Plants

19 pages, 14024 KiB

Open AccessArticle

Silencing of Putative Plasmodesmata-Associated Genes PDLP and SRC2 Reveals Their Differential Involvement during Plant Infection with Cucumber Mosaic Virus

by Richita Saikia, Athanasios Kaldis, Carl Jonas Spetz, Basanta Kumar Borah and Andreas Voloudakis

Plants 2025, 14(3), 495; https://doi.org/10.3390/plants14030495 - 6 Feb 2025

Abstract

Plant viruses utilize a subset of host plasmodesmata-associated proteins to establish infection in plants. In the present study, we aimed to understand the role of two plant genes, one encoding a putative plasmodesma located protein (PDLP) and a homolog of soybean gene regulated [...] Read more.

Plant viruses utilize a subset of host plasmodesmata-associated proteins to establish infection in plants. In the present study, we aimed to understand the role of two plant genes, one encoding a putative plasmodesma located protein (PDLP) and a homolog of soybean gene regulated by cold 2 protein (SRC2) during Cucumber mosaic virus (CMV) infection. Virus-induced gene silencing (VIGS) was used to silence PDLP and SRC2 genes in Nicotiana benthamiana and in two related solanaceous plants, N. tabacum and Capsicum chinense Jacq. (Bhut Jolokia). Up to 50% downregulation in the expression of the PDLP gene using the TRV2-PDLP VIGS construct was observed in N. benthamiana and N. tabacum while, using the same gene construct, 30% downregulation of the target mRNA was observed in C. chinense. Similarly, using the TRV2-SRC2 VIGS construct, a 60% downregulation of the SRC2 mRNA was observed in N. benthamiana, N. tabacum, and a 40% downregulation in C. chinense as confirmed by qRT-PCR analysis. Downregulation of the PDLP gene in N. benthamiana resulted in delayed symptom appearance up to 7–12 days post inoculation with reduced CMV accumulation compared to the control plants expressing TRV2-eGFP. In contrast, SRC2-silenced plants showed enhanced susceptibility to CMV infection compared to the control plants. Our data suggest that the PDLP gene might facilitate infection of CMV, thus being a susceptibility factor, while the SRC2 gene could play a role in resistance to CMV infection in N. benthamiana. Full article

(This article belongs to the Special Issue Physiological Aspects of Plant Response to Pathogens and Abiotic Stress—2nd Edition)

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18 pages, 4337 KiB

Open AccessArticle

Widely Targeted Metabolomics Analyses Provide Insights into the Transformation of Active Ingredients During Drying and the Mechanisms of Color Change for Forest Ginseng (Panax ginseng C. A. Mey. cv. Sativi-nemoralis)

by Junjia Xing, Limin Yang, Lianxue Zhang, Jiahong Han and Enbo Cai

Plants 2025, 14(3), 494; https://doi.org/10.3390/plants14030494 - 6 Feb 2025

Abstract

In this study, we investigated the mechanism of conversion of active components as well as the color change of forest ginseng (FG) during the drying process with the self-developed negative-pressure circulating airflow-assisted desiccator (PCAD) drying method, using a widely targeted metabolomics analytical method [...] Read more.

In this study, we investigated the mechanism of conversion of active components as well as the color change of forest ginseng (FG) during the drying process with the self-developed negative-pressure circulating airflow-assisted desiccator (PCAD) drying method, using a widely targeted metabolomics analytical method based on ultraperformance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). During the drying process, a total of 1862 metabolites were identified in FG, along with 748 differential abundant metabolites (DAMs). Further analysis of the types and metabolic pathways of the DAMs revealed that both primary and secondary metabolites changed by 50–70% moisture content (MC); secondary metabolites dominated with a 30–50% MC, and primary metabolites dominated with a 10–30% MC, which revealed the differences in the transformation of the active ingredients in the drying process. In addition, the results showed the browning characteristics during the drying process. MC-50 and MC-10 showed the smallest and largest color changes, as well as enzyme activities, compared to the other MCs, respectively. As drying proceeded, browning reactions were mainly related to lipid and nucleotide metabolism and phenylpropane and flavonoid biosynthesis. In conclusion, the present study provides theoretical support for the mechanisms of active ingredient transformation as well as the color change of FG during PCAD drying. Full article

(This article belongs to the Special Issue Biosynthetic Pathways and Molecular Regulatory Mechanisms of Active Ingredients in Medicinal Plants)

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16 pages, 3204 KiB

Open AccessArticle

Ultraviolet-A Radiation (UV_A) as a Stress and the Influence of Provenance and Leaf Age on the Expression of Phenolic Compounds by Eucalyptus camaldulensis ssp. camaldulensis

by Santosh Khanal, Simone J. Rochfort and Martin J. Steinbauer

Plants 2025, 14(3), 493; https://doi.org/10.3390/plants14030493 - 6 Feb 2025

Abstract

Ultraviolet radiation (UV) represents a significant abiotic stress, affecting green plants. Phenolic compounds have been suggested as components involved in plant photoprotective adaptation. We used a unique combination of experimental (LED lighting and leaf tagging) and analytical (unbiased, or untargeted, metabolomics) approaches to [...] Read more.

Ultraviolet radiation (UV) represents a significant abiotic stress, affecting green plants. Phenolic compounds have been suggested as components involved in plant photoprotective adaptation. We used a unique combination of experimental (LED lighting and leaf tagging) and analytical (unbiased, or untargeted, metabolomics) approaches to study the effects of high (approximating mid-summer) and low (approximating winter) levels of UV_A on the expression of phenolic compounds. These consisted of river red gum (Eucalyptus camaldulensis ssp. camaldulensis) of five provenances. The geographically separated provenances used in our study spanned the lowest and highest latitudes of the range of this subspecies. The concentrations of gallotannins and ellagitannins (i.e., hydrolysable tannins) increased most under high levels of UV_A, but responses only differed slightly among provenances. The most substantial changes in the composition of phenolic compounds were associated with leaf age. Overall, 3-month-old (herein, termed ‘young’) leaves had substantially different phenolic compositions to 6- and 12-month-old (‘old’) leaves. Hydrolysable tannins were more abundant in young leaves, whereas pedunculagin, catechin, and kaempferol galloyl glucoses were more abundant in old leaves. High levels of UV_A altered the expression of phenolic compounds, but our experimental saplings were unlikely to experience photoinhibition because they were not exposed to high levels of light and low temperatures, nor were they nitrogen-limited. We expect that changes in phenolic compounds would have been more pronounced if we had induced photoinhibition. Full article

(This article belongs to the Special Issue Plant Phenolic Compounds: From Biosynthesis to Functional Profiling)

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20 pages, 1509 KiB

Open AccessReview

L-Theanine Metabolism in Tea Plants: Biological Functions and Stress Tolerance Mechanisms

by Qianying Wang, Jingbo Yu, Wenchao Lin, Golam Jalal Ahammed, Wenli Wang, Ruihong Ma, Mengyao Shi, Shibei Ge, Ahmed S. Mohamed, Liyuan Wang, Qingyun Li and Xin Li

Plants 2025, 14(3), 492; https://doi.org/10.3390/plants14030492 - 6 Feb 2025

Abstract

L-theanine, a unique non-protein amino acid predominantly found in tea plants (Camellia sinensis), plays a pivotal role in plant responses to abiotic stress and significantly influences tea quality. In this review, the metabolism and transport mechanisms of L-theanine are comprehensively discussed, [...] Read more.

