Plants

15 pages, 2132 KB

Open AccessArticle

Anatomical Changes in the Peel of Sun-Damaged Pomegranates (Punica granatum L. cv. Hicaznar)

by Keziban Yazıcı, Muhammad Tanveer Altaf and Lami Kaynak

Plants 2026, 15(6), 987; https://doi.org/10.3390/plants15060987 - 23 Mar 2026

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Pomegranate (Punica granatum L.) is a major fruit crop in tropical and subtropical regions, but changing climatic conditions—especially rising temperatures and intense solar radiation—are increasing physiological disorders. Sunburn, a key heat- and light-induced disorder, causes peel discoloration and tissue damage. This results [...] Read more.

Pomegranate (Punica granatum L.) is a major fruit crop in tropical and subtropical regions, but changing climatic conditions—especially rising temperatures and intense solar radiation—are increasing physiological disorders. Sunburn, a key heat- and light-induced disorder, causes peel discoloration and tissue damage. This results in significant yield loss and reduced fruit quality. The objective of this study was to characterize sunburn-induced anatomical changes in the widely grown, highly sensitive Hicaznar cultivar in Türkiye, and to identify the optimal phenological stage for the application of sunburn-preventive practices. For this purpose, pomegranate fruit peels were fixed in FAA (Formalin–Acetic Acid–Alcohol) solution, embedded in paraffin blocks, and sectioned at a thickness of 5–7 µm. The sections were stained using the hematoxylin–eosin method and examined under a light microscope. The images captured with a digital camera wereanalyzed and revealed that sunburn damage in the pomegranate peel first appears in the cuticle layer, followed by disruption and fragmentation of the cutaneous and epidermal layers beneath it, and ultimately leads to damage of the parenchyma cells. Furthermore, Light microscopy showed that before visible discoloration, cells near the epidermis undergo phenolic accumulation, cell-wall thickening, and lignification, which are early indicators of sunburn. These microscopic changes provide early diagnostic features for detecting sunburn damage before external symptoms manifest. The study concluded that anatomical changes begin before the visible symptoms of sunburn appear on the fruit, and the most appropriate timing for applying preventive measures against sunburn has been identified. Light microscopy showed that before visible discoloration, cells near the epidermis undergo phenolic accumulation, cell-wall thickening, and lignification, which are early indicators of sunburn. Full article

(This article belongs to the Special Issue Plant Fruit Development and Abiotic Stress)

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29 pages, 6654 KB

Open AccessArticle

Improving Rice Root Development and Soil Health in Saline Soils: A Biochar and Microbial-Inoculated Biochar with Nitrogen Approach

by Hafiz Muhammad Mazhar Abbas, Song Li, Wentao Zhou, Haider Sultan, Mohammad Nauman Khan, Asad Shah, Ashar Tahir, Hamza Iltaf, Yixue Mu and Lixiao Nie

Plants 2026, 15(6), 986; https://doi.org/10.3390/plants15060986 - 23 Mar 2026

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Abstract

This study investigated the combined effects of microbial-inoculated biochar and nitrogen (N) on rice growth and soil properties under saline conditions. A randomized complete block design with three replications was employed to evaluate three factors: (i) salinity level (non-saline, S0; saline, 0.4% NaCl, [...] Read more.

This study investigated the combined effects of microbial-inoculated biochar and nitrogen (N) on rice growth and soil properties under saline conditions. A randomized complete block design with three replications was employed to evaluate three factors: (i) salinity level (non-saline, S0; saline, 0.4% NaCl, S1), (ii) biochar type (20 t/ha BC, BF, BB, and BFB), and (iii) nitrogen application rate (60 and 120 kg ha⁻¹). Soil physicochemical and biological properties, along with rice root development, were assessed. Salinity significantly reduced soil organic matter (OM) by 9%, nitrate nitrogen (NO₃⁻-N) by 16%, ammonium nitrogen (NH₄⁺-N) by 8.18%, and available phosphorus (AP) by 6.81%. Soil enzyme activities, including catalase (CAT), acid phosphatase (ACP), polyphenol oxidase (POX), and β-D-glucosidase (BG), decreased by 32.69%, 29%, 39.18%, and 19.44%, respectively, resulting in suppressed root growth compared with non-saline conditions. The combined treatment of microbial biochar (BFB) and N at 120 kg ha⁻¹ (BFB + N120) markedly improved saline soil quality and rice root performance by maintaining a favorable K⁺/Na⁺ balance in roots. Specifically, BFB+N120 increased OM by 145% and 120% compared with N120 and BC alone, respectively, and enhanced NO₃⁻-N, NH₄⁺-N, and soil enzyme activities (CAT, ACP, POX, and BG). These improvements were strongly associated with enhanced root development. Under saline conditions, BFB+N120 increased root dry mass by 429% and 1185.71%, and root length by 63% and 83%, compared with N120 and BC alone, respectively, in the cultivar Jing Liang You 534. Overall, the results demonstrate that microbial-modified biochar combined with nitrogen fertilizer mitigates salt-induced soil degradation by improving physicochemical and biological properties, thereby enhancing nutrient availability, ionic homeostasis, and root growth. This study provides mechanistic insights into the combined role of microbial biochar and nitrogen in the remediation of saline soils. Full article

(This article belongs to the Special Issue Fertilizer Management for Crop Resilience Under Abiotic Stress)

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18 pages, 3397 KB

Open AccessArticle

Integrating BSA-Seq and RNA-Seq to Identify Major QTLs and Candidate Genes Conferring Resistance to Fusarium Ear Rot in Maize

by Shufeng Sun, Jie Xu, Jiaxin Huang, Yuying Fan, Gongjian Li, Zhuanfang Hao, Jianfeng Weng, Zhennan Xu and Xinhai Li

Plants 2026, 15(6), 985; https://doi.org/10.3390/plants15060985 - 23 Mar 2026

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Abstract

Fusarium ear rot (FER), caused by Fusarium verticillioides, is a devastating disease that substantially reduces maize yield and compromises kernel quality. To investigate the genetic and molecular basis of resistance, an F₂ population derived from a cross between the resistant inbred [...] Read more.

Fusarium ear rot (FER), caused by Fusarium verticillioides, is a devastating disease that substantially reduces maize yield and compromises kernel quality. To investigate the genetic and molecular basis of resistance, an F₂ population derived from a cross between the resistant inbred line 3IBZ2 and the susceptible inbred line KW5G321 was analysed. By integrating bulked segregant analysis sequencing (BSA-Seq) with RNA sequencing (RNA-Seq), a major quantitative trait locus (QTL), designated qFER4, was identified on chromosome 4. Genetic analysis further demonstrated that qFER4 confers resistance through partial dominance. Transcriptome profiling of the resistant line revealed 7684 and 7906 differentially expressed genes (DEGs) at 36 and 72 h post inoculation (hpi), respectively. These DEGs were significantly enriched in defence-related biological processes and pathways, including phenylpropanoid biosynthesis, jasmonic acid signalling, MAPK cascades, and plant-pathogen interactions. By combining QTL mapping with transcriptome analyses, four candidate genes within the qFER4 interval were screened. Sequence analysis identified extensive structural variations in the promoter and coding regions of Zm00001d053393, including a premature stop codon predicted to lead to a gain-of-function mutation. In contrast, the other three genes exhibited only minor promoter polymorphisms with identical coding sequences between the parental lines. Overall, this study identifies a novel major-effect QTL and candidate gene associated with FER resistance, providing a foundation for gene function and a valuable genetic resource for breeding FER-resistant maize varieties. Full article

(This article belongs to the Special Issue Identification of Resistance of Maize Germplasm Resources to Disease)

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24 pages, 3504 KB

Open AccessArticle

Synergistic Effects of Supplemental Irrigation and Foliar Selenium Application on Dynamics Characteristics of Soil Respiration and Its Components in Millet Field

by Xiaoli Gao, Xuan Yang, Binbin Cheng, Haowen Wang and Yamin Jia

Plants 2026, 15(6), 984; https://doi.org/10.3390/plants15060984 - 23 Mar 2026

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Abstract

Soil respiration (Rs) plays a pivotal role in carbon cycling within semi-arid ecosystems. In our millet field experiment, we measured Rs, autotrophic respiration (Ra), heterotrophic respiration (Rh), water consumption (ET), yield (Y), water use efficiency (WUE), and key soil environmental properties to examine [...] Read more.

