Growth-regulating factors (GRFs) are plant-specific transcription factors that play important roles in plant growth and development. However, no systematic analysis of GRF genes has been reported in oat (Avena sativa). In this study, we conducted a comprehensive characterization of the GRF [...] Read more.

Growth-regulating factors (GRFs) are plant-specific transcription factors that play important roles in plant growth and development. However, no systematic analysis of GRF genes has been reported in oat (Avena sativa). In this study, we conducted a comprehensive characterization of the GRF gene family in oat, including their physicochemical properties, chromosomal distribution, phylogenetic relationships, gene structure, conserved domains, promoter cis-elements, duplication events, and drought-responsive expression. In total, 28 GRF genes were identified in oat. Phylogenetic analysis classified them into two main groups, which could be further subdivided into five subgroups. Gene structure and conserved motif analyses revealed that AsGRF genes are largely group-specific and relatively highly conserved within each subgroup. Segmental duplication has been the primary driver of AsGRF gene family expansion, and these genes have undergone strong purifying selection during evolution. Transcriptomic analysis identified 13 AsGRF genes expressed under drought stress. Subsequent qRT-PCR analysis revealed that six of these genes were significantly up-regulated. Notably, AsGRF3 showed the highest expression level, was localized to the nucleus, and lacked transcriptional self-activation activity. In conclusion, this study provides a comprehensive analysis of the AsGRF gene family and serves as a valuable reference for further functional characterization of these genes in drought stress responses in oat. Full article

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

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17 pages, 9949 KB

Open AccessArticle

Aluminum Alleviation of Iron Deficiency Chlorosis Is Conserved in Wild Rice Relative Oryza rufipogon and in Maize

by Jover da Silva Alves, Yugo Lima-Melo, Andriele Wairich, Vic Martini Sasso, Vitor L. Nascimento, Raul Antonio Sperotto, Luciane Almeri Tabaldi, Gustavo Brunetto and Felipe Klein Ricachenevsky

Plants 2026, 15(1), 159; https://doi.org/10.3390/plants15010159 - 5 Jan 2026

Viewed by 297

Abstract

Aluminum (Al), an element that has no biological function described in plants, is commonly found in acidic soils, reducing plant growth, despite some beneficial effects reported in the literature. Iron (Fe) is an essential nutrient for plants, and Fe deficiency causes leaf interveinal [...] Read more.

Aluminum (Al), an element that has no biological function described in plants, is commonly found in acidic soils, reducing plant growth, despite some beneficial effects reported in the literature. Iron (Fe) is an essential nutrient for plants, and Fe deficiency causes leaf interveinal chlorosis. Remarkably, rice (Oryza sativa), a C₃ crop considered tolerant to Al, shows alleviation of Fe deficiency chlorosis when exposed to Al, suggesting that Al can positively impact Fe homeostasis. However, whether this effect is observed only in rice or is common to other plant species is unknown. The rice wild progenitor Oryza rufipogon is closely related to the domesticated species, sharing several traits such as a semi-aquatic habit and use of the combined strategy for Fe uptake. Maize (Zea mays), on the other hand, is a C₄ plant, adapted to well-aerated soils, and uses a classic chelation-based strategy for Fe uptake. Here we used these two Poaceae representatives to determine whether Al excess could alleviate Fe deficiency chlorosis in species other than rice. Although Al caused toxicity irrespective of Fe levels, its addition essentially abolished chlorosis in Fe-deficient plants. The expression of Fe deficiency-induced marker genes was reduced to control levels in both species, suggesting that the Al alleviation effect leads to systemic signaling and down-regulation of Fe uptake mechanisms. Al alleviation partially rescued photosynthetic machinery inhibited by Fe deficiency, suggesting that leaves are maintaining photosynthetic activity when Al is present even under low Fe conditions. Taken together, our data show that the Al alleviation effect is shared by two other Poaceae species in addition to O. sativa and suggest that it might not be directly linked to domestication, changes in C₃/C₄ metabolism, or Al tolerance levels found in different species. Full article

(This article belongs to the Special Issue Molecular Regulation of Plant Stress Responses)

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24 pages, 5920 KB

Open AccessArticle

Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress

by Cínthia Carla Claudino Grangeiro Nunes, Agnes Angélica Guedes de Barros, Jéssica Barboza da Silva, Wilson Dias de Oliveira, Flávia Layse Belém Medeiros, José Ribamar Costa Ferreira-Neto, Roberta Lane de Oliveira-Silva, Eliseu Binneck, Reginaldo de Carvalho and Ana Maria Benko-Iseppon

Plants 2026, 15(1), 158; https://doi.org/10.3390/plants15010158 - 4 Jan 2026

Viewed by 642

Abstract

Stylosanthes scabra, a legume native to the Brazilian semiarid region, exhibits remarkable drought tolerance and represents a valuable model for studying molecular adaptation in legumes. Transcription factors of the AP2/ERF superfamily play central roles in plant development and stress response. This study [...] Read more.