L-theanine, a unique non-protein amino acid predominantly found in tea plants (Camellia sinensis), plays a pivotal role in plant responses to abiotic stress and significantly influences tea quality. In this review, the metabolism and transport mechanisms of L-theanine are comprehensively discussed, highlighting its spatial distribution in tea plants, where it is most abundant in young leaves and less so in roots, stems, and older leaves. The biosynthesis of L-theanine occurs through the enzymatic conversion of glutamate and ethylamine, catalyzed by theanine synthase, primarily in the roots, from where it is transported to aerial parts of the plant for further catabolism. Environmental factors such as temperature, light, drought, elevated CO₂, nutrient unavailability, and heavy metals significantly affect theanine biosynthesis and hydrolysis, with plant hormones and transcription factors playing crucial regulatory roles. Furthermore, it has been demonstrated that applying L-theanine exogenously improves other crops’ resistance to a range of abiotic stresses, suggesting its potential utility in improving crop resilience amid climate change. This review aims to elucidate the physiological mechanisms and biological functions of L-theanine metabolism under stress conditions, providing a theoretical foundation for enhancing tea quality and stress resistance in tea cultivation. Full article

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

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19 pages, 990 KiB

Open AccessArticle

Assessment of Tamarix smyrnensis for Phytoremediation Capacity of Laterite Mine Spoils

by Petroula Seridou, Vasiliki Karmali, Evdokia Syranidou, Konstantinos Komnitsas, Georgios Kolliopoulos and Nicolas Kalogerakis

Plants 2025, 14(3), 491; https://doi.org/10.3390/plants14030491 - 6 Feb 2025

Abstract

The phytoremediation potential of the halophytic plant, Tamarix smyrnensis (T. smyrnensis), was examined in toxic metal spoils assisted by biochar and irrigation by air nanobubbles. The substrate (spoil) used in the present study was derived from areas close to laterite (Ni-containing [...] Read more.

The phytoremediation potential of the halophytic plant, Tamarix smyrnensis (T. smyrnensis), was examined in toxic metal spoils assisted by biochar and irrigation by air nanobubbles. The substrate (spoil) used in the present study was derived from areas close to laterite (Ni-containing ores) mines. The efficiency of biochar addition in two rates (5 t/ha and 20 t/ha) to improve microbial properties and stabilize soil aggregates was also examined. Furthermore, the effect of irrigation with air-nanobubble-supplemented water was evaluated for the remediation of toxic metal spoils. The physiological condition of the plant species was investigated in terms of biomass, height, chlorophyll content, and antioxidant enzymes. The alkali and heavy metal accumulation and their distribution in the plant parts were assessed to explore whether toxic metals could accumulate in the root and further translocate to the aboveground tissues. The growth of T. smyrnensis was not adversely affected by its cultivation in lateritic spoil, and the highest rate of biochar exhibited a beneficial effect on plant growth in terms of weight (aerial and subterranean biomass). The highest biochar application rate led to significant increases in total chlorophyll content, showing a 97.6% increase when biochar is used alone and a 136% increase when combined with nanobubble irrigation. Remarkably, only when combining irrigation with air nanobubbles and low biochar supplementation did the translocation of the metals from soil to the aboveground tissues occur as the translocation factor was estimated to be greater than unity (TF > 1). The bioconcentration factors remained below 1.0 (BCF < 1) across all treatments, demonstrating limited mobilization from soil to plant tissues despite the application of soil amendments. Finally, the application of nanobubbles increased slightly but not substantially the total uptake of metals, which showed a significant decrease compared to the control groups when the lower dosage of biochar was utilized. Full article

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

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16 pages, 2088 KiB

Open AccessArticle

Genetic Basis of Seedling Root Traits in Common Wheat (Triticum aestivum L.) Identified by Genome-Wide Linkage Mapping

by Xiaole Ma, Juncheng Wang, Hong Zhang, Lirong Yao, Erjing Si, Baochun Li, Yaxiong Meng and Huajun Wang

Plants 2025, 14(3), 490; https://doi.org/10.3390/plants14030490 - 6 Feb 2025

Abstract

Common wheat production is significantly influenced by abiotic stresses. Identifying the genetic loci for seedling root traits and developing the available molecular markers are crucial for breeding high yielding and stable varieties. In this study, five wheat seedling root traits, including root length [...] Read more.

Common wheat production is significantly influenced by abiotic stresses. Identifying the genetic loci for seedling root traits and developing the available molecular markers are crucial for breeding high yielding and stable varieties. In this study, five wheat seedling root traits, including root length (RL), root surface area (RA), root volume (RV), number of root tips (RT), and root dry weight (RW), were measured in the Wp-072/Wp-119 recombinant inbred line (RIL) population. Genotyping was conducted for the RIL population and their parents using the wheat 90K single-nucleotide polymorphism (SNP) chip. In total, three quantitative trait loci (QTLs) for RL (QRL.gau-1DS, QRL.gau-1DL and QRL.gau-4AL), two QTLs for RA (QRA.gau-1D and QRA.gau-2DL), one locus for RV (QRV.gau-6AS), two loci for RW (QRW.gau-2DL and QRW.gau-2AS), and two loci for RT (QRT.gau-3AS and QRT.gau-6DL) were identified, with each explaining 4.5–8.4% of the phenotypic variances, respectively. Among these, QRT.gau-3AS, QRL.gau-4AL, and QRV.gau-6AS overlapped with the previous reports, whereas the other seven QTLs were novel. The favorable alleles of QRL.gau-1DS, QRL.gau-1DL, QRL.gau-4AL, QRA.gau-1D, QRW.gau-2AS, QRV.gau-6AS, QRT.gau-3AS, and QRT.gau-6DL were contributed by Wp-072, whereas the other two loci originated from Wp-119. Additionally, five kompetitive allele-specific PCR (KASP) markers, KASP-RL-1DL for RL, KASP-RA-1D and KASP-RA-2DL for RA, KASP-RW-2AS and KASP-RW-2DL for RW, were developed and validated successfully in 149 wheat accessions. Furthermore, seven candidate genes mainly for plant hormones were selected and validated by quantitative real-time PCR (qRT-PCR). This study provides new loci, new candidate genes, available KASP markers, and varieties for optimizing wheat root system architecture. Full article

(This article belongs to the Special Issue Recent Advances in the Genetics, Genomics and Breeding of Cereal Crops)

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15 pages, 1003 KiB

Open AccessReview

Adaptable Alchemy: Exploring the Flexibility of Specialized Metabolites to Environmental Perturbations Through Post-Translational Modifications (PTMs)

by Luca Cimmino, Annalisa Staiti, Domenico Carputo, Teresa Docimo, Vincenzo D’Amelia and Riccardo Aversano

Plants 2025, 14(3), 489; https://doi.org/10.3390/plants14030489 - 6 Feb 2025

Abstract

Plants are subjected to various stresses during the growth process, including biotic stresses, as well as abiotic stresses such as temperature, drought, salt, and heavy metals. To cope with these biotic and abiotic adversities, plants have evolved complex regulatory mechanisms during their long-term [...] Read more.