Soil respiration (Rs) plays a pivotal role in carbon cycling within semi-arid ecosystems. In our millet field experiment, we measured Rs, autotrophic respiration (Ra), heterotrophic respiration (Rh), water consumption (ET), yield (Y), water use efficiency (WUE), and key soil environmental properties to examine the effects of supplemental irrigation and selenium application on Rs dynamics and to clarify the controlling factors. The experiment was conducted from 2023 to 2024 with four treatments and three replicates per treatment each year. These treatments comprised conventional rainfed (CK), supplemental irrigation (SI, 50 mm), rainfed with Se addition (CS, 67.84 g·hm⁻²), and supplemental irrigation with Se addition (SIS). SI increased CO₂ emissions in the millet field, whereas selenium application (CS) suppressed them. Ra was the dominant component of Rs and was 1.03–4.01 times greater than Rh. SI and CS significantly affected cumulative CO₂ emissions through Ra (p < 0.05), whereas their effects on Rh were minor. The CS treatment resulted in the lowest cumulative CO₂ emissions at 4233 and 4009 g·m⁻² in 2023 and 2024, respectively. Diurnal variation patterns of Rs, Ra, and Rh differed across millet growth stages. Both supplemental irrigation and selenium application improved soil water retention, soil enzyme activity, and soil organic matter (SOM), and moderated soil temperature. Classification and Regression Tree (CART) algorithm analysis revealed that Ra was primarily driven by soil temperature, with a feature weight of 86.95% determined by CART based on machine learning, whereas Rh was mainly influenced by soil enzyme activity, with a feature weight of 76.11%. The CS treatment enhanced production while promoting emission mitigation. The combined SIS treatment achieved the highest WUE and maintained a lower Rs than SI. These findings suggest an environmentally sustainable management strategy for millet production in semi-arid regions. However, due to the limited number of parcels in this study, further field-scale validation and additional experimental research involving multiple levels of supplemental irrigation and Se addition are necessary. Full article

(This article belongs to the Topic Irrigation and Fertilization Management for Sustainable Agricultural Production)

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31 pages, 6766 KB

Open AccessArticle

Assessment of Heavy Metal Accumulation in Soils and Dominant Agricultural Crops in an Industrial Environment of Ridder, East Kazakhstan Region

by Dias Daurov, Kabyl Zhambakin, Ainash Daurova, Zagipa Sapakhova, Iskander Isgandarov, Raushan Ramazanova, Moldir Zhumagulova, Aidar Sumbembayev, Zhanar Abilda, Maxat Toishimanov, Rakhim Kanat and Malika Shamekova

Plants 2026, 15(6), 983; https://doi.org/10.3390/plants15060983 - 23 Mar 2026

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Abstract

Mining and metallurgical activities are among the main sources of heavy metal (HM) contamination of terrestrial ecosystems and the creation of persistent technogenic pollution hotspots. This study aimed to provide a comprehensive assessment of the accumulation of zinc (Zn), cooper (Cu), cadmium (Cd) [...] Read more.

Mining and metallurgical activities are among the main sources of heavy metal (HM) contamination of terrestrial ecosystems and the creation of persistent technogenic pollution hotspots. This study aimed to provide a comprehensive assessment of the accumulation of zinc (Zn), cooper (Cu), cadmium (Cd) and lead (Pb) in soils and vegetation under conditions of long-term industrial impact in Ridder, East Kazakhstan Region. A total of 52 soil samples were collected from 0–5 cm and 5–20 cm depths at 26 sites, and 44 species of natural vegetation, as well as three dominant agricultural crops, were examined. Soil concentrations of Zn (4415 mg·kg⁻¹), Cu (1177 mg·kg⁻¹), Cd (179 mg·kg⁻¹), and Pb (1996 mg·kg⁻¹) were classified as extremely high. Cadmium contributed most to the potential ecological risk (Cd > Pb > Zn > Cu). The industrial zone’s vegetation cover was predominantly formed by stress-tolerant and ruderal species, including Artemisia vulgaris, Calamagrostis epigeios, Bunias orientalis, Dactylis glomerata, Convolvulus arvensis, and Urtica dioica. The agricultural crops (Helianthus annuus, Avena sativa, and Triticum aestivum) mainly accumulated HMs in their root systems, with limited translocation to their aboveground organs (TF < 1). This indicates the predominance of phytostabilisation mechanisms, and highlights the potential of locally adapted plants for managing contaminated areas. Full article

(This article belongs to the Section Plant Ecology)

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22 pages, 2186 KB

Open AccessArticle

ConvDeiT-Tiny: Adding Local Inductive Bias to DeiT-Ti for Enhanced Maize Leaf Disease Classification

by Damaris Waema, Waweru Mwangi and Petronilla Muriithi

Plants 2026, 15(6), 982; https://doi.org/10.3390/plants15060982 - 23 Mar 2026

Viewed by 463

Abstract

Reliable identification of maize leaf diseases is critical for mitigating crop losses, particularly in regions where farmers have limited access to experts. Although vision transformers (ViTs) have recently demonstrated strong performance in image recognition, their weak inductive bias and limited modeling of local [...] Read more.

Reliable identification of maize leaf diseases is critical for mitigating crop losses, particularly in regions where farmers have limited access to experts. Although vision transformers (ViTs) have recently demonstrated strong performance in image recognition, their weak inductive bias and limited modeling of local texture patterns make them non-ideal for fine-grained maize leaf disease classification. To address these limitations, we propose ConvDeiT-Tiny, a lightweight hybrid ViT that improves DeiT-Ti by placing depthwise convolutions in parallel with multi-head self-attention modules in the first three transformer blocks. The local and global features captured by the convolution and attention modules are concatenated along the embedding dimension and fused using a multilayer perceptron. This results in richer token representations without significantly increasing model size. Across three datasets, ConvDeiT-Tiny (6.9 M parameters) consistently outperformed DeiT-Ti, DeiT-Ti-Distilled, and DeiT-S (21.7 M parameters) when trained from scratch. With transfer learning, ConvDeiT-Tiny achieved an accuracy of 99.15%, 99.35%, and 98.60% on the CD&S, primary, and Kaggle datasets, respectively, surpassing many previous studies with far fewer parameters. For explainability, we present gradient-weighted transformer attribution visualizations showing the disease lesions driving model predictions. These results indicate that injecting local inductive bias in early transformer blocks is beneficial for accurate maize leaf disease classification. Full article

(This article belongs to the Special Issue AI-Driven Machine Vision Technologies in Plant Science)

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22 pages, 2270 KB

Open AccessArticle

Seed Zone Nutritional Sensitivity and Hormone-Independent Rooting in Sugar Pine (Pinus lambertiana Dougl.): A Two-Phase Evaluation of Nutrient Solutions and Rooting Environments

by Jaime Barros Silva Filho, Arnaldo R. Ferreira and Milton E. McGiffen, Jr.

Plants 2026, 15(6), 981; https://doi.org/10.3390/plants15060981 - 23 Mar 2026

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Abstract

Clonal propagation of rust-resistant sugar pine (Pinus lambertiana Dougl.) is currently limited by extreme rooting recalcitrance and highly variable donor responses to nursery management. This study identified seed zone-specific nutritional sensitivities and evaluated rooting success; we hypothesized that northern seed sources would [...] Read more.