Stylosanthes scabra, a legume native to the Brazilian semiarid region, exhibits remarkable drought tolerance and represents a valuable model for studying molecular adaptation in legumes. Transcription factors of the AP2/ERF superfamily play central roles in plant development and stress response. This study aimed to identify and characterize AP2/ERF genes in Stylosanthes scabra and to analyze their transcriptional response to root dehydration. Candidate genes were identified through a Hidden Markov Model (HMM) search using the AP2 domain profile (PF00847), followed by validation of conserved domains, physicochemical characterization, prediction of subcellular localization, phylogenetic and structural analyses, and functional annotation. A total of 295 AP2/ERF proteins were identified and designated as SscAP2/ERF, most of which were predicted to be localized in the nucleus. These proteins exhibited a wide range of molecular weights and isoelectric points, reflecting structural diversity, and were classified into four subfamilies: AP2, ERF, DREB, and RAV. Functional annotation revealed predominant roles in DNA binding and transcriptional regulation, while promoter analysis identified numerous stress-related cis-elements. A total of 32 transcripts were differentially expressed under 24 h of water deficit, and four selected genes had their expression patterns validated by qPCR. These findings provide new insights into the AP2/ERF gene subfamily in Stylosanthes scabra and lay the groundwork for future biotechnological approaches to enhance stress tolerance in legumes. Full article

(This article belongs to the Special Issue Genetic and Biochemical Mechanisms of Abiotic Stress Responses in Phototropic Organisms)

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21 pages, 6687 KB

Open AccessArticle

Effects of Toxic Concentrations of Cadmium, Lead, or Zinc on Leaf Morphology, Anatomy and Calcium Oxalate Content in Metallicolous and Non-Metallicolous Ecotypes of Dianthus carthusianorum L.

by Izabela Borkowska-Drela, Marcin Domaciuk, Ewa Szczuka, Jaco Vangronsveld and Małgorzata Wójcik

Plants 2026, 15(1), 157; https://doi.org/10.3390/plants15010157 - 4 Jan 2026

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Abstract

Tolerance to metals develops independently across plant species and even among populations of the same species under strong environmental pressure. This study compares the morphology and leaf anatomy of Dianthus carthusianorum L. originating from a Zn–Pb waste dump (metallicolous ecotype, M) and from [...] Read more.

Tolerance to metals develops independently across plant species and even among populations of the same species under strong environmental pressure. This study compares the morphology and leaf anatomy of Dianthus carthusianorum L. originating from a Zn–Pb waste dump (metallicolous ecotype, M) and from unpolluted areas (non-metallicolous ecotype, NM), exposed to toxic concentrations of Cd, Pb, or Zn under chronic (field) and acute (hydroponic) metal stress. The aim was to identify leaf anatomical adaptations that support growth of the M ecotype in metal-polluted environments and to assess structural changes induced by acute exposure in both ecotypes. In both ecotypes, metal exposure caused alterations of mesophyll cells and the formation of abundant calcium oxalate (CaOx) crystals. Two oxalate forms were determined: insoluble (CaOx crystals) and soluble oxalates, with the former predominating. Following metal treatment, the M ecotype accumulated nearly twice as much of both forms as the NM ecotype, indicating a key role of oxalates in metal detoxification via precipitation of excess metal ions as metabolically inactive CaOx. Interestingly, elevated CaOx levels were also observed in M ecotype leaves grown under control (no metal application) conditions, suggesting a genetically fixed adaptation to metal-rich environments. Full article

(This article belongs to the Special Issue In Vivo and In Vitro Studies on Heavy Metal Tolerance in Plants)

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15 pages, 776 KB

Open AccessArticle

In Vitro and Field Effectiveness of the Combination of Four Trichoderma spp. Against Sclerotinia sclerotiorum and Its Impact on Potato (Solanum tuberosum L.) Crop Production

by Gabriel Herrera-Rodriguez, Ruben Felix-Gastelum, Maria Belen Irazoqui-Acosta, Sara Elodia Armenta-Lopez, Rosa Maria Longoria-Espinoza, Francisco Javier Orduño-Espinoza and Jessica Maria Parra-Parra

Plants 2026, 15(1), 156; https://doi.org/10.3390/plants15010156 - 4 Jan 2026

Viewed by 382

Abstract

White mold (Sclerotinia sclerotiorum) reduces potato yield and quality in Sinaloa, Mexico. This study first evaluated the in vitro efficacy of Trichoderma azevedoi, T. afroharzianum, T. asperellum and T. asperelloides in inhibiting S. sclerotiorum mycelial growth and sclerotia production. [...] Read more.

White mold (Sclerotinia sclerotiorum) reduces potato yield and quality in Sinaloa, Mexico. This study first evaluated the in vitro efficacy of Trichoderma azevedoi, T. afroharzianum, T. asperellum and T. asperelloides in inhibiting S. sclerotiorum mycelial growth and sclerotia production. Field experiments then assessed a combination of these antagonists, their alternating application with synthetic fungicides, and a fungicide-alone treatment for disease control, sclerotia reduction and yield increase. In vitro, all four Trichoderma species significantly inhibited the pathogen, achieving 60.1–63.1% mycelial suppression in dual culture and 90.3–94.1% via volatile metabolites, with the latter also completely suppressing sclerotia formation. In the field, the Trichoderma combination significantly controlled white mold, reducing plant incidence and severity to 66.0 and 27.1% in 2021 and 55.6 and 18.8% in 2022, while lowering sclerotia production to 32.7 and 14.6 on ten plants, respectively. This control extended to tubers, where incidence and severity were reduced to 1.6% and 0.4% in 2021, and 1.3% and 0.3% in 2022. The alternating application of Trichoderma with synthetic fungicides proved statistically equivalent to the Trichoderma-alone treatment in disease control, while the fungicides-alone treatment was significantly less effective. Potato yield was highest in plots treated with the Trichoderma combination (46.0 and 52.9 t ha⁻¹ in 2021 and 2022, respectively). These results highlight the potential of using a mixture of these four Trichoderma species as a cornerstone of sustainable disease management in Sinaloa, offering effective control of potato white mold while significantly reducing dependence on synthetic fungicides. Full article