Plants are subjected to various stresses during the growth process, including biotic stresses, as well as abiotic stresses such as temperature, drought, salt, and heavy metals. To cope with these biotic and abiotic adversities, plants have evolved complex regulatory mechanisms during their long-term environmental adaptations. In a suddenly changing environment, protein modifiers target other proteins to induce post-translational modification (PTM) in order to maintain cell homeostasis and protein biological activity in plants. PTMs modulate the activity of enzymes and transcription factors in their respective metabolic pathways, enabling plants to produce essential compounds for their survival under stress conditions. Examples of post-translational mechanisms include phosphorylation, ubiquitination, glycosylation, acetylation, protein–protein interactions, and targeted protein degradation. Furthermore, the role of histone modifications in regulating secondary metabolism deserves attention due to its potential impact on heritability and its contribution to stress tolerance. Understanding the epigenetic aspect of these modifications can provide valuable insights into the mechanisms underlying stress response. In this context, also examining PTMs that impact the biosynthesis of secondary metabolites is meaningful. Secondary metabolites encompass a wide range of compounds such as flavonoids, alkaloids, and terpenoids. These secondary metabolites play a crucial role in plant defense against herbivores, pathogens, and oxidative stress. In this context, it is imperative to understand the contribution of secondary metabolism to plant tolerance to abiotic stresses and how this understanding can be leveraged to improve long-term survival. While many studies have focused on the transcriptional regulation of these metabolites, there is a growing interest in understanding various changes in PTMs, such as acetylation, glycosylation, and phosphorylation, that are able to modulate plants’ response to environmental conditions. In conclusion, a comprehensive exploration of post-translational mechanisms in secondary metabolism can enhance our understanding of plant responses to abiotic stress. This knowledge holds promise for future applications in genetic improvement and breeding strategies aimed at increasing plant resilience to environmental challenges. Full article

(This article belongs to the Special Issue Protein Metabolism in Plants and Algae under Abiotic Stress)

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16 pages, 1133 KiB

Open AccessArticle

Foliar Application of Equisetum arvense Extract Enhances Growth, Alleviates Lipid Peroxidation and Reduces Proline Accumulation in Tomato Plants Under Salt Stress

by Messaouda Boukhari, Rocío Asencio-Vicedo, Mar Cerdán, Antonio Sánchez-Sánchez, Juana D. Jordá and Borja Ferrández-Gómez

Plants 2025, 14(3), 488; https://doi.org/10.3390/plants14030488 - 6 Feb 2025

Abstract

Salinity is a major abiotic stress that affects physiological and biochemical processes in plants, reducing the growth, yield, and quality of crops. This problem has been intensified with the reduction of the cultivated area. This study evaluated the response of hydroponically grown tomato [...] Read more.

Salinity is a major abiotic stress that affects physiological and biochemical processes in plants, reducing the growth, yield, and quality of crops. This problem has been intensified with the reduction of the cultivated area. This study evaluated the response of hydroponically grown tomato plants under salt stress to foliar applications of E. arvense extracts. Macro- and micronutrients, as well as silicon and phenolic compounds, were extracted using magnetic stirring and water reflux methods, the latter being the most effective. To evaluate the efficacy of E. arvense extracts, spraying was applied at two different doses: EQ-R-1 (23.6 mg·L⁻¹ Si and 0.5 mM phenolic compounds) and EQ-R-2 (5.9 mg·L⁻¹ Si and 0.125 mM phenolic compounds). Foliar application of both extracts alleviated salinity effects by reducing sodium uptake. E. arvense extracts mitigated oxidative stress by a decrease in electrolyte leakage by 29% and malondialdehyde and H₂O₂ concentrations by 69% and 39%, respectively, for the extract with the lowest dose. In addition, EQ-R-2 was also more effective by reducing 51.5% proline accumulation. These findings showed the potential use of E. arvense extracts as biostimulants to enhance plant tolerance to salinity providing new perspectives in agricultural systems. Full article

(This article belongs to the Special Issue Abiotic Stress Responses in Plants)

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14 pages, 1521 KiB

Open AccessReview

Molecular Mechanisms of Alfalfa Response to Abiotic Stresses

by Wenxin Peng, Wenqi Cai, Jieyi Pan, Xinru Su and Liru Dou

Plants 2025, 14(3), 487; https://doi.org/10.3390/plants14030487 - 6 Feb 2025

Abstract

Alfalfa (Medicago sativa L.), a high-quality perennial legume forage, is pivotal in global animal husbandry and ecological systems. However, its growth and production are threatened by various abiotic stresses, including drought, salinity, low temperatures, and heavy metal toxicity. This review summarizes recent [...] Read more.

Alfalfa (Medicago sativa L.), a high-quality perennial legume forage, is pivotal in global animal husbandry and ecological systems. However, its growth and production are threatened by various abiotic stresses, including drought, salinity, low temperatures, and heavy metal toxicity. This review summarizes recent research on the molecular mechanisms underlying alfalfa’s responses to these environmental adversities. It provides a theoretical foundation for enhancing the stress resistance of alfalfa, offering a valuable reference for breeding high-quality, stress-resistant alfalfa varieties. Full article

(This article belongs to the Special Issue Advances in Forage Stress Biology: Mechanisms and Adaptation Strategies)

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16 pages, 4120 KiB

Open AccessArticle

The WRKY28-BRC1 Transcription Factor Module Controls Shoot Branching in Brassica napus

by Ka Zhang, Jinfang Zhang, Cheng Cui, Liang Chai, Benchuan Zheng, Liangcai Jiang and Haojie Li

Plants 2025, 14(3), 486; https://doi.org/10.3390/plants14030486 - 6 Feb 2025

Abstract

The trade-off between growth and defense is common in plants. We previously demonstrated that BnaA03.WRKY28 weakened resistance strength but promoted shoot branching in Brassica napus (rapeseed). However, the molecular mechanism by which WRKY28 promotes branching formation is still obscure. In this study, we [...] Read more.

The trade-off between growth and defense is common in plants. We previously demonstrated that BnaA03.WRKY28 weakened resistance strength but promoted shoot branching in Brassica napus (rapeseed). However, the molecular mechanism by which WRKY28 promotes branching formation is still obscure. In this study, we found that BnaA01.BRC1, BnaC01.BRC1, and BnaC03.BRC1 are mainly expressed in the leaf axils and contained W-box cis-acting elements in the promoter regions. BnaA03.WRKY28 directly bound to the promoter regions of these three copies and inhibited their expression. The brc1 mutants, the BnaA01.BRC1, BnaC01.BRC1 BnaA03.BRC1 and BnaC03.BRC1 were simultaneously knocked out, mediated by CRISPR/Cas9, and exhibited excessive branching. The expression level of the ABA biosynthesis encoding gene NCED3 was significantly reduced in the mutant compared to that in the WT. Instead, the expression level of the ABA catabolism encoding gene CYP707A3 was significantly higher than that in WT. These results suggest that the excessive branching of the brc1 mutant may be caused by the release of ABA-mediated bud dormancy. This study provides direct evidence for the potential mechanism of the WRKY28-BRC1 transcription factor module contributing to shoot branching in rapeseed. Full article

(This article belongs to the Special Issue Advancement in Gene Expression Regulation in Plants: Coordinating Growth, Development, and Stress Resilience)

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15 pages, 2922 KiB

Open AccessArticle

Combined Use of Biostimulation and Deficit Irrigation Improved the Fruit Quality in Table Grape

by Susana Zapata-García, Pablo Berríos, Abdelmalek Temnani, Pedro J. Espinosa, Claudia Monllor and Alejandro Pérez-Pastor

Plants 2025, 14(3), 485; https://doi.org/10.3390/plants14030485 - 6 Feb 2025

Abstract

This study aims to determine the effects of four different biostimulation treatments—composed of microorganisms, seaweed, and plant extracts—on the yield and quality traits of table grapes. Those treatments are compared with an untreated control treatment and tested under two different irrigation schedules: (i) [...] Read more.