Clonal propagation of rust-resistant sugar pine (Pinus lambertiana Dougl.) is currently limited by extreme rooting recalcitrance and highly variable donor responses to nursery management. This study identified seed zone-specific nutritional sensitivities and evaluated rooting success; we hypothesized that northern seed sources would exhibit greater sensitivity to high nutrient loads and that stable microclimates would outperform high-intensity rooting systems. In Study 1, seedlings from five United States Department of Agriculture seed zones were grown for 27 weeks in five nutrient solutions (tap-water control, modified Hoagland, Foliage-Pro^®, Andrejow, and FloraNova^®) spanning 0.72–3.00 dS m⁻¹. The nutrient-rich Foliage-Pro^® and FloraNova^® solutions defined the upper end of the nutrient-intensity range and revealed strong seed zone contrasts: northern zones (526, 550) showed marked sensitivity, with survival declining from 70 to 100% in the control to 15–40% under the highest-EC formulations, whereas southern zones (992, 993) maintained high survival (≥75%) across all treatments and exhibited increased branching (up to 3.7 branches plant⁻¹) under higher-nutrient solutions. In Study 2, stem cuttings were rooted in three environments (non-mist, hydroponic, and aeroponic) and four hormone treatments (control, Clonex^®, Dip’n Grow^®, and IBA + Ethrel). Rooting occurred exclusively in the non-mist propagator; untreated controls achieved 65% success and outperformed all hormone treatments (0–10%). These results demonstrate that P. lambertiana propagation depends on seed zone-specific donor nutrition and stable, hormone-independent rooting environments. Full article

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

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14 pages, 2104 KB

Open AccessArticle

Chemical Profile, Antimicrobial and Anti-AChE of the Volatile Fraction of the Unexplored Bryophyte Polytrichadelphus purpureus Mitt. from Ecuador

by James Calva and Yamil Andrade

Plants 2026, 15(6), 980; https://doi.org/10.3390/plants15060980 - 22 Mar 2026

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Abstract

Polytrichadelphus purpureus is a bryophyte distributed in tropical and subtropical regions. It represents an underexploited source of bioactive metabolites. In this study, the volatile fraction (VF) obtained by steam distillation was analyzed by gas chromatography (GC-MS and GC-FID) on a DB-5ms capillary column, [...] Read more.

Polytrichadelphus purpureus is a bryophyte distributed in tropical and subtropical regions. It represents an underexploited source of bioactive metabolites. In this study, the volatile fraction (VF) obtained by steam distillation was analyzed by gas chromatography (GC-MS and GC-FID) on a DB-5ms capillary column, identifying 86 volatile compounds, representing the 97% of the volatile profile. Sesquiterpene hydrocarbons (23.6%), alcohols (15.6%), and alkanes (14.1%) were the major group compounds. Major components include (Z)-falcarinol (14%), hexacosane (4%), β-Curcumene (3%), and oleic acid (3%), among others. In addition, the volatile fraction exhibited moderate in vitro inhibitory activity against Gram-positive bacteria (E. faecium, S. aureus), fungus A. niger at concentrations of 250 µg/mL and 500 µg/mL, respectively, and E. faecalis and L. monocytogenes (250–500 µg/mL) and a weak inhibition of acetylcholinesterase (IC₅₀: 392 µg/mL). These effects were evaluated for the first time in this species. While they are within the range reported for other plant-derived volatile fraction, they do not, on their own, justify claims of therapeutic efficacy. This study primarily advances our understanding of the genus Polytrichadelphus, suggesting potential as a source of bioactive sesquiterpenes for future phytochemical screening. Full article

(This article belongs to the Special Issue Plant-Derived Bioactive Compounds: Extraction, Isolation, Biological Activities and Therapeutic Potential)

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17 pages, 7121 KB

Open AccessArticle

Habitat Filtering Shapes Root Endophytic Microbiome Assembly and Its Association with Fruit Quality in Lycium ruthenicum from the Tarim Basin

by Aihua Liang, Fengjiao Wang, Tianyi Liu, Yuting Liao and Zixin Mu

Plants 2026, 15(6), 979; https://doi.org/10.3390/plants15060979 - 22 Mar 2026

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Abstract

Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria [...] Read more.

Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe–host–environment interactions and the quality improvement of desert medicinal plants. Full article

(This article belongs to the Special Issue Forage and Sustainable Agriculture)

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17 pages, 9520 KB

Open AccessArticle

Two Optimized Methods for Efficient, Stable and Transient Transformation of Broccoli (Brassica oleracea Var. Italica)

by Alberto Coronado-Martín, Alejandro Atarés, Rosa Porcel, Lynne Yenush and José M. Mulet

Plants 2026, 15(6), 978; https://doi.org/10.3390/plants15060978 - 22 Mar 2026

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Abstract

Broccoli (Brassica oleracea var. italica) is an important crop valued for its nutritional and health-promoting properties, yet its biotechnological improvement is limited by low effectivity and genotype-dependent transformation protocols. The absence of reliable transient expression systems further constrains functional genomics and genome-editing [...] Read more.

Broccoli (Brassica oleracea var. italica) is an important crop valued for its nutritional and health-promoting properties, yet its biotechnological improvement is limited by low effectivity and genotype-dependent transformation protocols. The absence of reliable transient expression systems further constrains functional genomics and genome-editing applications. Here, we optimized regeneration and transformation protocols for different broccoli genotypes. Endoreduplication patterns in young tissues were analyzed by flow cytometry to identify suitable explants, and combinations of plant growth regulators were tested to develop an efficient organogenic medium. Stable transformation was achieved via Agrobacterium tumefaciens using nptII and eGFP markers. Cotyledons and hypocotyls up to day 7 showed similar endoreduplication patterns, with abundant 2n cells, but hypocotyls exhibited higher regeneration capacity. The optimized medium supported efficient organogenesis while maintaining diploidy. Transformation efficiency reached 10.4% in ‘S1’ and 2.8% in ‘Naxos’, highlighting genotype dependence. In parallel, a transient expression system was established using cotyledon-derived protoplasts and electroporation-mediated DNA delivery. GFP expression was confirmed through fluorescence microscopy, confocal imaging, and Western blotting. These protocols provide a robust toolkit for broccoli genetic manipulation, facilitating molecular biology studies in the native plant, functional genomics and genome-editing strategies, including CRISPR-based approaches. Full article

(This article belongs to the Special Issue In Vitro Plant Regeneration and Biotechnological Approaches for Crop Improvement)

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14 pages, 2152 KB

Open AccessArticle

Genetic Interaction Effects of Heading Date Genes Hd1 and Ghd7 on Photosynthetic Traits at the Heading Stage in Rice

by Jun Shi, Yi-Jie Yan, Zhen-Hua Zhang, Ye-Yang Fan, De-Run Huang, Yu-Jun Zhu and Bo Shen

Plants 2026, 15(6), 977; https://doi.org/10.3390/plants15060977 - 22 Mar 2026

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Abstract

In this study, we dissect the genetic effects of two major rice heading date genes, Heading date 1 (Hd1) and Grain number, plant height, and heading date 7 (Ghd7), in the regulation of six photosynthesis-related traits: the chlorophyll a [...] Read more.

In this study, we dissect the genetic effects of two major rice heading date genes, Heading date 1 (Hd1) and Grain number, plant height, and heading date 7 (Ghd7), in the regulation of six photosynthesis-related traits: the chlorophyll a/b contents, net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), and transpiration rate (Tr). Using two sets of near-isogenic lines (Z43 and Z44) derived from a Zhenshan97/Milyang46 cross, functional Hd1 increased the chlorophyll contents but decreased the photosynthesis-related parameters; however, functional Ghd7 consistently inhibited all six traits. More importantly, there is a significant epistatic interaction between them: Hd1 only enhances the photosynthetic capacity under the non-functional background of ghd7 but intensifies its photosynthesis inhibition under the functional background of Ghd7. Transcriptome analysis showed that functional Ghd7 mainly down-regulated the expression of genes related to photosynthesis and chloroplast development, and the inhibitory effect was significantly enhanced in the presence of functional Hd1. GO enrichment analysis further confirmed that the chlorophyll synthesis, photosystem assembly, and electron transfer pathways were downregulated in the bifunctional allele combination. Although Hd1 promotes chlorophyll accumulation, it reduces the actual photosynthetic efficiency, indicating that it has different regulatory paths for chlorophyll synthesis and photosynthetic function. Both physiological and molecular evidence showed that the Hd1-Ghd7 module coordinated the regulation of the heading date and photosynthetic capacity, forming a trade-off relationship between “early heading–high photosynthesis” and “late heading–low photosynthesis”. This study reveals the pleiotropy of genes at the heading stage and provides a theoretical basis for the optimization of the source–sink balance in high-yield rice breeding. Full article

(This article belongs to the Special Issue Rice Physiology, Genetics and Breeding)

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25 pages, 3484 KB

Open AccessArticle

Temporal Variation in the Essential Oil Production of Piper aduncum L.: Influence of Circadian Rhythms and Insights into Dillapiole Production Dynamics

by Jeferson A. S. Assunção, Camila G. Oliveira, Jessica S. Felisberto, Daniel B. Machado, Ygor Jesse Ramos and Davyson de Lima Moreira

Plants 2026, 15(6), 976; https://doi.org/10.3390/plants15060976 - 21 Mar 2026

Viewed by 548

Abstract

Piper aduncum L. (Piperaceae) is a neotropical species widely recognized for its bioactive essential oils (EOs), which exhibit antifungal, insecticidal, larvicidal, and antimicrobial properties. This study investigates the influence of circadian rhythms on the chemical composition and yield of P. aduncum EOs cultivated [...] Read more.