(This article belongs to the Special Issue Advances in Plant–Fungal Pathogen Interaction—2nd Edition)

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20 pages, 11309 KB

Open AccessArticle

Elucidating Scent and Color Variation in White and Pink-Flowered Hydrangea arborescens ‘Annabelle’ Through Multi-Omics Profiling

by Yanguo Ke, Dongdong Wang, Zhongjian Fang, Ying Zou, Zahoor Hussain, Shahid Iqbal, Yiwei Zhou and Farhat Abbas

Plants 2026, 15(1), 155; https://doi.org/10.3390/plants15010155 - 4 Jan 2026

Viewed by 416

Abstract

The color and scent of flowers are vital ornamental attributes influenced by a complex interaction of metabolic and transcriptional mechanisms. Comparative analyses were performed to determine the molecular rationale for these features in Hydrangea arborescens, between the white-flowered variety ‘Annabelle’ (An) and [...] Read more.

The color and scent of flowers are vital ornamental attributes influenced by a complex interaction of metabolic and transcriptional mechanisms. Comparative analyses were performed to determine the molecular rationale for these features in Hydrangea arborescens, between the white-flowered variety ‘Annabelle’ (An) and its pink-flowered variant ‘Pink Annabelle’ (PA). Gas chromatography–mass spectrometry (GC–MS) detected 25 volatile organic compounds (VOCs) in ‘An’ and 21 in ‘PA’, with 18 chemicals common to both types. ‘An’ exhibited somewhat higher VOC diversity, whereas ‘PA’ emitted much bigger quantities of benzenoid and phenylpropanoid volatiles, including benzaldehyde, benzyl alcohol, and phenylethyl alcohol, resulting in a more pronounced floral scent. UPLC–MS/MS metabolomic analysis demonstrated obvious clustering of the two varieties and underscored the enrichment of phenylpropanoid biosynthesis pathways in ‘PA’. Transcriptomic analysis revealed 11,653 differentially expressed genes (DEGs), of which 7633 were elevated and linked to secondary metabolism. Key biosynthetic genes, including PAL, 4CL, CHS, DFR, and ANS, alongside transcription factors such as MYB—specifically TRINITY_DN5277_c0_g1, which is downregulated in ‘PA’ (homologous to AtMYB4, a negative regulator of flavonoid biosynthesis)—and TRINITY_DN23167_c0_g1, which is significantly upregulated in ‘PA’ (homologous to AtMYB90, a positive regulator of anthocyanin synthesis), as well as bHLH, ERF, and WRKY (notably TRINITY_DN25903_c0_g1, highly upregulated in ‘PA’ and homologous to AtWRKY75, associated with jasmonate pathway), demonstrating a coordinated activation of color and fragrance pathways. The integration of metabolomic and transcriptome data indicates that the pink-flowered ‘PA’ variety attains its superior coloring and aroma via the synchronized transcriptional regulation of the phenylpropanoid and flavonoid pathways. These findings offer novel molecular insights into the genetic and metabolic interplay of floral characteristics in Hydrangea. Full article

(This article belongs to the Special Issue Anthocyanins, Carotenoids, and Betalains in Plants: From Biosynthesis to Function)

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28 pages, 6853 KB

Open AccessArticle

Colors for Resources: Reward-Linked Visual Displays in Orchids

by Gabriel Coimbra, Carlos E. Pereira Nunes, Pedro J. Bergamo, João M. R. B. V. Aguiar and Leandro Freitas

Plants 2026, 15(1), 154; https://doi.org/10.3390/plants15010154 - 4 Jan 2026

Viewed by 472

Abstract

Pollination syndromes reflect the convergence of floral traits among plants sharing the same pollinator guild. However, bee-pollinated orchids exhibit striking variation in color and size. This diversity reflects the multiple reward strategies that evolved within the family, each interacting differently with bee sensory [...] Read more.

Pollination syndromes reflect the convergence of floral traits among plants sharing the same pollinator guild. However, bee-pollinated orchids exhibit striking variation in color and size. This diversity reflects the multiple reward strategies that evolved within the family, each interacting differently with bee sensory biases. Here, we tested whether the complex floral visual displays of orchids differ in signal identity and intensity among reward systems. We also considered intrafloral modularity, measured as the color differentiation among flower parts, and color–size integration. For this, we measured and modeled floral morphometric and reflectance data from sepals, petals, lip tips, and lip bases under bee vision from 95 tropical Epidendroid species to compare chromatic and achromatic contrasts, spectral purity, and mean reflectance across wavebands, plus flower and display size, among reward systems. Reward types included 19 food-deceptive, 8 nectar-offering, 10 oil-offering, 11 fragrance-offering, and 47 orchid species of unknown reward strategy. Principal component analyses on 34 color and 9 size variables summarized major gradients of visual trait variation: first component (19.1%) represented overall green-red reflectance and achromatic contrasts, whereas the second (16.5%) captured chromatic contrast–size covariation. Reward systems differed mostly in signal identity rather than signal intensity. Flower chromatic contrasts presented strong integration with flower size, while achromatic contrasts were negatively associated with display size. While deceptive and nectar-offering orchids tend toward larger solitary flowers with bluer and spectrally purer displays, oil- and fragrance-offering orchids tend toward smaller, brownish, or yellow to green flowers, with larger inflorescences. Rewardless orchids presented more achromatically conspicuous signals than rewarding orchids, but smaller displays. Orchid species clustered by reward both in PCA spaces and in bee hexagon color space. Deceptive orchids were typically associated with UV + White colors, oil orchids with UV + Yellow lip tips, and fragrance orchids with UV-Black lip bases and UV-Green lip tips. Together, these results indicate that orchid reward systems promote qualitative rather than quantitative differentiation in visual signals, integrating display color and size. These long-evolved distinct signals potentially enable foraging bees to discriminate among resource types within the community floral market. Our results demonstrate that color and flower display size are important predictors of reward strategy, likely used by foraging bees for phenotype-reward associations, thus mediating the evolution of floral signals. Full article