This study aims to determine the effects of four different biostimulation treatments—composed of microorganisms, seaweed, and plant extracts—on the yield and quality traits of table grapes. Those treatments are compared with an untreated control treatment and tested under two different irrigation schedules: (i) Farmer Irrigation (FI), according to farmer criteria, and (ii) a deficit irrigation program, Precision Irrigation (PI), irrigated as FI, except during the post-veraison period when a 10% soil water depletion was allowed to mitigate the lixiviation. The water inputs in the treatments under PI were reduced by 30% without affecting the total yield but still promoting harvest precocity—an effect that was enhanced by the biostimulated treatments. This deficit irrigation program also stimulated berry growth and a higher maturity index. The different biostimulation treatments led to an improvement in the physical and chemical quality traits of the grapes; under FI, they showed a bigger size and a greater weight than the non-biostimulated treatment, while under PI, they showed a higher soluble sugar concentration and maturity index. Regardless of the irrigation program, the commercial berry color proportion was increased in all the biostimulated treatments, reducing the percentage of green berries. The combined use of biostimulation and PI can promote more efficient and sustainable farming practices, promoting fruit yield precocity and quality of the grapevine in drought-prone regions. Full article

(This article belongs to the Special Issue Grapevine Response to Abiotic Stress)

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18 pages, 1149 KiB

Open AccessReview

A Guide to Metabolic Network Modeling for Plant Biology

by Xiaolan Rao and Wei Liu

Plants 2025, 14(3), 484; https://doi.org/10.3390/plants14030484 - 6 Feb 2025

Abstract

Plants produce a diverse array of compounds that play crucial roles in growth, in development, and in responses to abiotic and biotic stresses. Understanding the fluxes within metabolic pathways is essential for guiding strategies aimed at directing metabolism for crop improvement and the [...] Read more.

Plants produce a diverse array of compounds that play crucial roles in growth, in development, and in responses to abiotic and biotic stresses. Understanding the fluxes within metabolic pathways is essential for guiding strategies aimed at directing metabolism for crop improvement and the plant natural product industry. Over the past decade, metabolic network modeling has emerged as a predominant tool for the integration, quantification, and prediction of the spatial and temporal distribution of metabolic flows. In this review, we present the primary methods for constructing mathematical models of metabolic systems and highlight recent achievements in plant metabolism using metabolic modeling. Furthermore, we discuss current challenges in applying network flux analysis in plants and explore the potential use of machine learning technologies in plant metabolic modeling. The practical application of mathematical modeling is expected to provide significant insights into the structure and regulation of plant metabolic networks. Full article

(This article belongs to the Special Issue Deciphering Plant Molecular Data Using Computational Methods)

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24 pages, 6429 KiB

Open AccessArticle

Infiltration-RNAseq Reveals Enhanced Defense Responses in Nicothiana benthamiana Leaves Overexpressing the Banana Gene MaWRKY45

by Sergio García-Laynes, Carlos Ligne Calderón-Vázquez, Carlos Puch-Hau, Virginia Aurora Herrera-Valencia and Santy Peraza-Echeverria

Plants 2025, 14(3), 483; https://doi.org/10.3390/plants14030483 - 6 Feb 2025

Abstract

The banana gene MaWRKY45 gene encodes a WRKY transcription factor (TF) that is closely related to OsWRKY45, which is a master regulator of defense responses in rice. MaWRKY45 is a transcription factor with proven transactivation activity and nuclear localization. Its expression is [...] Read more.

The banana gene MaWRKY45 gene encodes a WRKY transcription factor (TF) that is closely related to OsWRKY45, which is a master regulator of defense responses in rice. MaWRKY45 is a transcription factor with proven transactivation activity and nuclear localization. Its expression is upregulated by the defense phytohormones salicylic acid (SA) and jasmonic acid (JA). Despite these findings, its transcriptome-wide impact during overexpression remains unexplored. Accordingly, the present study employed the Infiltration-RNAseq method to identify differentially expressed genes (DEGs) resulting from the overexpression of MaWRKY45 in the leaves of the model plant Nicotiana benthamiana. A total of 2473 DEGs were identified in N. benthamiana leaves overexpressing the banana gene MaWRKY45. Of these, 1092 were up-regulated and 1381 were down-regulated. Among the genes that were found to be up-regulated, those encoding proteins that are involved in plant immunity were identified. These included disease resistance receptors, proteins that are involved in cell wall reinforcement, proteins that possess antimicrobial and insecticidal activities, and defense-related TFs. It was thus concluded that the function of the banana gene MaWRKY45 is associated with the plant immune system, and that its overexpression can lead to enhance defense responses. Full article

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

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3 pages, 167 KiB

Open AccessEditorial

QTL Mapping of Seed Quality Traits in Crops

by Moulay Abdelmajid Kassem

Plants 2025, 14(3), 482; https://doi.org/10.3390/plants14030482 - 6 Feb 2025

Abstract

The ability to map quantitative trait loci (QTLs) has revolutionized plant genetics, providing an essential toolkit for dissecting the genetic basis of agronomic traits [...] Full article

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

20 pages, 7023 KiB

Open AccessArticle

Genetic Diversity Analysis and GWAS of Plant Height and Ear Height in Maize Inbred Lines from South-East China

by Changjin Wang, Wangfei He, Keyu Li, Yulin Yu, Xueshi Zhang, Shuo Yang, Yongfu Wang, Li Yu, Weidong Huang, Haibing Yu, Lei Chen and Xinxin Cheng

Plants 2025, 14(3), 481; https://doi.org/10.3390/plants14030481 - 6 Feb 2025

Abstract

Maize is a critical crop for food, feed, and bioenergy worldwide. This study characterized the genetic diversity and population structure of 212 important inbred lines collected from the Southeast China breeding program using the Maize6H-60K single nucleotide polymorphism (SNP) array. To investigate the [...] Read more.

Maize is a critical crop for food, feed, and bioenergy worldwide. This study characterized the genetic diversity and population structure of 212 important inbred lines collected from the Southeast China breeding program using the Maize6H-60K single nucleotide polymorphism (SNP) array. To investigate the genetic architecture of plant height (PH) and ear height (EH), genome-wide association analysis (GWAS) was performed on this population in 2021 and 2022. Cluster analysis and population genetic structure analysis grouped the 212 maize inbred lines into 10 distinct categories. GWAS identified significant associations for PH, EH, and the EH/PH ratio. A total of 40 significant SNP (p < 8.55359 × 10⁻⁷) were detected, including nine associated with PH, with phenotypic variation explained (PVE) ranging from 3.42% to 25.92%. Additionally, 16 SNP were linked to EH, with PVE ranging from 2.49% to 38.49%, and 15 SNP were associated with the EH/PH ratio, showing PVE between 3.43% and 16.83%. Five stable SNP, identified across two or more environments, were further analyzed. Three of these SNP loci are reported for the first time in this study: two loci associated with the PH, AX-108020973, and AX-108022922, as well as one new locus, AX-108096437, which was significantly associated with the EH/PH ratio. Additionally, two other significant SNP (AX-247241325 and AX-108097244) were located within a 2 Mb range of previously identified QTL and/or related SNP. Within the 200 kb confidence intervals of these five stable SNP loci, 76 functionally annotated genes were identified. Further functional analysis indicated that 14 of these genes may play a role in regulating plant morphology, which is primarily involved in hormone synthesis, microtubule development, root growth, and cell division regulation. For instance, the homologous genes GRMZM2G375249 and GRMZM2G076029 in maize correspond to OsPEX1 in rice, a protein similar to extension proteins that are implicated in lignin biosynthesis, plant growth promotion, and the negative regulation of root growth through gibberellin-mediated pathways. The candidate gene corresponding to AX-108097244 is GRMZM2G464754; previous studies have reported its involvement in regulating EH in maize. These findings enhance the understanding of QTL associated with maize plant-type traits and provide a foundation for cloning PH, EH-related genes. Therefore, the results also support the development of functional markers for target genes and the breeding of improved maize varieties. Full article

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

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14 pages, 5415 KiB

Open AccessArticle

Tetraploidization Altered Phenotypic Traits and Metabolite Profile of Java Ginseng (Talinum paniculatum (Jacq.) Gaertn.)

by Yingying Liu, Xiao Huang, Xinsheng Gao, Xiaofei Zhang, Huasun Huang, Weiguo Li and Yuanyuan Zhang

Plants 2025, 14(3), 480; https://doi.org/10.3390/plants14030480 - 6 Feb 2025

Abstract

Polyploidization is a beneficial technique for enhancing the biomass of and secondary metabolite concentrations in plants. Java ginseng (Talinum paniculatum (Jacq.) Gaertn.) can be used as an alternative source of nutrition and has both ornamental and medicinal value. To improve the biomass [...] Read more.