Piper aduncum L. (Piperaceae) is a neotropical species widely recognized for its bioactive essential oils (EOs), which exhibit antifungal, insecticidal, larvicidal, and antimicrobial properties. This study investigates the influence of circadian rhythms on the chemical composition and yield of P. aduncum EOs cultivated under agroecological conditions in the Rio de Janeiro Botanical Garden. Fresh leaves were collected every three hours over a 24 h cycle during both dry (July 2023) and rainy (February 2024) seasons. EOs were extracted by hydrodistillation and analyzed using GC-MS and GC-FID. A total of 20 compounds were identified in the dry season, while 10 were detected in the rainy season. Dillapiole was the predominant constituent in both periods, ranging from 75.78% to 88.27% (dry) and 75.90% to 90.86% (rainy). The highest EO yield was observed at 3:00 p.m. (0.73%) in the dry season and at 12:00 p.m. (0.61%) in the rainy season. Despite seasonal variations in chemical diversity, dillapiole content remained stable, reinforcing its biotechnological potential. The results highlight the importance of optimized harvesting times to maximize EO yield and composition, contributing to the sustainable exploitation of P. aduncum for medicinal and agricultural applications. Full article

(This article belongs to the Special Issue Circadian Regulation of Growth, Development and Metabolism in Plants/Microorganisms)

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23 pages, 3811 KB

Open AccessReview

Jasmonates Alleviate Abiotic Stress and Enhance Fruit Quality in Crop Plants: An Updated Review

by María Emma García-Pastor, Alex Erazo-Lara, Pedro Antonio Padilla-González, Domingo Martínez-Romero, María Serrano, Daniel Valero and Vicente Agulló

Plants 2026, 15(6), 975; https://doi.org/10.3390/plants15060975 - 21 Mar 2026

Viewed by 669

Abstract

Jasmonic acid (JA) and its derivative, methyl jasmonate (MeJa), are naturally occurring plant hormones involved in alleviating abiotic stresses, such as exposure to extreme temperatures (cold or heat), flooding and drought. JA content increased following MeJa applications at pre- or postharvest, regulating several [...] Read more.

Jasmonic acid (JA) and its derivative, methyl jasmonate (MeJa), are naturally occurring plant hormones involved in alleviating abiotic stresses, such as exposure to extreme temperatures (cold or heat), flooding and drought. JA content increased following MeJa applications at pre- or postharvest, regulating several physiological and biochemical processes during fruit growth and ripening. As a preharvest treatment, MeJa increased crop yield and improved the organoleptic quality of the fruit. Regarding postharvest applications, MeJa reduced the chilling injury symptoms in sensitive fruits when they were stored at cold temperatures. In addition, there is some evidence of crosstalk between JA and other plant hormones. In this review, we highlight the mechanisms by which jasmonates contribute to plant stress resistance, regulating the biosynthesis and metabolism of abiotic stress and improving fruit quality. Full article

(This article belongs to the Special Issue The Role of Plant Growth Regulators in Plant Response to Stress Factors)

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22 pages, 2533 KB

Open AccessArticle

Environmental and Cultivation Effects on Growth and Phytochemical Profiles of Chicory (Cichorium intybus L.) in Soil, Hydroponics, and Aquaponics

by Lorenzo Maria Curci, Sara Carrozzo, Gabriele Pecatelli, Teodoro Semeraro, Cosimo Tafuro, Marcello Salvatore Lenucci and Monica De Caroli

Plants 2026, 15(6), 974; https://doi.org/10.3390/plants15060974 - 21 Mar 2026

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Abstract

The increasing demand for sustainable food production has intensified interest in controlled-environment agriculture and soilless cultivation systems. This study evaluated the performance of local chicory (Cichorium intybus L., cultivar “Otrantina”) grown for 45 days in soil, hydroponics, and decoupled aquaponics under two [...] Read more.

The increasing demand for sustainable food production has intensified interest in controlled-environment agriculture and soilless cultivation systems. This study evaluated the performance of local chicory (Cichorium intybus L., cultivar “Otrantina”) grown for 45 days in soil, hydroponics, and decoupled aquaponics under two different environments: a fully controlled growth chamber and a naturally variable greenhouse. Morphological, anatomical, biochemical, and physiological traits were analyzed to assess the combined influence of growth environment and cultivation system on plant development and nutritional quality. Across all parameters, the growth environment emerged as the main driver of plant performance. Greenhouse-grown plants exhibited greater leaf expansion, enhanced mesophyll and vascular development, and higher fresh and dry biomass than those cultivated in the growth chamber. Within each environment, hydroponics consistently supported vigorous growth, whereas aquaponics produced smaller leaves and pronounced root elongation, likely reflecting nutrient and pH instability in the decoupled system. Biochemical analyses revealed system-specific adaptive responses. Soilless cultivation promoted higher lipid accumulation and, under growth chamber conditions, increased protein content. Aquaponically grown plants, particularly in the greenhouse, accumulated elevated levels of soluble sugars and phenolic antioxidants, consistent with stress-related metabolic activation. In contrast, soil-grown plants displayed the highest flavonoid concentrations, suggesting a prominent role of rhizosphere–microbiome interactions in modulating secondary metabolism. Overall, these results indicate that, under the tested conditions, environmental control exerts a stronger influence than cultivation systems on chicory growth and metabolism. Hydroponics proved to be the most efficient system for biomass production, whereas aquaponics requires improved nutrient management to ensure stable growth and quality. The distinct metabolic profiles associated with each cultivation system highlight opportunities to tailor chicory nutraceutical traits within sustainable controlled-environment agriculture. Full article

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21 pages, 11405 KB

Open AccessArticle

Defining the Optimal Microspore Developmental Window for Efficient Anther-Derived Somatic Embryogenesis in Rubber Tree (Hevea brasiliensis)

by Yinglian Wu, Naushad Alam, Xing Bao, Suna Peng, Rizhi Wu, Chenrui Gu, Xinran Ou, Haobin Liu, Xiaoyi Wang and Tiandai Huang

Plants 2026, 15(6), 973; https://doi.org/10.3390/plants15060973 - 21 Mar 2026

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Abstract

Anther-derived somatic embryogenesis is a valuable approach in rubber tree (Hevea brasiliensis) breeding; however, its effectiveness is highly influenced by the developmental stage of the microspores. The present investigation focused on male flower buds of the cultivar Reyan 73397 at successive [...] Read more.

Anther-derived somatic embryogenesis is a valuable approach in rubber tree (Hevea brasiliensis) breeding; however, its effectiveness is highly influenced by the developmental stage of the microspores. The present investigation focused on male flower buds of the cultivar Reyan 73397 at successive developmental stages to examine the relationship between visible bud characteristics and internal microspore development, assess how microspore developmental stage affects callus induction and somatic embryo formation, and identify the stage with the greatest embryogenic potential. Cytological observations distinguished six well-defined phases of microspore development, spanning from microspore mother cells to fully mature pollen grains, each reliably linked to particular bud diameters, coloration, and anther morphology. Anthers corresponding to each developmental phase were cultured in vitro, and their ability to initiate callus and produce somatic embryos was systematically evaluated. Anthers containing uninucleate microspores exhibited the highest rates of both callus formation and somatic embryogenesis, with the early-uninucleate stage showing the strongest response. This stage consistently matched flower buds measuring 1.42–1.57 mm in transverse diameter and displaying a green to yellowish-green appearance. In contrast, anthers collected at the microspore mother cell and tetrad stages did not produce embryogenic responses. Histological evidence has indicated that both callus and somatic embryos originate from diploid somatic tissues of the anther wall, particularly connective parenchyma cells, rather than from microspores themselves. Based on these findings, a rapid, non-destructive selection method integrating bud diameter, bud color, and sieve-based size separation was developed to identify responsive explants efficiently. Overall, this study defines the optimal developmental window for anther culture in rubber trees, verifies the somatic origin of embryogenic tissues, and provides a practical morphological and cytological basis for improving anther culture efficiency in rubber tree breeding programs. Full article

(This article belongs to the Section Plant Development and Morphogenesis)

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28 pages, 6442 KB

Open AccessArticle

Chemical Profiling and Photoprotective Activity of Extracts from Colombian Passiflora Byproducts

by María Cabeza, Cindy Lucero López, Geison Modesti Costa, Mónica Ávila-Murillo, Freddy A. Ramos, Yolima Baena, Marcela Aragón Novoa and Leonardo Castellanos

Plants 2026, 15(6), 972; https://doi.org/10.3390/plants15060972 - 21 Mar 2026

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Abstract

Agro-industrial byproducts from Colombian Passiflora species represent an underexplored source of chemically diverse metabolites with promising cosmetic and pharmaceutical potential. This study investigated the chemical profiles and photoprotective potential of polar extracts obtained from byproducts (leaves, pericarps, and seeds) of six commercially relevant [...] Read more.