(This article belongs to the Special Issue Interaction Between Flowers and Pollinators)

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21 pages, 14183 KB

Open AccessArticle

Root–Canopy Coordination Drives High Yield and Nitrogen Use Efficiency in Dryland Winter Wheat

by Meng Li, Limin Zhang, Yuanxin Li, Yunxuan Cao, Yueran Zhang, Zhiqiang Gao, Dongsheng Zhang and Wen Lin

Plants 2026, 15(1), 153; https://doi.org/10.3390/plants15010153 - 4 Jan 2026

Viewed by 326

Abstract

Improving yield and nitrogen-use efficiency (NUE) is essential for dryland winter wheat. We hypothesized that cultivars classified as high-yield and high-efficiency (HH) achieve superior performance through coordinated root–canopy traits that enhance water and nitrogen acquisition, sustain post-anthesis photosynthesis, and maintain assimilate and nitrogen [...] Read more.

Improving yield and nitrogen-use efficiency (NUE) is essential for dryland winter wheat. We hypothesized that cultivars classified as high-yield and high-efficiency (HH) achieve superior performance through coordinated root–canopy traits that enhance water and nitrogen acquisition, sustain post-anthesis photosynthesis, and maintain assimilate and nitrogen remobilization. A two-year field experiment was conducted using ten regionally representative cultivars, which were grouped into HH, high-yield and low-efficiency (HL), low-yield and high-efficiency (LH), and low-yield and low-efficiency (LL) types based strictly on grain yield and NUE. Measurements included yield components, grain-filling, dry matter accumulation and partitioning, soil water use, nitrogen uptake and remobilization, and root–canopy structural traits. HH increased yield by 41.5% and water-use efficiency by 24.1% relative to LH, supported by denser shallow roots, moderate deeper-root development, higher leaf area index, and more compact canopies. HH also exhibited stronger post-anthesis dry matter and nitrogen translocation, resulting in a larger grain number per unit area and improved sink capacity. Correlation analyses further demonstrated positive associations among root–canopy traits, water and nitrogen dynamics, and yield formation. These results support the hypothesis that a coordinated root–canopy structure underlies the superior yield and NUE performance of HH cultivars in dryland systems, providing a physiological basis for cultivar improvement. Full article

(This article belongs to the Special Issue Modern Technologies in Water and Fertilizer Management for Sustainable Crop Production)

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29 pages, 2645 KB

Open AccessArticle

Influence of β-Cyclodextrin on the Overall Antioxidant Activity and DPPH· Reaction Kinetics of Fresh Raspberry (Rubus idaeus L.) and Dehydrated Strawberry (Fragaria × ananassa Duch.) Extracts

by Marinela Fiţoiu (Voin), Anamaria Pop (Mateuţ), Elena Vladu, Roxana Poja, Lavinia-Alexandra Toporîşte, Carina Elena Molnar, Mărioara Drugă, Gabriel Stelian Bujancă, Ioan David, Adina Horablaga, Nicoleta-Gabriela Hădărugă and Daniel-Ioan Hădărugă

Plants 2026, 15(1), 152; https://doi.org/10.3390/plants15010152 - 4 Jan 2026

Viewed by 376

Abstract

The influence of natural β-cyclodextrin (β-CD) on the overall antioxidant activity of berry extracts is presented in this study. Raw raspberry (Rubus idaeus L.) and β-CD-assisted dehydrated strawberry (Fragaria × ananassa Duch.) ethanolic extracts (RB and SB, respectively) were spectrophotometrically monitored [...] Read more.

The influence of natural β-cyclodextrin (β-CD) on the overall antioxidant activity of berry extracts is presented in this study. Raw raspberry (Rubus idaeus L.) and β-CD-assisted dehydrated strawberry (Fragaria × ananassa Duch.) ethanolic extracts (RB and SB, respectively) were spectrophotometrically monitored in the presence of 1 mM 2,2-diphenyl-1-picrylhydrazyl (DPPH·) solution in the absence or presence of β-CD. Cyanidin 3-O-glucoside (Cy3G) was used as standard compound, being identified by RP-HPLC in both RB and SB at 14.62 and only 0.15 mg/100 g fresh weight (fw). Pelargonidin 3-O-glucoside (Plg3G) was the most concentrated anthocyanin in SB (estimated at 2.46 mg/100 g fw). Higher antioxidant activities (expressed as the radical scavenging activity, RSA, %) were obtained for SB dehydrated in the presence of β-CD. The RSA values increased by 35% in comparison with the SB dehydrated by the classical method. On the other hand, the DPPH· reaction kinetic parameters significantly differed for RB extracts evaluated in the presence of 1 mM β-CD (in water). The DPPH· reaction rate in the 3–15 min time range was 25% higher for the RB extracts obtained from the β-CD-assisted dehydrated samples. This study demonstrates for the first time the protection capacity of β-CD against the degradation of antioxidants during the classical dehydration process of berries. This technology can be extended to other fruits and scaled up for obtaining high-quality fruit-based products. Full article

