Plants

25 pages, 1162 KiB

Open AccessArticle

Geobotanical Study and Preservation of Rare and Endangered Rosaceae Species

by Natalya V. Romadanova, Alina S. Zemtsova, Nazira A. Altayeva, Natalya A. Artimovich, Alyona M. Alexandrova, Svetlana V. Kushnarenko and Jean Carlos Bettoni

Plants 2025, 14(10), 1526; https://doi.org/10.3390/plants14101526 - 19 May 2025

Abstract

The loss of plant species, especially endangered and endemic ones, poses a significant threat to global biodiversity. These species cannot easily be replaced when their populations decline or become extinct, which makes their loss particularly devastating. This study focuses on the geobotanical study [...] Read more.

The loss of plant species, especially endangered and endemic ones, poses a significant threat to global biodiversity. These species cannot easily be replaced when their populations decline or become extinct, which makes their loss particularly devastating. This study focuses on the geobotanical study of nine Rosaceae species (Cotoneaster karatavicus, Crataegus ambigua, Malus niedzwetzkyana, Malus sieversii, Prunus tenella, Prunus ulmifolia, Sibiraea laevigata, Sorbus persica, and Spiraeanthus schrenkianus) and the development of ex situ approaches for the conservation of Rosaceae species listed in the Red Book of Kazakhstan. The geobotanical study revealed an alarming trend of biodiversity loss in five regions of Kazakhstan. This loss is driven by threats from diseases and pests, as well as the aging of plants, small population sizes, weak in situ fruiting, and other factors, such as climate change. We have established an in vitro collection for the short- and medium-term conservation of seeds, embryos and shoots taken either directly from field-grown plants or from budwood cuttings forced indoors. We also use long-term sexual conservation methods, such as the cryopreservation of seed and embryonic axes, alongside conventional seed banking at −20 °C. Ex situ conservation efforts that use multiple propagules and storage methods for the same species are well-suited to a diverse genebank facility. These efforts enable future generations to use this valuable reservoir of genetic diversity for crop improvement and may also serve as a basis for propagating planting material to restore degraded populations. Full article

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

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32 pages, 6649 KiB

Open AccessArticle

Elevated Growth Temperature Modifies Drought and Shade Responses of Fagus sylvatica Seedlings by Altering Growth, Gas Exchange, Water Relations, and Xylem Function

by Faustino Rubio, Ismael Aranda, Rosana López and Francisco Javier Cano

Plants 2025, 14(10), 1525; https://doi.org/10.3390/plants14101525 - 19 May 2025

Abstract

Climate change is increasing global temperatures and imposing new constraints on tree regeneration, especially in late-successional species exposed to simultaneous drought and low-light conditions. To disentangle the effects of warming from those of atmospheric drought, we conducted a multifactorial growth chamber experiment on [...] Read more.

Climate change is increasing global temperatures and imposing new constraints on tree regeneration, especially in late-successional species exposed to simultaneous drought and low-light conditions. To disentangle the effects of warming from those of atmospheric drought, we conducted a multifactorial growth chamber experiment on Fagus sylvatica seedlings, manipulating temperature (25 °C and +7.5 °C above optimum), soil moisture (well-watered vs. water-stressed), and light intensity (high vs. low), while maintaining constant vapor pressure deficit (VPD). We assessed growth, biomass allocation, leaf gas exchange, water relations, and xylem hydraulic traits. Warming significantly reduced total biomass, leaf area, and water-use efficiency, while increasing transpiration and residual conductance, especially under high light. Under combined warming and drought, seedlings exhibited impaired osmotic adjustment, reduced leaf safety margins, and diminished hydraulic performance. Unexpectedly, warming under shade promoted a resource-acquisitive growth strategy through the production of low-cost leaves. These results demonstrate that elevated temperature, even in the absence of increased VPD, can compromise drought tolerance in beech seedlings and shift their ecological strategies depending on light availability. The findings underscore the need to consider multiple, interacting stressors when evaluating tree regeneration under future climate conditions. Full article

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

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17 pages, 3106 KiB

Open AccessArticle

Integrative Transcriptomics and Metabolomics Reveal the Key Metabolic Pathways in Endophyte-Infected Rice Seedlings Resistance to Na₂CO₃ Stress

by Xinnan Wang, Yanan Li, Hefei Sun, Lihong Zhang and Xuemei Li

Plants 2025, 14(10), 1524; https://doi.org/10.3390/plants14101524 - 19 May 2025

Abstract

Soil saline-alkalization is a key factor affecting rice growth and physiological metabolism, which leads to reduced yields. Endophyte EF0801 significantly promoted growth and improved its saline-alkali resistance. We investigated growth parameters and physiological indices of endophyte EF0801-infected and control rice seedlings under sodium [...] Read more.