Agro-industrial byproducts from Colombian Passiflora species represent an underexplored source of chemically diverse metabolites with promising cosmetic and pharmaceutical potential. This study investigated the chemical profiles and photoprotective potential of polar extracts obtained from byproducts (leaves, pericarps, and seeds) of six commercially relevant Passiflora species cultivated in Colombia (P. ligularis, P. edulis var. edulis, P. edulis var. flavicarpa, P. maliformis, P. quadrangularis and P. tarminiana × P. tripartita). Butanolic fractions from leaves and pericarps and hydroethanolic seed extracts were analyzed using ¹H NMR, GC-FID, GC-MS and UHPLC-qTOF. NMR profiling revealed aromatic signals mainly associated with flavonoids and stilbenoids in leaves and pericarps, while seeds exhibited abundant fatty acids, particularly linoleic acid. Molecular networking enabled the visualization of chemical diversity and supported the identification of 74 metabolites, including flavonoids, saponins, and stilbenoids, using Global Natural Products Social Molecular Networking (GNPS), SIRIUS (Version 6.0.5) software, and comparison with the literature. In vitro spectrophotometric photoprotective evaluation using the Mansur equation at 200 ppm showed that leaf extracts exhibited the highest sun protection factor (SPF) values, followed by seeds and pericarps, consistent with their phenolic composition. All active extracts demonstrated broad-spectrum protection, with high UVA ratios and critical wavelength values. These findings highlight the potential of Passiflora byproducts as sustainable sources of natural photoprotective agents for cosmetic applications. Full article

(This article belongs to the Special Issue Bioactive Compounds from Fruit and Vegetable By-Products: Recovery, Characterization, and Potential Applications)

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22 pages, 4360 KB

Open AccessArticle

Silicon Nanoparticles Modulate C:N:P Homeostasis and the Efficiencies of Nutrient Uptake, Translocation, and Use in Sugarcane Under Calcium Deficiency and Sufficiency

by João Victor da Silva Santos, Milton Garcia Costa, João Vitor Silva e Silva, Francisco Sales Ferreira dos Santos, Júnior and Renato de Mello Prado

Plants 2026, 15(6), 971; https://doi.org/10.3390/plants15060971 - 21 Mar 2026

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Abstract

Calcium (Ca) deficiency is a major nutritional constraint for sugarcane, impairing stoichiometric homeostasis and biomass accumulation. In this context, silicon dioxide nanoparticles (nSiO₂) have emerged as a promising alternative due to their high reactivity and potential to modulate mineral homeostasis. This [...] Read more.

Calcium (Ca) deficiency is a major nutritional constraint for sugarcane, impairing stoichiometric homeostasis and biomass accumulation. In this context, silicon dioxide nanoparticles (nSiO₂) have emerged as a promising alternative due to their high reactivity and potential to modulate mineral homeostasis. This study evaluated the effects of nSiO₂ on C:N:P:Si homeostasis and on nutrient uptake, translocation, and use efficiencies in sugarcane plants grown under Ca deficiency and sufficiency. The experiment was conducted in a greenhouse using a 2 × 2 factorial design, with two Ca conditions (0 and 3 mmol L⁻¹) and two nSiO₂ conditions (0 and 1.77 mmol L⁻¹ of Si), with four replications. Calcium deficiency reduced nutrient accumulation and nutritional efficiencies of several macro- and micronutrients, disrupted stoichiometric ratios, and decreased shoot dry mass. The application of nSiO₂ under Ca deficiency increased Si concentration and accumulation along with other nutrients, reduced C:Si ratios, enhanced nutrient uptake, translocation, and use efficiencies, and resulted in increased shoot biomass. Under Ca-sufficient conditions, nSiO₂ promoted nutritional adjustments and improved nutrient efficiencies but did not affect biomass production. Overall, the results demonstrate that nSiO₂ acts as a nutritional modulator and is more effective in mitigating the adverse effects of Ca deficiency through stoichiometric rebalancing and improved nutrient use efficiencies. Full article

(This article belongs to the Special Issue Silicon and Its Physiological Role in Plant Growth and Development)

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24 pages, 6500 KB

Open AccessArticle

Integrated Analysis of Physiological and Transcriptional Mechanisms in Response to Drought Stress in Scaevola taccada Seedlings

by Yaqin Wang, Wenlan Liu, Cunwu Zuo, Yongzhong Luo and Mengting Huang

Plants 2026, 15(6), 970; https://doi.org/10.3390/plants15060970 - 21 Mar 2026

Viewed by 524

Abstract

Scaevola taccada, as a key dominant plant in coastal ecosystems, plays an irreplaceable role in sand fixation, shoreline protection, and maintaining the ecological stability of coastal zones. To investigate the effects of drought stress on the Binghai plant Scaevola taccada seedlings, a [...] Read more.

Scaevola taccada, as a key dominant plant in coastal ecosystems, plays an irreplaceable role in sand fixation, shoreline protection, and maintaining the ecological stability of coastal zones. To investigate the effects of drought stress on the Binghai plant Scaevola taccada seedlings, a natural drought treatment was applied. Physiological indicators were measured at 0, 10, 25, and 40 days of stress, and 5 days after rewatering. Transcriptome sequencing and long non-coding RNA (lncRNA) analysis were also conducted to reveal the drought response mechanisms and molecular regulatory networks. The results showed that: (1) Prolonged drought significantly inhibited growth, with relative height increase, leaf number, and relative water content declining by 46.8%, 37.2%, and 63.4%, respectively, at T40 compared to the control. (2) In terms of photosynthetic physiology, Rubisco activity, RCA activity, SPAD value, Fv/Fm, and qP all continuously declined with increasing stress, while NPQ increased, suggesting damage to the photosynthetic system but also the activation of energy dissipation mechanisms to alleviate photooxidative stress. (3) The antioxidant system played a crucial role in the drought response. Under drought stress, the activities of SOD, POD, and CAT, and MDA content, underwent significant changes, with antioxidant enzyme activities rebounding notably after rewatering. (4) Transcriptome analysis revealed that differentially expressed mRNAs and lncRNA-targeted genes were significantly enriched in the ‘photosynthesis’ and ‘carbon metabolism’ pathways. Key genes involved, including PSAD-1, PSAL, NPQ4, six LHCs, BAM3, BAM1, SSII-A, and FRK1, were identified as core components of the regulatory network. In summary, Scaevola taccada effectively responds to drought stress through multi-level mechanisms, including photosynthetic regulation, carbon metabolism regulation, antioxidant defense, and transcriptional reprogramming, demonstrating strong drought resistance and post-rewatering recovery potential. These findings provide scientific evidence for plant selection and application in ecological restoration projects in coastal areas in the context of global climate extremes. Full article

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

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20 pages, 19943 KB

Open AccessArticle

MBMSA-UNet: A Multi-Scale Attention-Based Instance Segmentation Model for Moso Bamboo Cells

by Xue Zhou, Ziwei Cheng, Long Chen, Jiawei Pei, Yingyu Liao, Weizhang Liu, Chunyin Wu and Changyu Liu

Plants 2026, 15(6), 969; https://doi.org/10.3390/plants15060969 - 20 Mar 2026

Viewed by 3191

Abstract

Instance segmentation of moso bamboo cells is a critical step in quantitative structural analysis of bamboo materials and plant phenomics research. Moso bamboo tissues are mainly composed of vascular bundles and parenchyma cells. Within vascular bundles, fiber cells exhibit thick cell walls and [...] Read more.