Polyploidization is a beneficial technique for enhancing the biomass of and secondary metabolite concentrations in plants. Java ginseng (Talinum paniculatum (Jacq.) Gaertn.) can be used as an alternative source of nutrition and has both ornamental and medicinal value. To improve the biomass and content of medicinal ingredients, this study established an in vitro system that was used to induce polyploidy of java ginseng. Tetraploids were successfully produced by exposing the axillary buds to colchicine. The most favorable medium for inducing polyploidy was Murashige and Skoog medium devoid of hormonal substances, while immersing stem segments in a solution of 1–3 mg/mL colchicine for 48 h could achieve tetraploidy induction with a maximum rate of 18.03%. Tetraploids were distinguished from diploids by flow cytometry, with the tetraploids exhibiting darker and thicker leaves, bigger fruit and pollen, and larger stomata but lower stomatal density, while the aboveground biomass yield was reduced significantly compared with that of the diploids. Tetraploidization also altered the metabolite profile, with 22 metabolite concentrations being significantly increased (p < 0.05) and 74 metabolite concentrations being significantly decreased (p < 0.05) in the leaves of the tetraploids. The autotetraploid produced in this study could provide novel insights into artificial polyploid breeding and could be utilized as a germplasm to generate new polyploids. Full article

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

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11 pages, 1143 KiB

Open AccessReview

Root Exudates in Soilless Culture Conditions

by Brechtje de Haas, Emmy Dhooghe and Danny Geelen

Plants 2025, 14(3), 479; https://doi.org/10.3390/plants14030479 - 6 Feb 2025

Abstract

Root metabolite secretion plays a critical role in increasing nutrient acquisition, allelopathy, and shaping the root-associated microbiome. While much research has explored the ecological functions of root exudates, their relevance to horticultural practices, particularly soilless cultivation, remains underexplored. Steering root exudation could help [...] Read more.

Root metabolite secretion plays a critical role in increasing nutrient acquisition, allelopathy, and shaping the root-associated microbiome. While much research has explored the ecological functions of root exudates, their relevance to horticultural practices, particularly soilless cultivation, remains underexplored. Steering root exudation could help growers enhance the effectiveness of plant growth-promoting bacteria. This review summarizes current knowledge on root exudation in soilless systems, examining its process and discussing environmental influences in the context of soilless cultivation. Plants in soilless systems exhibit higher total carbon exudation rates compared to those in natural soils, with exudation profiles varying across systems and species. Root exudation decreases with plant age, with most environmental adaptations occurring during early growth stages. Several environmental factors unique to soilless systems affect root exudation. For instance, nutrient availability has a major impact on root exudation. Light intensity reduces exudation rates, and light quality influences exudation profiles in a species- and environment-dependent manner. Elevated CO₂ and temperature increase exudation. Factors related to the hydroponic nutrient solution and growing media composition remain insufficiently understood, necessitating further research. Full article

(This article belongs to the Special Issue Effect of Growing Media on Plant Performance)

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20 pages, 6189 KiB

Open AccessArticle

Comparative Transcriptomic Analyses of Anthocyanin Biosynthesis Genes in Eggplant Under Low Temperature and Weak Light

by Baoying Shen, Hongqi Wu, Xinxin Xie, Bo Zhao, Peiqiang Chen, Deyong Ao, Heli Pan and Biying Lin

Plants 2025, 14(3), 478; https://doi.org/10.3390/plants14030478 - 6 Feb 2025

Abstract

Low temperature, weak light, and the combination of low temperature and weak light can have an impact on the growth, development, and quality of eggplants. The color of the eggplant peel is affected by the anthocyanin content. To better understand the influence of [...] Read more.

Low temperature, weak light, and the combination of low temperature and weak light can have an impact on the growth, development, and quality of eggplants. The color of the eggplant peel is affected by the anthocyanin content. To better understand the influence of low temperature, weak light, and the combination of low temperature and weak light on the regulation of anthocyanins in the eggplant peel, four treatments were carried out on the eggplants, respectively: low temperature (18/13 °C, 250 μmol/(m²·s)), weak light intensity (WL, 25/20 °C, 120 μmol/(m²·s)), low temperature combined with weak light intensity (LW, 18/13 °C, 120 μmol/(m²·s)), and the control (CK, 25/20 °C, 250 μmol/(m²·s)). The effects of low temperature and weak light on the anthocyanin content in various parts of the eggplant were analyzed, and transcriptome analysis was performed on the eggplant peel under the treatments of low temperature, weak light, and the combination of low temperature and weak light using RNA sequencing. The anthocyanin content in eggplants increased under low temperature and the combination of low temperature and weak light treatments, while it decreased under weak light. KEGG analysis showed that three pathways, namely phenylpropanoid biosynthesis, flavonoid biosynthesis, and anthocyanin biosynthesis, were involved in the anthocyanin biosynthesis of eggplants. Pearson correlation coefficients indicated that the anthocyanin content in the eggplant peel under low temperature and the combination of low-temperature and weak-light treatments was significantly correlated with SmPAL, Sm4CL, SmCYP73A100, SmCHS, SmCHI, F3H, DFR, ANS, and 3GT, and also significantly correlated with MYB, bHLH, and AP2/ERF. Under low-temperature and the combination of low-temperature and weak-light stress, the anthocyanin content increased due to the significant down-regulation of 3GT. Full article

(This article belongs to the Special Issue Horticultural Plant Cultivation and Fruit Quality Enhancement)

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14 pages, 3206 KiB

Open AccessArticle

A Gemini Virus-Derived Autonomously Replicating System for HDR-Mediated Genome Editing of the EPSP Synthase Gene in Indica Rice

by Bhabesh Borphukan, Muslima Khatun, Dhirendra Fartyal, Donald James and Malireddy K. Reddy

Plants 2025, 14(3), 477; https://doi.org/10.3390/plants14030477 - 6 Feb 2025

Abstract

CRISPR/Cas9-mediated homology-directed repair (HDR) is a powerful tool for precise genome editing in plants, but its efficiency remains low, particularly for targeted amino acid substitutions or gene knock-ins. Successful HDR requires the simultaneous presence of Cas9, guide RNA, and a repair template (RT) [...] Read more.

CRISPR/Cas9-mediated homology-directed repair (HDR) is a powerful tool for precise genome editing in plants, but its efficiency remains low, particularly for targeted amino acid substitutions or gene knock-ins. Successful HDR requires the simultaneous presence of Cas9, guide RNA, and a repair template (RT) in the same cell nucleus. Among these, the timely availability of the RT at the double-strand break (DSB) site is a critical bottleneck. To address this, we developed a sequential transformation strategy incorporating a deconstructed wheat dwarf virus (dWDV)-based autonomously replicating delivery system, effectively simplifying the process into a two-component system. Using this approach, we successfully achieved the targeted editing of the OsEPSPS gene in rice with a 10 percent HDR efficiency, generating three lines (TIPS1, TIPS2, and TIPS3) with amino acid substitutions (T172I and P177S) in the native EPSPS protein. The modifications were confirmed through Sanger sequencing and restriction digestion assays, and the edited lines showed no yield penalties compared to wild-type plants. This study demonstrates the utility of viral replicons in delivering gene-editing tools for precise genome modification, offering a promising approach for efficient HDR in crop improvement programs. Full article

(This article belongs to the Special Issue Plant Biotechnological Approaches Towards Crop Improvement)

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26 pages, 4979 KiB

Open AccessArticle

The Role of Reproductive Modes in Shaping Genetic Diversity in Polyploids: A Comparative Study of Selfing, Outcrossing, and Apomictic Paspalum Species

by A. Verena Reutemann, Mara Schedler, Diego H. Hojsgaard, Elsa A. Brugnoli, Alex L. Zilli, Carlos A. Acuña, Ana I. Honfi and Eric J. Martínez

Plants 2025, 14(3), 476; https://doi.org/10.3390/plants14030476 - 6 Feb 2025

Abstract

Exploring the genetic diversity and reproductive strategies of Paspalum species is essential for advancing forage grass improvement. We compared morpho-phenological, molecular, and genotypic variation in five tetraploid Paspalum species with contrasting mating systems and reproductive modes. Contrary to previous findings, selfing (Paspalum [...] Read more.