Soil saline-alkalization is a key factor affecting rice growth and physiological metabolism, which leads to reduced yields. Endophyte EF0801 significantly promoted growth and improved its saline-alkali resistance. We investigated growth parameters and physiological indices of endophyte EF0801-infected and control rice seedlings under sodium carbonate (Na₂CO₃) stress. The results showed that endophyte-infected rice seedlings showed plant height increase by 1.25-fold, root length shortening by 0.79-fold, sucrose synthase (SS), sucrose phosphosynthase (SPS), hexokinase (HXK), and α-glucosidase (α-GC) activities increased by 0.15-fold, 0.29-fold, 0.06-fold, and 1.45-fold, respectively, and β-glucosidase (β-GC) activity decreased by 0.12-fold. Utilizing gas chromatography and mass spectrometry (GC-MS) technology and RNA sequencing (RNA-seq) technology, we identified 419 differentially expressed genes (DEGs) and 37 differentially accumulated metabolites (DAMs). Comprehensive enrichment analysis of DAMs and DEGs showed that 6 DEGs and 6 DAMs were strongly correlated with the mitigating effects of endophytes on rice leaves under Na₂CO₃ treatment, highlighting the co-enrichment in starch and sucrose metabolism, as well as alanine, aspartate, and glutamate metabolism. The gene encoding HXK was found to be upregulated in endophyte-infected rice seedlings under Na₂CO₃ stress. HXK plays a key role in the conversion of fructose and glucose to fructose 6-phosphate (F-6-P) and glucose 6-phosphate (G-6-P), which are important intermediates in cellular energy metabolism and glycolytic pathways, providing energy and biosynthesis of precursor substances. Our findings provide a potential perspective for unraveling the molecular response of endophyte-mediated saline-alkali resistance in rice leaves and a theoretical rationale for exploring the mechanisms of growth-promoting effects by endophytes. Full article

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

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27 pages, 3147 KiB

Open AccessArticle

Insights into the Red Seaweed Asparagopsis taxiformis Using an Integrative Multi-Omics Analysis

by Min Zhao, Tomas Lang, Zubaida Patwary, Andrew L. Eamens, Tianfang Wang, Jessica Webb, Giuseppe C. Zuccarello, Ana Wegner-Thépot, Charlotte O’Grady, David Heyne, Lachlan McKinnie, Cecilia Pascelli, Nori Satoh, Eiichi Shoguchi, Alexandra H. Campbell, Nicholas A. Paul and Scott F. Cummins

Plants 2025, 14(10), 1523; https://doi.org/10.3390/plants14101523 - 19 May 2025

Abstract

The red seaweed Asparagopsis taxiformis (Bonnemaisoniaceae, Rhodophyta) produces a bioactive natural product, bromoform, which, when fed to ruminant livestock, can eradicate methane emissions. However, to cultivate enough A. taxiformis to produce a yield that would have a meaningful impact on global greenhouse gas [...] Read more.

The red seaweed Asparagopsis taxiformis (Bonnemaisoniaceae, Rhodophyta) produces a bioactive natural product, bromoform, which, when fed to ruminant livestock, can eradicate methane emissions. However, to cultivate enough A. taxiformis to produce a yield that would have a meaningful impact on global greenhouse gas emissions, we need to advance our current understanding of the biology of this seaweed species. Here, we used both a domesticated diploid tetrasporophyte (>1.5 years in culture) and wild samples to establish a high-quality draft nuclear genome for A. taxiformis (lineage 6 based upon phylogenetic analyses using the cox2-3 spacer). The constructed nuclear genome is 142 Mb in size (including 70.67% repeat regions) and was determined to encode for approximately 10,474 protein-coding genes, including those associated with secondary metabolism, photosynthesis, and defence. To obtain information regarding molecular differences between cultured and wild tetrasporophytes, we further explored differential gene expression relating to their different growth environments. Cultured tetrasporophytes, which contained a relatively higher level of bromoform compared to wild tetrasporophytes, demonstrated an enrichment of regulatory factors, such as protein kinases and transcription factors, whereas wild tetrasporophytes were enriched for the expression of defence and stress-related genes. Wild tetrasporophytes also expressed a relatively high level of novel secretory genes encoding proteins with von Willebrand factor A protein domains (named rhodophyte VWAs). Gene expression was further confirmed by proteomic investigation of cultured tetrasporophytes, resulting in the identification of over 400 proteins, including rhodophyte VWAs, and numerous enzymes and phycobiliproteins, which will facilitate future functional characterisation of this species. In summary, as the most comprehensive genomic resource for any Asparagopsis species, this resource for lineage 6 provides a novel avenue for seaweed researchers to interrogate genomic information, which will greatly assist in expediating production of Asparagopsis to meet demand by both aquaculture and agriculture, and to do so with economic and environmental sustainability. Full article