(This article belongs to the Special Issue Phytochemicals in Plants: Recent Developments on the Occurrence, Composition, Stability, Health, Food and Pharmaceutical Applications—2nd Edition)

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13 pages, 1194 KB

Open AccessCommunication

Progress in Flax Genome Assembly from Nanopore Sequencing Data

by Elena N. Pushkova, Alexander A. Arkhipov, Nadezhda L. Bolsheva, Tatiana A. Rozhmina, Alexander A. Zhuchenko, Elena V. Borkhert, Nikolai M. Barsukov, Gavriil A. Oleshnya, Alina V. Milovanova, Olesya D. Moskalenko, Fedor D. Kostromskoy, Elizaveta A. Ivankina, Ekaterina M. Dvorianinova, Daiana A. Krupskaya, Nataliya V. Melnikova and Alexey A. Dmitriev

Plants 2026, 15(1), 151; https://doi.org/10.3390/plants15010151 - 4 Jan 2026

Viewed by 396

Abstract

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford [...] Read more.

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford Nanopore Technologies (ONT) simplex R10.4.1 data and the Hifiasm algorithm optimized for ONT reads. The K-3018 genome assembly was 491.1 Mb and consisted of thirteen full-length chromosomes and two one-gap chromosomes. The Svyatogor genome assembly was 497.8 Mb and consisted of twelve full-length chromosomes and three one-gap chromosomes. All chromosomes had telomeric repeats at their ends for both varieties. Hi-C contact maps and Illumina genomic data supported the accuracy of the obtained assemblies. The K-3018 and Svyatogor genome assemblies surpassed the quality of the best currently available flax genome assembly of variety T397, which serves as a reference for L. usitatissimum in the NCBI Genome database. Comparative analysis revealed that the flax genomes are generally quite similar at the chromosome level, with only a few large-scale differences. Thus, two near-T2T (telomere-to-telomere) flax genomes were assembled from the ONT simplex R10.4.1 reads using Hifiasm ONT without involving Pacific Biosciences (PacBio) HiFi or ultra-long ONT reads as well as optical maps. High-quality flax genomes are essential for improving the efficiency of genetic research, evaluating genetic diversity at the whole-genome level, and developing breeding and genome editing approaches of this valuable multipurpose crop. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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19 pages, 8050 KB

Open AccessArticle

Optimization of Gene Gun-Mediated Transient Transformation and Explant Suitability in Coconut

by Mingjun Ma, Hanlu Su, Hao Nie, Xiaomeng Fang, Saeed Rauf, Saira Batool, Yin Min Htwe, Dapeng Zhang, Peng Shi, Zhiying Li, Qun Yu, Xiangman He and Yong Wang

Plants 2026, 15(1), 150; https://doi.org/10.3390/plants15010150 - 4 Jan 2026

Viewed by 362

Abstract

Coconut genetic improvement remains challenging due to low regeneration efficiency and limited transformation success. We optimized major components of a gene gun-mediated transient transformation system and evaluated explant types to support future establishment of a stable transformation pipeline. Three reporter genes (eGFP, GUS [...] Read more.

Coconut genetic improvement remains challenging due to low regeneration efficiency and limited transformation success. We optimized major components of a gene gun-mediated transient transformation system and evaluated explant types to support future establishment of a stable transformation pipeline. Three reporter genes (eGFP, GUS, and RUBY) were compared in coconut callus, and eGFP was selected as the most suitable due to its strong and non-destructive fluorescence. Background interference in GUS staining was reduced by adjusting the methanol–GUS ratio to 4:10. Single-factor optimization using callus tissue identified 0.4 M mannitol, 300–500 μg gold particles, 1.5 μg plasmid DNA, a 6.5 cm target distance, and 7 MPa pressure as effective parameters for biolistic delivery. Among the callus types, spongy callus showed strong transient eGFP expression but displayed loose and watery morphology consistent with non-embryogenic callus. In contrast, crumbly and smooth callus exhibited compact structures previously associated with embryogenic competence, although transient expression levels were lower. Among differentiated tissues, germinated zygotic embryo plumules and distal young leaflets exhibited moderate transient expression, supporting their suitability as transformation targets. These findings provide practical guidance on reporter selection, parameter refinement, and explant choice for future establishment of an efficient genetic transformation system in coconut. Full article

(This article belongs to the Special Issue Genetic Variation and Adaptation in Crops: Unraveling Molecular Mechanisms of Stress Tolerance)

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54 pages, 4696 KB

Open AccessReview

Molecular Mechanisms and Experimental Strategies for Understanding Plant Drought Response

by Adrianna Michalak, Karolina Małas, Kinga Dąbrowska, Kinga Półrolniczak, Lidia Bronowska, Anna Misiewicz, Angelika Maj, Maja Stabrowska, Iga Wnuk and Katarzyna Kabała

Plants 2026, 15(1), 149; https://doi.org/10.3390/plants15010149 - 4 Jan 2026

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Abstract

Drought severely limits plant growth, threatening global food security and biodiversity. This review provides a comprehensive overview of the recent advances in plant responses to drought, ranging from initial sensing to physiological adaptation, as well as guidelines for experimental design. We focus on [...] Read more.