Exploring the genetic diversity and reproductive strategies of Paspalum species is essential for advancing forage grass improvement. We compared morpho-phenological, molecular, and genotypic variation in five tetraploid Paspalum species with contrasting mating systems and reproductive modes. Contrary to previous findings, selfing (Paspalum regnellii and P. urvillei) and outcrossing (P. durifolium and P. ionanthum) species exhibited similar phenotypic diversity patterns, with low intrapopulation variability and no morphological differentiation among populations. The apomictic species (P. intermedium) exhibited low intrapopulation phenotypic variation but high population differentiation, indicative of genetic drift and local adaptation. Outcrossing species showed greater intrapopulation genotypic variation than selfing species, which displayed a high population structure due to restricted pollen migration. The apomictic species exhibited the lowest intrapopulation molecular diversity, forming uniclonal populations with high interpopulation differentiation, highlighting the fixation of distinct gene pools via apomixis. This is the first report about genetic diversity in populations of sexual allopolyploid species of Paspalum. Population structure in these allotetraploid Paspalum species is primarily shaped by how reproductive modes, mating systems, and geographic distribution influence gene flow via pollen and seeds. Our findings contribute significantly to the conservation and genetic improvement of forage grasses, particularly for developing cultivars with enhanced adaptability and productivity. Full article

(This article belongs to the Special Issue Genetic Resources and Improvement of Forage Plants)

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13 pages, 2823 KiB

Open AccessArticle

Biocontrol of Crown Gall Disease of Cherry Trees by Bacillus velezensis

by Yongfeng Li, Zhaoliang Gao, Weiliang Kong, Yueting Xiao, Mark Owusu Adjei and Ben Fan

Plants 2025, 14(3), 475; https://doi.org/10.3390/plants14030475 - 5 Feb 2025

Abstract

Crown gall disease (CGD), caused by Agrobacterium tumefaciens, is a common plant disease that leads to significant economic losses. Biological control is a sustainable and scalable method for managing CGD. In this study, we isolated three Bacillus strains from the rhizosphere soil [...] Read more.

Crown gall disease (CGD), caused by Agrobacterium tumefaciens, is a common plant disease that leads to significant economic losses. Biological control is a sustainable and scalable method for managing CGD. In this study, we isolated three Bacillus strains from the rhizosphere soil of healthy cherry trees and investigated their biocontrol activities and the underlying mechanisms against CGD of cherry trees. The results demonstrate that the three Bacillus strains can effectively inhibit the growth of the pathogenic A. tumefaciens strain XYT58 in vitro under different culture conditions. The pot experiments showed that the three strains could prevent CGD in cherry seedlings. Using PCR amplification, we identified the genes responsible for the synthesis of difficidin, macrolactin, and bacilysin in the three strains. In addition, inoculation with strains WY66 and WY519 significantly enhanced the expression of JA, ET, and SA pathway-related genes in cherry plants. The presence of antibiotic synthesis-related genes in the Bacillus strains and the trigger of plant ISR may explain their ability to control CGD in cherry trees. The findings of this study provide a theoretical basis for the application and development of plant growth-promoting rhizobacteria Bacillus strains in the control of CGD. Full article

(This article belongs to the Special Issue Biological Control of Agricultural and Forestry Plant Diseases)

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13 pages, 2232 KiB

Open AccessArticle

Effects of Water and Wind Stress on Phytochemical Diversity, Cannabinoid Composition, and Arthropod Diversity in Hemp

by Ericka R. Kay, Casey S. Philbin, Lora A. Richards, Matthew L. Forister, Christopher Jeffrey and Lee A. Dyer

Plants 2025, 14(3), 474; https://doi.org/10.3390/plants14030474 - 5 Feb 2025

Abstract

Phytochemical diversity is increasingly appreciated as an important attribute of plants that affects their interactions with other organisms and can have substantial effects on arthropod communities, but this axis of diversity is less studied for agricultural plants. For both managed and natural systems, [...] Read more.

Phytochemical diversity is increasingly appreciated as an important attribute of plants that affects their interactions with other organisms and can have substantial effects on arthropod communities, but this axis of diversity is less studied for agricultural plants. For both managed and natural systems, understanding how extreme weather events, such as droughts, floods, and extreme wind, affect phytochemical diversity is an important part of predicting responses of plant–arthropod interactions to climate change. In an outdoor field experiment with two distinct varieties of hemp (Cannabis sativa L., Cannabaceae), we investigated the effects of simulated water stress from reduced water availability and flooding, along with an unplanned extreme wind event on phytochemical diversity and cannabinoid profiles. We also examined how changes in chemistry affected the diversity of the associated arthropods. Our results indicate that both genetic variety and environmental stress have substantial effects on variation in hemp phytochemical diversity and cannabinoid composition, and these effects cascaded to alter the arthropod communities on flowers. The largest differences in chemistry were found between different varieties, which accounted for over 10% of the variation in phytochemical diversity. Stress from wind and floods reduced the phytochemical diversity of flowers, wind had negative effects on cannabidiol (CBD) concentrations, and both water deficit and flooding caused subtle shifts in cannabinoid composition. The subsequent cascading effects of chemistry depended on how it was characterized, with increases in CBD causing higher arthropod richness, while increased phytochemical diversity reduced arthropod diversity. These results provide insights into the potential effects of extreme weather on hemp chemistry, as well as the consequences of hemp phytochemical diversity on colonizing arthropods. Full article

(This article belongs to the Special Issue Phytochemical Diversity and Interactions with Herbivores)

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27 pages, 5727 KiB

Open AccessArticle

Genome-Wide Identification, Characterization, and Expression Analysis of BES1 Family Genes in ‘Tieguanyin’ Tea Under Abiotic Stress

by Yanzi Zhang, Yanlin Zhang, Zhicheng Yang, Qingyan Li, Weixiang Chen, Xinyan Wen, Hao Chen and Shijiang Cao

Plants 2025, 14(3), 473; https://doi.org/10.3390/plants14030473 - 5 Feb 2025

Abstract

The BRI1-EMS-SUPPRESSOR 1 (BES1) family comprises plant-specific transcription factors, which are distinguished by atypical bHLH domains. Over the past two decades, genetic and biochemical studies have established that members of the BRI1-EMS-SUPPRESSOR 1 (BES1) family are crucial for regulating [...] Read more.