(This article belongs to the Special Issue Molecular Research of the Seaweeds)

22 pages, 3384 KiB

Open AccessArticle

Seed Morphometry Reveals Two Major Groups in Spanish Grapevine Cultivars

by José Javier Martín-Gómez, José Luis Rodríguez-Lorenzo, Francisco Emanuel Espinosa-Roldán, Félix Cabello Sáenz de Santamaría, Gregorio Muñoz-Organero, Ángel Tocino and Emilio Cervantes

Plants 2025, 14(10), 1522; https://doi.org/10.3390/plants14101522 - 19 May 2025

Abstract

Seed morphological description requires quantitative methods for further comparison. Here, traditional measurements, curvature analysis, and the J-index (percentage of similarity to a geometric model) were applied to the average contours (Acs) of 271 Vitis cultivars from the Spanish collection at IMIDRA (Madrid, [...] Read more.

Seed morphological description requires quantitative methods for further comparison. Here, traditional measurements, curvature analysis, and the J-index (percentage of similarity to a geometric model) were applied to the average contours (Acs) of 271 Vitis cultivars from the Spanish collection at IMIDRA (Madrid, Spain), including 9 different Vitis species and several sylvestris seeds (i.e., those derived from plants that once grew in the wild). Acs are graphical representations of the shape in seed populations, which can be obtained either from image analysis programs or computationally opening the way to quantitative analysis. A geometric model is a geometrically defined, closed curve, used as a reference for shape quantification. Based on existing differences between the Hebén cultivar (collected in 2020 and 2024; Hebén model, for morphotype 1) and the European varieties Chenin and Gewurztraminer (Chenin model, for morphotype 2), we created two models. The comparisons were based on a J-index, resulting in four groups: Group 1 contained all seeds with values lower than 90 for both models and included all Vitis species other than V. vinifera and most sylvestris seeds; Groups 2 and 3 contained seeds with J-index values higher than 94 for the Hebén and Chenin models, respectively. Group 4 consisted of seeds not included in the other groups. Based on J-index values, differences in curvature and solidity, and PCA analysis with Fourier coefficients, this work defines two new morphotypes associated with the Hebén (Group 2) and Chenin (Group 3) models, related to Iberian and Western European varieties, respectively. Full article

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

24 pages, 6093 KiB

Open AccessArticle

Evaluation and Source Analysis of Plant Heavy Metal Pollution in Kalamaili Mountain Nature Reserve

by Jialin Li, Abdugheni Abliz, Buasi Nueraihemaiti, Dongping Guo and Xianhe Liu

Plants 2025, 14(10), 1521; https://doi.org/10.3390/plants14101521 - 19 May 2025

Abstract

Plants serve as vital components of ecosystems, with their contamination status acting as sensitive indicators of environmental pollution. Therefore, the precise assessment of plant heavy metal contamination and source identification are crucial for regional ecological conservation and sustainable development. This study investigated heavy [...] Read more.