Drought severely limits plant growth, threatening global food security and biodiversity. This review provides a comprehensive overview of the recent advances in plant responses to drought, ranging from initial sensing to physiological adaptation, as well as guidelines for experimental design. We focus on key regulatory components, specifically the ABA signaling core (PYR/PYL/RCARs, PP2C phosphatases, and SnRK2 kinases) and ROS signaling. We provide a detailed description of transcriptional networks, highlighting the pivotal roles of DREB, NAC, and MYB transcription factors in coordinating gene expression. Furthermore, we explore downstream tolerance strategies, including osmoprotectant (e.g., proline) accumulation, cell wall remodeling involving expansins and pectin methylesterases, as well as stomatal regulation. We also discuss how combining genetics with multi-omics and high-throughput phenotyping bridges the gap between molecular mechanisms and whole-plant physiological performance. Ultimately, these insights provide a foundation for refining research approaches and accelerating the development of drought-resilient crops to sustain agricultural productivity and ecosystem stability in increasingly arid environments. Full article

(This article belongs to the Special Issue Molecular Mechanisms Associated with Plant Tolerance upon Abiotic Stress—2nd Edition)

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27 pages, 6009 KB

Open AccessArticle

Integrating Molecular Analysis and the Pharmacology Network to Discover the Antioxidative Effects of Zanthoxylum piperitum Fruits

by Ducdat Le, Thinhulinh Dang, Thientam Dinh, Soojung Yu, Vinhquang Truong, Minhee Kim, Su-Yun Lyu, Kwang Seok Ahn and Mina Lee

Plants 2026, 15(1), 148; https://doi.org/10.3390/plants15010148 - 4 Jan 2026

Viewed by 462

Abstract

Zanthoxylum piperitum is a food and culinary plant commonly used in East Asia. In traditional medicine, its fruits, seeds, and bark have been utilized to treat digestive disorders, pain, and stomachache. Prior research has demonstrated its health benefits, particularly its significant antioxidant properties. [...] Read more.

Zanthoxylum piperitum is a food and culinary plant commonly used in East Asia. In traditional medicine, its fruits, seeds, and bark have been utilized to treat digestive disorders, pain, and stomachache. Prior research has demonstrated its health benefits, particularly its significant antioxidant properties. However, limited research has investigated the specific metabolites responsible for these pharmacological effects. In this study, the antioxidant activities (EC₅₀: 9.1–1084.5 μg/mL) and metabolite profiles of different organs (fruits, pericarps, and seeds) of Z. piperitum collected from different regions were comparatively analyzed. Chemical structures of 91 metabolites from different organs were identified using UHPLC-Orbitrap-MS/MS based on untargeted metabolomics. The LC-DPPH method was employed to screen antioxidants from the extracts of the most active organ (the pericarps). The potential effects of the active compounds on oxidation-related diseases were evaluated by integrating compound–target interaction network analysis. Protein–protein interaction (PPI) networks revealed EGFR, STAT3, AKT1, TNF, BCL2, CASP3, ESR1, PPARA, CYP19A1, and CDK2 as central hub genes. The significance of compound and target interactions was further supported by molecular docking studies, which demonstrated favorable binding affinities, with most proteins exhibiting docked scores below −4.27 kcal/mol. The extracts of Z. piperitum fruits and pericarps also exhibited antioxidative activity against ROS production in LPS-stimulated RAW264.7 cells. Our findings demonstrate the application of an optimized extraction process and underscore the medicinal value of this food-plant by characterizing its bioactive constituents. The results indicate that Z. piperitum may serve not only as a health-promoting food but also has the potential for prevention or treatment of oxidative-stress-related diseases. Future research should focus on in vivo studies by exploring the therapeutic mechanisms of actions of the active extracts. Full article

(This article belongs to the Special Issue Antioxidant and Anti-Inflammatory Activities of Plant Extracts and Phytochemicals)

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39 pages, 1754 KB

Open AccessReview

Eco-Physiological and Molecular Roles of Zinc Oxide Nanoparticles (ZnO-NPs) in Mitigating Abiotic Stress: A Comprehensive Review

by Erick H. Ochoa-Chaparro, Luis U. Castruita-Esparza and Esteban Sánchez

Plants 2026, 15(1), 147; https://doi.org/10.3390/plants15010147 - 4 Jan 2026

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Abstract

Mitigation of abiotic stress of crops is currently one of the primary issues for modern agriculture to secure food supply. On that point, it is acknowledged that climate change is leading to an increase in temperature and solar radiation, while also contributing to [...] Read more.