The BRI1-EMS-SUPPRESSOR 1 (BES1) family comprises plant-specific transcription factors, which are distinguished by atypical bHLH domains. Over the past two decades, genetic and biochemical studies have established that members of the BRI1-EMS-SUPPRESSOR 1 (BES1) family are crucial for regulating the expression of genes involved in brassinosteroid (BR) response in rapeseed. Due to the significance of the BES1 gene family, extensive research has been conducted to investigate its functional properties. This study presents a comprehensive identification and computational analysis of BES1 genes in ‘Tieguanyin’ (TGY) tea (Camellia sinensis). A total of 10 BES1 genes were initially identified in the TGY genome. Through phylogenetic tree analysis, this study uniquely revealed that CsBES1.2 and CsBES1.5 cluster with SlBES1.8 from Solanum lycopersicum, indicating their critical roles in fruit growth and development. Synteny analysis identified 20 syntenic genes, suggesting the conservation of their evolutionary functions. Analysis of the promoter regions revealed two types of light-responsive cis-elements, with CsBES1.4 exhibiting the highest number of light-related cis-elements (13), followed by CsBES1.9 and CsBES1.10. Additional validation via qRT-PCR experiments showed that CsBES1.9 and CsBES1.10 were significantly upregulated under light exposure, with CsBES1.10 reaching approximately six times the expression level of the control after 4 h. These results suggest that CsBES1.9 and CsBES1.4 could play crucial roles in responding to abiotic stress. This study offers novel insights into the functional roles of the BES1 gene family in ‘Tieguanyin’ tea and establishes a significant foundation for future research, especially in exploring the roles of these genes in response to abiotic stresses, such as light exposure. Full article

(This article belongs to the Special Issue Responses of Crops to Abiotic Stress)

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15 pages, 8553 KiB

Open AccessArticle

Highly Efficient Homozygous CRISPR/Cas9 Gene Editing Based on Single-Cell-Originated Somatic Embryogenesis in Liriodendron tulipifera

by Cairong Li, Pengshuo Jiang, Jiaji Zhang, Dingjie Yang, Lu Lu, Zhaodong Hao, Yingxuan Ma, Jisen Shi and Jinhui Chen

Plants 2025, 14(3), 472; https://doi.org/10.3390/plants14030472 - 5 Feb 2025

Abstract

The clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is the most widely used gene-editing tool to date. However, its application in the genetic improvement of forestry trees has been largely limited. Here, we first established a highly efficient multi-target editing [...] Read more.

The clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is the most widely used gene-editing tool to date. However, its application in the genetic improvement of forestry trees has been largely limited. Here, we first established a highly efficient multi-target editing system in the magnoliid woody plant Liriodendron tulipifera. Using phytoene desaturase gene (PDS) as an example, we systematically compared CRISPR/Cas9 and CRSPR/Cpf1 expression systems for loss-of-function analysis and conducted genetic transformations using transient and stable transformation. Ultimately, our findings indicated that the CRISPR/Cas9 system, when applied to transformation based on single-cell-originated somatic embryogenesis, yielded the highest gene-editing efficiency, with mutation rates of nearly 100%. Furthermore, we obtained a total of 137 regeneration plantlets via somatic embryogenesis, of which 82.48% exhibited an albino phenotype. The Illumina sequencing results of albino seedlings and the callus tissue obtained from dedifferentiation of mutant plants revealed that the mutation at the T1 target site was homozygous. These results indicate that CRISPR/Cas9-based multiplex genome-editing technology can not only accelerate the identification of gene function but also be incorporated into the genetic improvement and breeding of tulip trees, supporting the scale propagation of genome-edited plantlets via somatic embryogenesis. Full article

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

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13 pages, 2233 KiB

Open AccessArticle

Interpopulational Variation in Cyclotide Production in Heavy-Metal-Treated Pseudometallophyte (Viola tricolor L.)

by Rebecca Miszczak, Blazej Slazak, Klaudia Sychta, Ulf Göransson, Anna Nilsson and Aneta Słomka

Plants 2025, 14(3), 471; https://doi.org/10.3390/plants14030471 - 5 Feb 2025

Abstract

It remains an open question whether violets use universal mechanisms, such as the production of metallothioneins, phytochelatins, and organic acids and/or rely on specific mechanisms like the production of antimicrobial cyclic peptides (cyclotides) for heavy metal tolerance. To contribute to the understanding of [...] Read more.

It remains an open question whether violets use universal mechanisms, such as the production of metallothioneins, phytochelatins, and organic acids and/or rely on specific mechanisms like the production of antimicrobial cyclic peptides (cyclotides) for heavy metal tolerance. To contribute to the understanding of the role of cyclotides, we used seed-derived plants from metallicolous (M) and non-metallicolous (NM) populations of Viola tricolor, a pseudometallophyte tolerant to Zn and Pb. Eight- to ten-week-old plants were treated with 1000 μM of Zn or Pb for 3 or 7 days and subsequently measured for cyclotides and heavy metal content using MALDI-MS and Atomic Absorption Spectrometry (AAS), respectively. Individuals from the M population accumulated a similar amount of Zn but occasionally more Pb in comparison with the NM population. Of the 18 different cyclotides included in the analysis, some showed statistically significant changes under the heavy metal treatment. In general, a decrease was observed in the M population, whereas an increase was observed in the NM population (except for the 3-day treatment with Zn). The day of treatment and dose of metal and their interaction played a crucial role in the explained variance for cyclotides produced by the M individuals but not for the NM plants. This unravels the importance of this antimicrobial compound in heavy metal tolerance and indicates that, in V. tricolor, cyclotides are involved in heavy metal tolerance, but specimens from two populations have developed different strategies and tolerance mechanisms involving cyclotides to mitigate heavy metal stress. Full article

(This article belongs to the Special Issue Heavy Metal Tolerance in Plants and Algae—2nd Edition)

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24 pages, 2898 KiB

Open AccessReview

Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology

by Abel Lucido, Oriol Basallo, Alberto Marin-Sanguino, Abderrahmane Eleiwa, Emilce Soledad Martinez, Ester Vilaprinyo, Albert Sorribas and Rui Alves

Plants 2025, 14(3), 470; https://doi.org/10.3390/plants14030470 - 5 Feb 2025

Abstract

Global food insecurity and environmental degradation highlight the urgent need for more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology offers the potential for enhanced crop traits, it also entails risks [...] Read more.

Global food insecurity and environmental degradation highlight the urgent need for more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology offers the potential for enhanced crop traits, it also entails risks of extensive environmental damage. This review highlights the complexities and risks associated with plant synthetic biology, while presenting the potential of multiscale mathematical modeling to assess and mitigate those risks effectively. Despite its potential, applying multiscale mathematical models in plants remains underutilized. Here, we advocate for integrating technological advancements in agricultural data analysis to develop a comprehensive understanding of crops across biological scales. By reviewing common modeling approaches and methodologies applicable to plants, the paper establishes a foundation for creating and utilizing integrated multiscale mathematical models. Through modeling techniques such as parameter estimation, bifurcation analysis, and sensitivity analysis, researchers can identify mutational targets and anticipate pleiotropic effects, thereby enhancing the safety of genetically engineered species. To demonstrate the potential of this approach, ongoing efforts are highlighted to develop an integrated multiscale mathematical model for maize (Zea mays L.), engineered through synthetic biology to enhance resilience against Striga (Striga spp.) and drought. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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51 pages, 948 KiB

Open AccessReview

Pharmacological Significance, Medicinal Use, and Toxicity of Extracted and Isolated Compounds from Euphorbia Species Found in Southern Africa: A Review

by Ipeleng Kopano Rosinah Kgosiemang, Relebohile Lefojane, Ayodeji Mathias Adegoke, Oludare Ogunyemi, Samson Sitheni Mashele and Mamello Patience Sekhoacha

Plants 2025, 14(3), 469; https://doi.org/10.3390/plants14030469 - 5 Feb 2025

Abstract

This study documents the Euphorbiaceae family of plants in Southern Africa, with a focus on their traditional medicinal applications, pharmacological properties, toxicity, and active secondary metabolites. A review of the literature from scientific journals, books, dissertations, and conference papers spanning from 1962 to [...] Read more.