Instance segmentation of moso bamboo cells is a critical step in quantitative structural analysis of bamboo materials and plant phenomics research. Moso bamboo tissues are mainly composed of vascular bundles and parenchyma cells. Within vascular bundles, fiber cells exhibit thick cell walls and extremely dense arrangements, whereas vessel cells are characterized by large diameters and complex internal structures. These features frequently lead to blurred boundaries, structural complexity, and local overexposure in microscopic images, making it difficult for traditional segmentation algorithms to achieve stable and accurate results. Although the U-Net has demonstrated outstanding performance in biological microscopic image analysis, its feature extraction capability and boundary recognition stability remain insufficient when dealing with the composite structure of moso bamboo. To address these challenges, this study proposes an improved model based on a multi-scale attention mechanism, termed MBMSA-UNet (Moso Bamboo Multi-Scale Attention U-Net). Building upon the encoder–decoder architecture of U-Net, the proposed model introduces a multi-scale channel-spatial attention block, aiming to handle the pronounced morphological and scale differences among vessels, fibers, and parenchyma cells. By adaptively reweighting features at different scales, the model enhances cross-layer feature fusion and strengthens responses to key regions, thereby effectively suppressing local overexposure interference and emphasizing boundary features between different cell types. Experimental results demonstrate that, compared with the U-Net and several of its improved variants, MBMSA-UNet achieves higher segmentation accuracy and greater robustness on microscopic images of moso bamboo, providing a solid foundation for fine-grained quantitative analysis of complex bamboo tissues. Full article

(This article belongs to the Special Issue Advanced Remote Sensing and AI Techniques in Agriculture and Forestry)

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24 pages, 5291 KB

Open AccessArticle

Roles of Cultivar, Light and Carbohydrates in Rooting of Cuttings of Hydrangea macrophylla

by Uwe Druege and Sindy Chamas

Plants 2026, 15(6), 968; https://doi.org/10.3390/plants15060968 - 20 Mar 2026

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Abstract

The roles of light and carbohydrates in adventitious root formation of Hydrangea macrophylla cuttings of the cultivars ‘Caipirinha’ and ‘Clarissa’ were investigated. Cuttings were planted immediately or dark-stored for seven days prior to cultivation under light. The leaf and rooting phenotype, relative chlorophyll [...] Read more.

The roles of light and carbohydrates in adventitious root formation of Hydrangea macrophylla cuttings of the cultivars ‘Caipirinha’ and ‘Clarissa’ were investigated. Cuttings were planted immediately or dark-stored for seven days prior to cultivation under light. The leaf and rooting phenotype, relative chlorophyll content, carbohydrate levels in different cutting sections and rooting response to hexose were analyzed. Surprisingly, pronounced leaf yellowing and reddening and a strong hexose accumulation in the cutting leaves indicated that the hydrangea cuttings experienced light stress under a photosynthetic photon flux density (PPFD) of 100 µmol m⁻² s⁻¹. Reduction in PPFD to 50 µmol m⁻² s⁻¹ decreased these symptoms and increased chlorophyll content, but impaired rooting. The effects of dark storage depended on cultivar, PPFD, and hydration of cuttings. ‘Clarissa’ exhibited lower rooting success, particularly after dark storage and low light, and showed lower hexose-to-sucrose ratios and hexose concentrations in the stem base than ‘Caipirinha’. Rooting of ‘Clarissa’ could not be rescued by sugar supplementation, whereas application of 27 mM glucose plus 30 mM fructose for 24 h before planting enhanced rooting of ‘Caipirinha’. The lower hexose level in the stem base of ‘Clarissa’ does not appear to be the critical factor underlying its low rooting capacity. Full article

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

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18 pages, 2949 KB

Open AccessArticle

Chromatin-Remodeling Factor CHR5 Promotes Defense Gene Expression and SA Accumulation

by Xueru Liu, Ning Cui, Zhengxi Gong, Hainan Tian, Yuelin Zhang and Xin Li

Plants 2026, 15(6), 967; https://doi.org/10.3390/plants15060967 - 20 Mar 2026

Viewed by 529

Abstract

Chromatin remodelers play essential roles in modulating nucleosome structure and enabling dynamic transcriptional control. Arabidopsis calmodulin-binding transcription activators CAMTA1/2/3 negatively regulate plant immunity by suppressing the expression of biosynthesis genes of major defence hormones salicylic acid (SA) and N-hydroxy-pipecolic acid (NHP). The autoimmunity [...] Read more.

Chromatin remodelers play essential roles in modulating nucleosome structure and enabling dynamic transcriptional control. Arabidopsis calmodulin-binding transcription activators CAMTA1/2/3 negatively regulate plant immunity by suppressing the expression of biosynthesis genes of major defence hormones salicylic acid (SA) and N-hydroxy-pipecolic acid (NHP). The autoimmunity of the camta2/3 mutant is partially suppressed by loss of the NHP biosynthesis enzyme SAR deficient 4 (SARD4). During a forward genetic screen with the mildly autoimmune camta2/3 sard4 mutant, we identified chromatin-remodelling factor 5 (chr5) as its partial suppressor. The chr5 single mutants displayed decreased SA biosynthesis and compromised basal immunity. Further RNA-sequencing with chr5 defined immune-related genes that were downregulated in the mutants, including those involved in SA and NHP biosynthesis and signalling, PTI and ETI pathways. Our analysis highlights the roles of CHR5 in immune-specific chromatin remodelling events, contributing to transcriptional reprogramming during plant defence responses. Full article

(This article belongs to the Special Issue Innate Immunity and Stress Responses in Plants: Mechanisms and Resilience)

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19 pages, 2013 KB

Open AccessArticle

Genetic Basis Analysis for Candidate QTLs and Functional Genes Controlling Four-Seeded Pods at Lower-Node in Soybean (Glycine max) Plant

by Ramiz Raja, Yihan Huang, Shicheng Ning, Bo Hu, Mahfishan Siyal, Wen-Xia Li and Hailong Ning

Plants 2026, 15(6), 966; https://doi.org/10.3390/plants15060966 - 20 Mar 2026

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Abstract

Soybean (Glycine max L. Merr.) is a globally significant oilseed crop. The number of four-seeded pods in the lower part (FSPL) serves as a critical yield component under high-density planting. To date, numerous crop-specific traits have been investigated in multiple breeding studies [...] Read more.

Soybean (Glycine max L. Merr.) is a globally significant oilseed crop. The number of four-seeded pods in the lower part (FSPL) serves as a critical yield component under high-density planting. To date, numerous crop-specific traits have been investigated in multiple breeding studies of soybean; however, little attention has been paid to studies on FSPL. Hence, in this study, we investigated the genetic basis of FSPL using a recombinant inbred line population (RIL3613) across four environments. The segregated genetic mapping population was cultivated during the field experiments, and the collected phenotypic dataset of FSPL exhibited quantitative genetics and high broad-sense heritability (0.724), indicating stable genetic control. Further, we performed quantitative trait locus (QTL) mapping using raw means in each environment and identified 10 QTL, explaining phenotypic variations (PVE) ranging from 0.10% to 2.94%. Among the identified environmentally stable QTL, qFSPL-15-1 was consistently detected across all environments. Two candidate genes [Glyma.15G034100 (encoding lysophosphatidic acid acyltransferase 2) and Glyma.15G034200 (encoding an RNA-binding protein)] were predicted within the flanking genomic interval. The allele frequencies of haplotype combinations of Hap1: Pro2 + CDS1 for Glyma.15G034100 and Hap3: Pro3 + CDS1 for Glyma.15G034200 in wild soybeans (26.6–30.0%) were larger than improved cultivars (52.6–53.4%). We believe that our current findings elucidate the molecular mechanisms regulating lower-pod formation and provide precise genetic targets for marker-assisted selection in high-yield soybean breeding. Full article

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

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24 pages, 7181 KB

Open AccessArticle

Integrated Transcriptomics and Metabolomics with Machine Learning Identify Flavonoids as Key Effectors in Wheat Root Thermotolerance

by Wenyuan Shen, Qingming Ren, Yiyang Dai, Yu Zhang and Fei Xiong

Plants 2026, 15(6), 965; https://doi.org/10.3390/plants15060965 - 20 Mar 2026

Viewed by 814

Abstract

Root plasticity is vital for crop survival amid global warming. Yet, the molecular mechanisms governing wheat root thermotolerance remain largely unknown. In this study, we combined phenomics, transcriptomics, and metabolomics with machine learning to analyze the performance of heat-tolerant cultivar YM158 and heat-sensitive [...] Read more.