Mitigation of abiotic stress of crops is currently one of the primary issues for modern agriculture to secure food supply. On that point, it is acknowledged that climate change is leading to an increase in temperature and solar radiation, while also contributing to prolonged drought events. In contrast, saline soil and heavy metal pollution have been globally problematic, affecting a large part of crops. In this review, we have provided an overview of the eco-physiological and molecular aspects of zinc oxide nanoparticles (ZnO-NPs) as a novel technology for alleviating abiotic stress in plants. It is reported that the presence of ZnO-NPs has positive benefits in physiological processes, such as photosynthetic efficiency, osmotic regulation, ionic homeostasis, and the activation of antioxidant defense systems through gene modifications and the regulation of genes that are regulated under stress conditions. These are positive results for yields, nutrition, and resistance levels in cereals, legumes, and horticultural crops. Furthermore, essential details are reported, suggesting that the addition of ZnO-NPs to crops may be involved in regulating plant metabolism. Nonetheless, we recognize that this technology poses significant challenges for validation on a large scale, particularly in uncontrolled environments. Full article

(This article belongs to the Special Issue Climate Change and Plant Survival Strategies: Physiological and Biochemical Adaptations)

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21 pages, 3444 KB

Open AccessArticle

The Wheat Nucleoredoxin TaNRX1-2D Gene Ameliorates Salt Tolerance in Wheat (Triticum aestivum L.)

by Jianfei Zhou, Xiling Chang, Yaning Bu, Tianqi Song, Ling Kang, Yan Dong, Xinpeng Lei, Yuxin Wang, Xiaoxing Wang, Jiandong Ren, Jishan Xiang, Dongsheng Chen and Xiaoke Zhang

Plants 2026, 15(1), 146; https://doi.org/10.3390/plants15010146 - 4 Jan 2026

Viewed by 342

Abstract

Wheat is one of the most important crops contributing to global food and nutritional security. However, the gradual increase in soil salt content significantly impairs wheat growth and development, ultimately resulting in reduced yields. Therefore, enhancing the salt tolerance of wheat is of [...] Read more.

Wheat is one of the most important crops contributing to global food and nutritional security. However, the gradual increase in soil salt content significantly impairs wheat growth and development, ultimately resulting in reduced yields. Therefore, enhancing the salt tolerance of wheat is of significant importance. Salt stress commonly induces oxidative stress in plants, and nucleoredoxin (NRX) has been shown to effectively maintain redox homeostasis under stress conditions. However, the functional role and molecular mechanism of the NRX gene in regulating salt tolerance in wheat remain to be elucidated. The results of this study demonstrated that TaNRX1-2D homologous overexpression (OE) lines exhibited significantly enhanced tolerance to salt stress. The survival rate and antioxidant enzyme activities (including superoxide dismutase and catalase) in the OE lines were higher than those in the wild type (WT). In contrast, the levels of superoxide anion (O₂⁻), hydrogen peroxide (H₂O₂), and malondialdehyde (MDA) in the OE lines were markedly lower than those in the WT. Conversely, the RNA interference (RNAi) lines displayed opposing trends. The results of yeast one-hybrid (Y1H) and dual luciferase assays (D-LUC) demonstrated that the TaERD15L-3B transcription factor positively regulated the expression of the TaNRX1-2D gene by binding to the ABRERATCAL cis-acting element in the TaNRX1-2D promoter. Through luciferase complementation assay (LCA), bimolecular fluorescence complementation (BiFC) assay, and a “mutation capture strategy”, it was found that TaNRX1-2D (C54, 327S) interacted with TaCAT2-B, indicating that TaCAT2-B was the target protein of TaNRX1-2D. The results of data-independent acquisition (DIA) proteomics analysis indicated that TaNRX1-2D may mediate salt tolerance in wheat through the positive regulation of nsLTP protein abundance and the negative regulation of hexokinase protein abundance. In general, the TaERD15L-3B/TaNRX1-2D regulatory module played a crucial role in conferring salt tolerance in wheat. This study provided an important theoretical basis and identified a potential gene target for developing salt-tolerant wheat varieties through molecular breeding approaches. Full article

(This article belongs to the Special Issue Abiotic Stress of Crops: Molecular Genetics and Genomics—3rd Edition)

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18 pages, 5588 KB

Open AccessArticle

Regulation of Plasmodesmata Function Through Lipid-Mediated PDLP7 or PDLP5 Strategies in Arabidopsis Leaf Cells

by Xin Chen, Ning-Jing Liu, Jia-Rong Hu, Hao Shi, Jin Gao and Yu-Xian Zhu

Plants 2026, 15(1), 145; https://doi.org/10.3390/plants15010145 - 4 Jan 2026

Viewed by 613

Abstract

Plasmodesmata (PDs) are enriched in sphingolipids and sterols, creating a specialized environment for regulatory proteins like plasmodesmata-localized proteins (PDLPs). How PDLPs regulate PD function in a specific lipid environment remains poorly understood. Here, we provide a unique insight from the interaction network of [...] Read more.