This study documents the Euphorbiaceae family of plants in Southern Africa, with a focus on their traditional medicinal applications, pharmacological properties, toxicity, and active secondary metabolites. A review of the literature from scientific journals, books, dissertations, and conference papers spanning from 1962 to 2023 was conducted for 15 Euphorbia species. Recent findings indicate that specific compounds found in Euphorbia plants exhibit significant biological and pharmacological properties. However, the white sticky latex sap they contain is highly toxic, although it may also have medicinal applications. Phytochemical analyses have demonstrated that these plants exhibit beneficial effects, including antibacterial, antioxidant, antiproliferative, anticancer, anti-inflammatory, antiviral, antifungal, and anti-HIV activities. Key phytochemicals such as euphol, cycloartenol, tirucallol, and triterpenoids contribute to their therapeutic efficacy, along with various proteins like lectin and lysozyme. Despite some Euphorbiaceae species undergoing screening for medicinal compounds, many remain insufficiently examined, highlighting a critical gap in the research literature. Given their historical usage, further investigations are essential to evaluate the medicinal significance of Euphorbia species through detailed studies of isolated compounds and their pharmacokinetics and pharmacodynamics. This research will serve as a valuable resource for future inquiries into the benefits of lesser-studied Euphorbia species. Full article

(This article belongs to the Special Issue Phytochemical Analysis, Antioxidant, Antimicrobial, and Cytotoxic Activity of Plant Extracts)

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20 pages, 5647 KiB

Open AccessArticle

VM-YOLO: YOLO with VMamba for Strawberry Flowers Detection

by Yujin Wang, Xueying Lin, Zhaowei Xiang and Wen-Hao Su

Plants 2025, 14(3), 468; https://doi.org/10.3390/plants14030468 - 5 Feb 2025

Abstract

Computer vision technology is widely used in smart agriculture, primarily because of its non-invasive nature, which avoids causing damage to delicate crops. Nevertheless, the deployment of computer vision algorithms on agricultural machinery with limited computing resources represents a significant challenge. Algorithm optimization with [...] Read more.

Computer vision technology is widely used in smart agriculture, primarily because of its non-invasive nature, which avoids causing damage to delicate crops. Nevertheless, the deployment of computer vision algorithms on agricultural machinery with limited computing resources represents a significant challenge. Algorithm optimization with the aim of achieving an equilibrium between accuracy and computational power represents a pivotal research topic and is the core focus of our work. In this paper, we put forward a lightweight hybrid network, named VM-YOLO, for the purpose of detecting strawberry flowers. Firstly, a multi-branch architecture-based fast convolutional sampling module, designated as Light C2f, is proposed to replace the C2f module in the backbone of YOLOv8, in order to enhance the network’s capacity to perceive multi-scale features. Secondly, a state space model-based lightweight neck with a global sensitivity field, designated as VMambaNeck, is proposed to replace the original neck of YOLOv8. After the training and testing of the improved algorithm on a self-constructed strawberry flower dataset, a series of experiments is conducted to evaluate the performance of the model, including ablation experiments, multi-dataset comparative experiments, and comparative experiments against state-of-the-art algorithms. The results show that the VM-YOLO network exhibits superior performance in object detection tasks across diverse datasets compared to the baseline. Furthermore, the results also demonstrate that VM-YOLO has better performances in the mAP, inference speed, and the number of parameters compared to the YOLOv6, Faster R-CNN, FCOS, and RetinaNet. Full article

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

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23 pages, 897 KiB

Open AccessArticle

Invasive Plants as a Source of Polyphenols with High Radical Scavenging Activity

by Oskars Purmalis, Linards Klavins, Evelina Niedrite, Marcis Mezulis and Maris Klavins

Plants 2025, 14(3), 467; https://doi.org/10.3390/plants14030467 - 5 Feb 2025

Abstract

The wide occurrence and expansive nature of invasive plant species are worldwide problems because these plants by their competitive character can lead to the loss of biodiversity. As a result, they significantly disrupt ecosystems, create economic damage and threats to human health, and [...] Read more.

The wide occurrence and expansive nature of invasive plant species are worldwide problems because these plants by their competitive character can lead to the loss of biodiversity. As a result, they significantly disrupt ecosystems, create economic damage and threats to human health, and diminish the quality of recreational resources. Therefore, sustainable, bio-based solutions are needed for their control, focusing on the utilization of their biomass after eradication. To better understand the potential application possibilities of invasive plants and their potential role in bioeconomy, species such as Lupinus polyphyllus—Lindl., Impatiens glandulifera Royle, Heracleum sosnowskyi Manden, Solidago canadensis L., Echinocystis lobata (Michx.), and Elodea canadensis Michx. were studied. These plants are not only widely spread but also form dense mono-stands and produce substantial amounts of biomass, which provides more options for their harvesting. In particular, their composition was analysed to assess the feasibility of their use for bioactive compound extraction. The amount of total polyphenols and flavonoids was determined in various parts of the studied invasive plants, and their corresponding radical scavenging activities were determined using DPPH, ABTS, FRAP and CUPRAC. The studied invasive plants are rich sources of polyphenols, and the highest concentrations were found in Impatiens glandulifera leaves, reaching a concentration of 7.78–11.75 g GAE/100 g DW, but in Lupinus polyphyllus, the highest concentrations of polyphenols were identified in the extracts of the flowers (12.77 g GAE/100 g DW) and leaves (11.88 g GAE/100 g DW) of the plant. Among the various plant parts studied, the leaves and flowers consistently showed the highest concentrations of polyphenols and flavonoids, as well as the greatest antioxidant and radical scavenging activities. These findings underscore the potential of invasive plant biomass as a source of valuable bioactive substances, particularly polyphenols, after the eradication of these invasive species. Full article

(This article belongs to the Special Issue Uses & Efficient Valorisation of Plant Biomass in Biorefinery Context)

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15 pages, 1551 KiB

Open AccessArticle

Phytochemical Profiles, Antimicrobial and Antioxidant Activity of Knautia integrifolia (L.) Bertol. subsp. integrifolia

by Hilal Kılınc

Plants 2025, 14(3), 466; https://doi.org/10.3390/plants14030466 - 5 Feb 2025

Abstract

The genus Knautia (L.) (Caprifoliaceae) is widely distributed in the Mediterranean region and is represented by 11 species of flora in Turkey. This study conducted a detailed phytochemical investigation of the methanol extract of the whole plant of K. integrifolia using a combination [...] Read more.

The genus Knautia (L.) (Caprifoliaceae) is widely distributed in the Mediterranean region and is represented by 11 species of flora in Turkey. This study conducted a detailed phytochemical investigation of the methanol extract of the whole plant of K. integrifolia using a combination of LC-ESI-FT-MS and NMR analyses. According to the results of this analysis, 25 compounds were identified in the methanol extract of K. integrifolia. The extract is particularly rich in phenolic secondary metabolites, including phenolic acid derivatives, flavonoid glycosides, and flavones, along with the presence of triterpenoid compounds. Additionally, the total phenolic content of the K. integrifolia methanol extract was evaluated. Considering the pharmacological activities reported for Knautia species, the antioxidant potential of the methanol extract was assessed using the DPPH radical scavenging assay, resulting in a value of 77.5% when compared to the ascorbic acid standard. In this study, antimicrobial activity tests were performed on K. integrifolia methanol extract for the first time. The results indicated that the extract demonstrated greater susceptibility to Staphylococcus epidermidis compared to the control group. At the same time, Pseudomonas aeruginosa exhibited a minimum inhibitory concentration value, indicating high sensitivity to the methanol extract. Full article

(This article belongs to the Special Issue Natural Products of Medicinal Plants: Isolation, Purification and Bioactivity Evaluation)

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