Root plasticity is vital for crop survival amid global warming. Yet, the molecular mechanisms governing wheat root thermotolerance remain largely unknown. In this study, we combined phenomics, transcriptomics, and metabolomics with machine learning to analyze the performance of heat-tolerant cultivar YM158 and heat-sensitive cultivar YM15 under varying heat stress. While high temperatures (35 °C) severely inhibited root growth and caused oxidative damage in YM15, YM158 maintained robust root architecture and redox balance. Using weighted gene co-expression network analysis (WGCNA) alongside the random forest feature selection algorithm, we identified the flavonoid biosynthesis pathway as central to thermotolerance. Protein–protein interaction network analysis revealed that wheat root adaptability to high temperatures involves maintaining protein homeostasis via the endoplasmic reticulum protein processing system, specifically activating the flavonoid biosynthesis pathway and enhancing the antioxidant enzyme system. Furthermore, we identified a potential regulatory hub involving the cell wall sensor FERONIA (FER) and heat shock factors (HSFs), highlighting a complex interaction between hormonal signaling and secondary metabolism. Our study offers a detailed map of root heat adaptation and positions the flavonoid-mediated antioxidant system as a promising target for breeding climate-resilient crops. Full article

(This article belongs to the Special Issue Physiological Responses and Tolerance Mechanisms of Plants to Heat Stress)

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19 pages, 5980 KB

Open AccessArticle

Integrative Analysis of Transcriptome and Metabolome Reveals Regulatory Networks Associated with Flavonoids in Leaves of Rhododendron hainanense Under High-Temperature Stress

by Minghui Zhai, Enbo Wang, Jiaxuan Shi, Wendi Deng, Chengming Yan, Jian Wang, Xiqiang Song, Youhai Shi and Ying Zhao

Plants 2026, 15(6), 964; https://doi.org/10.3390/plants15060964 - 20 Mar 2026

Viewed by 464

Abstract

Heat stress severely impairs normal plant growth and yield, which significantly limits the horticultural and productive application of most Rhododendron species. In contrast, Rhododendron hainanense exhibits considerable heat tolerance due to its unique growing environment; however, the molecular mechanisms underlying its response to [...] Read more.

Heat stress severely impairs normal plant growth and yield, which significantly limits the horticultural and productive application of most Rhododendron species. In contrast, Rhododendron hainanense exhibits considerable heat tolerance due to its unique growing environment; however, the molecular mechanisms underlying its response to heat stress remain poorly understood. In this study, R. hainanense plants were subjected to heat stress treatment. Combined transcriptomic and metabolomic analyses identified 5454 differentially expressed genes and 152 differential metabolites. The results demonstrated that heat stress significantly induced the accumulation of flavonoids in R. hainanense. Notably, derivatives of myricetin, quercetin, and kaempferol were abundantly accumulated, suggesting their potential role in aiding plant defense against heat stress. The significant up-regulation of specific Rh4CL and RhFLS genes under high-temperature stress, coupled with the substantial accumulation of their flavonoid products (myricetin, quercetin, and kaempferol), indicates a potential role for these metabolites in the thermotolerance of Rhododendron hainanense. These findings provide novel insights into the heat stress response and flavonoid biosynthesis regulation in R. hainanense, highlighting the critical role of flavonoids in plant adaptation to heat stress. This study offers valuable references for the genetic improvement of Rhododendron cultivars with high stress resistance. Full article

(This article belongs to the Special Issue Physiological, Molecular and Genetic Mechanisms of Biotic and Abiotic Stress Tolerance in Trees)

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27 pages, 6066 KB

Open AccessArticle

Integrating Prognostic Breeding Approach Through Phenotypic and Marker-Assisted Selection for Yield and BCMV Resistance in Common Bean Greek Landraces

by Eirini N. Demertzi, Lefkothea Karapetsi, Chrysanthi I. Pankou, Nefeli Vasileiou, Eleftheria Georgiadou, Anastasia Kargiotidou, Varvara I. Maliogka, Dimitrios Vlachostergios, Panagiotis Madesis and Athanasios G. Mavromatis

Plants 2026, 15(6), 963; https://doi.org/10.3390/plants15060963 - 20 Mar 2026

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Abstract

Addressing principal challenges in common bean (Phaseolus vulgaris L.) breeding requires a holistic approach. A combined strategy was implemented to assess seven genotypes (landraces and commercial varieties) for yield potential, stability and resistance to bean common mosaic virus (BCMV) under Mediterranean low-input [...] Read more.

Addressing principal challenges in common bean (Phaseolus vulgaris L.) breeding requires a holistic approach. A combined strategy was implemented to assess seven genotypes (landraces and commercial varieties) for yield potential, stability and resistance to bean common mosaic virus (BCMV) under Mediterranean low-input conditions. Pure-line selection and prognostic breeding together with SSR and CAPS-SCAR marker-assisted selection (MAS) formed the core methodology. Significant variation was detected across 24 morpho-agronomic descriptors, while SSR revealed 48.57% polymorphic loci and private alleles in specific landraces. High genetic coefficients of variation and high heritability were recorded for yield-related traits. Phenotypical evaluation showed diverse responses to BCMV, with mild symptoms predominating (52.14%). Entries G1 (45%) and G5 (35%) exhibited the highest frequency of the symptomless resistant phenotype. Molecular screening at I and bc-3/eIF4E loci confirmed G5’s robust dominant I gene profile, while G1 included individuals carrying both the dominant I gene and recessive bc-3, offering a valuable source for pyramiding resistance. Additionally, G1 (LI = 2.35; 100%) performed strongly in productivity, whereas G2 (SI = 3.1; 100%) and G7 (SI = 2.8; 89.7%) exhibited exceptional stability. Overall, the mixed-model approach highlighted the complementary characteristics of the tested genotypes and identified G1, G2, G5 and G7 as promising candidates for future breeding programs targeting high yield, low-input adaptability and resistance to BCMV. Full article

(This article belongs to the Special Issue Bean Breeding)

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17 pages, 2730 KB

Open AccessArticle

Regulatory Effects of “Straw-Nitrogen Fertilizer” on Maize Yield Enhancement

by Yuchen Zhang, Mingxue Ye, Jinman Mei, Qiulai Song, Xiaochen Lyu and Chunmei Ma

Plants 2026, 15(6), 962; https://doi.org/10.3390/plants15060962 - 20 Mar 2026

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Abstract

To elucidate the regulatory mechanisms underlying the interaction between straw return and nitrogen (N) fertilization on yield formation, nutrient uptake, and soil N cycling in a continuous maize cropping system, a two-year positioning experiment was conducted. The study established two straw treatments (S0: [...] Read more.

To elucidate the regulatory mechanisms underlying the interaction between straw return and nitrogen (N) fertilization on yield formation, nutrient uptake, and soil N cycling in a continuous maize cropping system, a two-year positioning experiment was conducted. The study established two straw treatments (S0: 0 g/box; S1: 84 g/box) combined with three N levels (N0: 0 g/box; N1: 1.24 g/box; N2: 2.47 g/box). (The box refers to the cylinder used for planting maize.) The responses of maize yield, plant nutrient accumulation and partitioning, fertilizer-derived N ratio, nitrogen fertilizer use efficiency (NUE), and soil microenvironment were analyzed. Results indicated that under N1 conditions, straw return had a negligible effect on crop growth and yield formation. Conversely, under N2 conditions, straw return significantly enhanced maize yield and promoted the accumulation of N, phosphorus (P), and potassium (K) in plant tissues. ¹⁵N isotope tracing revealed a novel mechanism: rather than significantly altering direct fertilizer nitrogen use efficiency, straw return improved crop yield primarily by elevating indigenous soil N content and boosting the activities of N-transforming enzymes, thereby beneficially altering the ultimate environmental fate of the fertilizer N. Furthermore, straw return significantly boosted the activities of enzymes involved in N transformation and optimized the soil microenvironment. Collectively, straw return coupled with increased N application (specifically the S1N2 treatment) significantly maximizes maize yield, providing a theoretical basis for rational straw utilization and N management. Full article