Plasmodesmata (PDs) are enriched in sphingolipids and sterols, creating a specialized environment for regulatory proteins like plasmodesmata-localized proteins (PDLPs). How PDLPs regulate PD function in a specific lipid environment remains poorly understood. Here, we provide a unique insight from the interaction network of two different PDLPs together with sphingolipids and propose a concept that PDLPs form homo- or hetero-dimers only in the presence of sphingolipids. Located in the detergent resistance region, PDLP7 demonstrated the ability to influence the sphingolipid composition in PD-enriched fraction, particularly the GIPC content, and finally, modulating the membrane order. The presence of sphingolipids, in turn, affected the oligomeric state of PDLP7 in membranes. The PDLP7 recombinant protein existed as a monomer in vitro, but it formed self-aggregates in yeast and plant cells. We further examined PDLP5, another known phytosphinganine (t18:0)-specific binding PDLP, alongside PDLP7, and confirmed a similar interaction pattern: no direct interaction was observed in vitro, but interactions were noted in vivo. Co-overexpression of the two disrupted their PD localization and induced the upregulation of pathogenesis-related protein 1 (PR1). In summary, we gained insights into the network of PDLPs with lipids and propose that PDLPs were under precise regulation during plant development and stress responses. Full article

(This article belongs to the Section Plant Cell Biology)

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22 pages, 5901 KB

Open AccessReview

Advances in Micro- and Macrobiological Strategies for Pest Control in Berry Production Systems: A Critical Review

by Oscar Giovanni Gutiérrez-Cárdenas, Humberto Javier López-Macías, Kolima Peña-Calzada, Gerardo Arias-Robledo, Guadalupe Oyoque-Salcedo, Isaac Zepeda-Jazo, Pedro Damián Loeza-Lara, Martin Heil and Omar Fabián Hernández-Zepeda

Plants 2026, 15(1), 144; https://doi.org/10.3390/plants15010144 - 4 Jan 2026

Viewed by 676

Abstract

Berry crops such as strawberry Fragaria × ananassa (Weston), raspberry Rubus idaeus L., blackberry Rubus ulmifolius Schott, 1818, and blueberry Vaccinium myrtillus L. are economically and nutritionally valuable worldwide. However, the intensive use of synthetic pesticides for pest management in these crops has [...] Read more.

Berry crops such as strawberry Fragaria × ananassa (Weston), raspberry Rubus idaeus L., blackberry Rubus ulmifolius Schott, 1818, and blueberry Vaccinium myrtillus L. are economically and nutritionally valuable worldwide. However, the intensive use of synthetic pesticides for pest management in these crops has led to ecological imbalance, pest resistance, and negative effects on non-target organisms and human health. The integration of biological control agents into sustainable integrated pest management (IPM) systems represents an alternative. This review compiles and evaluates current advances in the application of baculoviruses (BVs), entomopathogenic fungi (EPFs), nematodes (EPNs), predatory mites (PMs), and parasitoid wasps (PWs) for pest suppression in berry crops. Emphasis was placed on their ecological interactions, host specificity, and compatibility within IPM frameworks. The combined use of micro- and macrobiological control agents effectively reduces key pest populations. However, field efficacy remains influenced by abiotic stressors such as UV radiation, temperature fluctuations, and chemical incompatibility. The integration of native micro- and macrobiological control agents of through conservation biological control (CBC) strategies can enhance sustainability in berry production systems. Future efforts should focus on formulation improvements, adaptive management under field conditions, and synergistic interactions among microbial and arthropod natural enemies. Full article

(This article belongs to the Special Issue Translating Ecological Research into Biological Control Strategies)

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25 pages, 6377 KB

Open AccessArticle

Increased Drought Stress Tolerance in Maize Seeds by Bacillus paralicheniformis Halotolerant Endophytes Isolated from Avicennia germinans

by Dinary Eloisa Durán-Sequeda, Zamira E. Soto-Valera, Ricardo Pizarro Castañeda, María José Torres, Luz Sandys Tobias, Claudia Vergel, Alejandra Paola Quintero Linero, Hernando José Bolívar-Anillo, Ricardo Amils and Maria Auxiliadora Iglesias-Navas

Plants 2026, 15(1), 143; https://doi.org/10.3390/plants15010143 - 4 Jan 2026

Viewed by 455

Abstract

Avicennia germinans, a representative of the marine coastal mangrove ecosystem, vital in the Colombian Caribbean, harbors a unique microbial diversity that could contain microorganisms with the potential to promote plant growth of agricultural species such as maize. The objective of this research [...] Read more.

Avicennia germinans, a representative of the marine coastal mangrove ecosystem, vital in the Colombian Caribbean, harbors a unique microbial diversity that could contain microorganisms with the potential to promote plant growth of agricultural species such as maize. The objective of this research was to evaluate A. germinans endophytes at different sampling sites and in diverse plant organs in order to identify the growth-promoting role of the most sodium chloride-tolerant endophyte found. These were then inoculated in maize seeds under drought stress conditions simulated by polyethylene glycol (PEG) in vitro. To this end, samples of adult A. germinans plants were collected from four mangrove ecosystems in the Colombian Caribbean. Several isolates were able to tolerate up to 15% NaCl (w/v), produce indole-3-acetic acid (IAA), show proteolytic activity, and inhibit phytopathogenic fungi. The best-performing strain, C1T-KM1901-B, was genomically identified as Bacillus paralicheniformis and evaluated as a bioinoculant in maize seeds under PEG-induced drought stress. Inoculation with B. paralicheniformis significantly increased germination potential and germination index of drought-resistant seeds compared to non-inoculated controls under severe drought stress conditions (40% PEG). In addition, inoculated seedlings exhibited significantly higher roots and shoot fresh and dry biomass at moderate to severe drought stress levels (15% and 20% PEG). These results are position B. paralicheniformis C1T-KM1901-B, isolated from Avicennia germinans, as a promising bioinoculant to enhance maize establishment under drought conditions. Full article

(This article belongs to the Special Issue Advances in Plant–Fungal Pathogen Interaction—2nd Edition)

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Plants, Volume 15, Issue 1 (January-1 2026) – 172 articles

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