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

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5 pages, 165 KB

Open AccessEditorial

Effect of Biotic and Abiotic Factors on the Physiology of Horticultural Plants

by Filippos Bantis and George Zervoudakis

Plants 2026, 15(6), 961; https://doi.org/10.3390/plants15060961 - 20 Mar 2026

Viewed by 467

Abstract

Horticultural crops comprise a diverse group of intensively cultivated plant species including vegetables, fruits, ornamental plants, and medicinal or aromatic crops, which are typically characterized by high economic value, intensive management, and strong dependence on environmental conditions [...] Full article

(This article belongs to the Special Issue Effect of Biotic and Abiotic Factors on the Physiology of Horticultural Plants)

19 pages, 1370 KB

Open AccessReview

Cold Stress Responses and Adaptation Mechanisms in Moringa oleifera Lam.: A Metabolite-Centred Review

by Blair Moses Kamanga, Donita L. Cartmill, Craig McGill and Andrea Clavijo McCormick

Plants 2026, 15(6), 960; https://doi.org/10.3390/plants15060960 - 20 Mar 2026

Viewed by 697

Abstract

Moringa oleifera Lam. (moringa) is a desirable crop for intensive cultivation because of its multiple uses in human and animal nutrition, medicine, and ecological applications. Its resilience and adaptability to various environmental conditions make it an attractive option for farmers seeking alternative cash [...] Read more.

Moringa oleifera Lam. (moringa) is a desirable crop for intensive cultivation because of its multiple uses in human and animal nutrition, medicine, and ecological applications. Its resilience and adaptability to various environmental conditions make it an attractive option for farmers seeking alternative cash crops that can thrive in challenging agricultural environments. While its resilience is well documented in tropical and subtropical climates, limited information exists on its growth dynamics and adaptation mechanisms to prolonged cold stress, which constrains its expansion and cultivation in temperate regions. This review synthesises current knowledge on cold stress adaptation mechanisms and the coordinated functional roles of primary and secondary metabolites in response to cold stress in plants, with a focus on moringa. Although considerable progress has been made in understanding morphological adjustments to cold stress in moringa plants, limited attention has been given to elucidating the physiological, metabolic, and genetic regulatory mechanisms underlying its cold-adaptive responses. Moreover, despite the potential roles of primary and secondary metabolites in coordinating protective functions against cold stress in plants, specific metabolites and their functional roles against cold stress remain insufficiently characterised in moringa. While genetic improvement and selective breeding have improved key agronomic traits, including growth rate, biomass yield, and nutritive value, breeding for enhanced cold stress tolerance remains insufficiently explored. Future studies should focus on integrative metabolite profiling, as well as the identification and selection of cold-tolerant provenances, to support the development of cold-tolerant gene pools to expand the cultivation range of moringa into temperate regions. Full article

(This article belongs to the Special Issue Cell Physiology and Stress Adaptation of Crops)

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12 pages, 3775 KB

Open AccessArticle

In Vitro Micropropagation of Native Ulluco (Ullucus tuberosus Caldas) from the Amazonas Region of Peru

by Deyli Mailita Fernández-Poquioma, Erika Llaja-Zuta, Angel David Hernández-Amasifuen and Jorge Alberto Condori-Apfata

Plants 2026, 15(6), 959; https://doi.org/10.3390/plants15060959 - 20 Mar 2026

Viewed by 533

Abstract

Ulluco (Ullucus tuberosus Caldas) is an Andean tuber crop of high nutritional and genetic importance. However, its vegetative propagation promotes the accumulation of pathogens and limits the availability of uniform, high-quality planting material. In this study, an efficient and reproducible in vitro [...] Read more.

Ulluco (Ullucus tuberosus Caldas) is an Andean tuber crop of high nutritional and genetic importance. However, its vegetative propagation promotes the accumulation of pathogens and limits the availability of uniform, high-quality planting material. In this study, an efficient and reproducible in vitro micropropagation protocol was established for an ulluco genotype from the Amazonas region of Peru. Nodal segments were cultured on MS (Murashige and Skoog) medium supplemented with 6-benzylaminopurine (BAP) or kinetin (KIN) at increasing concentrations (0.0–2.0 mg L⁻¹). For rooting, in vitro-derived shoots were transferred to MS medium supplemented with indole-3-butyric acid (IBA) or 1-naphthaleneacetic acid (NAA) at the same concentration range (0.0–2.0 mg L⁻¹). The explants exhibited a high basal morphogenetic capacity; however, the addition of cytokinins significantly enhanced the response. KIN at 2.0 mg L⁻¹ achieved 100% regeneration, whereas BAP at 0.2 mg L⁻¹ maximized shoot proliferation, producing 2.07 shoots per explant. Shoot elongation was greater with KIN at 1.0 mg L⁻¹, reaching 39.15 mm. In the rooting phase, the response varied depending on the type and concentration of auxin. NAA at 0.1 mg L⁻¹ resulted in 100% rooting and produced the greatest root length (41.93 mm), whereas IBA at 0.1 mg L⁻¹ maximized the number of roots (4.67), although roots were shorter. Rooted plantlets exhibited 100% survival after eight weeks of acclimatization. This protocol provides an effective system for the rapid production of vigorous and uniform clonal plants and represents a useful tool for the propagation, conservation, and future biotechnological improvement of ulluco. Full article

(This article belongs to the Collection Plant Tissue Culture)

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20 pages, 4377 KB

Open AccessArticle

Transcriptome-Based Dissection of the Molecular Mechanisms Underlying Flooding Stress Responses of Eastern Cottonwood in the Floodplains of the Middle and Lower Reaches of the Yangtze River

by Guowei Huang, Xueli Zhang, Xinye Zhang, Ning Liu, Changjun Ding, Jinhua Li, Fenfen Liu, Kailian Long, Chengcheng Gao, Jimeng Sun, Chenggong Liu and Qinjun Huang

Plants 2026, 15(6), 958; https://doi.org/10.3390/plants15060958 - 20 Mar 2026

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Abstract

Flooding, as a major abiotic stress, significantly impacts the growth and survival of poplar plantations in the floodplains of the middle and lower reaches of the Yangtze River. Elucidating the molecular mechanisms underlying flooding responses in poplar is crucial for enhancing plantation productivity. [...] Read more.

Flooding, as a major abiotic stress, significantly impacts the growth and survival of poplar plantations in the floodplains of the middle and lower reaches of the Yangtze River. Elucidating the molecular mechanisms underlying flooding responses in poplar is crucial for enhancing plantation productivity. In this study, two important eastern cottonwood cultivars, Populus deltoides ‘Jianghan 1’ (HBI) and P. deltoides Bartr. CL (CL), were investigated. By integrating long-term growth surveys and transcriptome sequencing, we analyzed their phenotypic traits and molecular responses to flooding stress. After 7 years of seasonal flooding, HBI exhibited a survival rate of 73.91%, along with superior height (23.1 m) and diameter at breast height (DBH, 26.3 cm), compared with CL, indicating HBI as a flooding-tolerant cultivar. Transcriptome analysis identified 1098 shared differentially expressed genes (DEGs) in the leaves of flooded HBI and CL, which were mainly enriched in stress signal perception, oxidative stress regulation, energy metabolism and circadian rhythm. Cultivar-specific DEG analysis revealed that CL mainly activated pathways related to oxidative stress and damage repair pathways, whereas HBI-specific genes were significantly enriched in hormone signal transduction, growth regulation, flavonoid synthesis and photosynthesis. Based on this distinct enrichment pattern in the tolerant cultivar HBI, we propose that it possesses adaptive advantages under flooding stress. Specifically, HBI likely coordinates multiple physiological processes by activating ethylene and other hormone-related genes, thereby regulating hypoxia adaptation, reoxygenation-induced oxidative stress, photosynthetic recovery, and flavonoid-mediated antioxidant defense. This coordinated regulation collectively sustains growth vigor and enhances survival under seasonal inundation. Our findings demonstrate clear transcriptomic divergence underlying flooding tolerance among poplar cultivars, laying a theoretical foundation for the selection of flooding-tolerant varieties and the sustainable development of forestry in flood-prone regions. Furthermore, these results broaden the current knowledge of flooding stress biology in woody plants. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Epigenetic Regulation of Abiotic Stress Tolerance in Plants)

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Plants, Volume 15, Issue 6 (March-2 2026) – 138 articles

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