Plants serve as vital components of ecosystems, with their contamination status acting as sensitive indicators of environmental pollution. Therefore, the precise assessment of plant heavy metal contamination and source identification are crucial for regional ecological conservation and sustainable development. This study investigated heavy metal pollution in four characteristic plant species (Anabasis aphylla L., Alhagi camelorum Fisch., Reaumuria songonica (PalL)Maxim., and Haloxylon ammodendron (C. A. Mey.) Bunge.) within the Kalamaili Mountain Nature Reserve, employing comprehensive methodologies including pollution indices, bioconcentration factors (BCFs), absolute principal component score–multiple linear regression (APCS-MLR), and the random forest model (RF). The key findings revealed the following: The soil exhibited severe Cd and Hg contamination. The plant Cr concentrations exceeded standard limits by 31.89 to 147 fold. The Pb, Hg, and As content in plants showed significant differences. The plants displayed differential metal enrichment capacities, ranked as Cr (BCF = 3.28) > Hg (1.22) > Cd (0.92) > Cu (0.25) > Zn (0.15) > Pb (0.125) > As (0.125), highlighting Cr, Hg, and Cd as priority ecological hazards. Complex interactions were observed, with Reaumuria songonica (PalL)Maxim. showing strong Cd soil–plant correlation (r = 0.78), whereas Alhagi camelorum Fisch. demonstrated negative associations (Cd: r = −0.21). APCS-MLR identified mining/smelting as primary contributors to Cd (63.49%), Zn (55.66%), and Cr (45.51%), while transportation dominated Pb emissions (72.92%). Mercury pollution originated from mixed sources (56.18%), likely involving atmospheric deposition, and RF modeling corroborated these patterns, confirming industrial and transportation synergies for Cd, Zn, Cr, Cu, Hg, and As, with Pb predominantly linked to vehicular emissions. This multidisciplinary approach provides scientific evidence for establishing heavy metal monitoring systems and formulating targeted remediation strategies in arid ecologically fragile regions. Full article

(This article belongs to the Topic Effect of Heavy Metals on Plants, 2nd Volume)

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21 pages, 5244 KiB

Open AccessArticle

Identification and Functional Validation of the PeDHN Gene Family in Moso Bamboo

by Yaqin Ye, Yanting Chang, Wenbo Zhang, Tiankui Chu, Hanchen Tian, Yayun Deng, Zehui Jiang, Yanjun Ma and Tao Hu

Plants 2025, 14(10), 1520; https://doi.org/10.3390/plants14101520 - 19 May 2025

Abstract

As climate change intensifies soil drought and salinization, enhancing the drought and salt tolerance of moso bamboo (Phyllostachys edulis) is urgent. DHN genes are crucial for plant stress responses and have gained attention in plant resistance to drought and salinity. This [...] Read more.

As climate change intensifies soil drought and salinization, enhancing the drought and salt tolerance of moso bamboo (Phyllostachys edulis) is urgent. DHN genes are crucial for plant stress responses and have gained attention in plant resistance to drought and salinity. This study identified nine DHN family members (PeDHN1–PeDHN9) from moso bamboo, which were classified into K₂S-type, YK₂S-type, and Y₂K₂S-type dehydrins based on their characteristic motifs. We employed integrated bioinformatics approaches to analyze their gene structure, phylogeny, biological properties, and expression patterns under various stress conditions. Five genes (PeDHN2/4/5/6/8), which may have significant functional roles in moso bamboo, were selected for cloning. Subcellular localization experiments showed that YK₂S-type dehydrins (PeDHN2/5/6) localized to both the nucleus and the plasma membrane, while K₂S-type dehydrins (PeDHN4/8) were exclusively localized to the plasma membrane, indicating functional differentiation. qRT-PCR analysis revealed that the expression of PeDHN2/4/5/6/8 was significantly responsive to stress treatments with ABA, NaCl, and PEG. Additionally, overexpressing these genes in rice significantly enhanced seed germination rates and root development under salt and ABA stress, further confirming that PeDHN2/4/5/6/8 contribute to enhancing plant stress tolerance. Yeast one-hybrid assays demonstrated that two PeABF1 proteins could bind to the promoter of PeDHN4, suggesting that PeDHN4 may regulate stress responses through the ABA signaling pathway. Thus, these findings demonstrate that PeDHN2/4/5/6/8 are closely related to the response of moso bamboo to drought and saline-alkali environments. This research offers insights for moso bamboo cultivation and theoretical foundations for bamboo genetic improvement in stress environments. Full article

(This article belongs to the Topic Tolerance to Drought and Salt Stress in Plants, 2nd volume)

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23 pages, 2335 KiB

Open AccessArticle

Effect of Combining Organic and Inorganic Fertilizers on the Growth of Hemp (Cannabis sativa L.) Plants and the Accumulation of Phytochemicals in Their Inflorescence

by Mariarosaria Sicignano, Romina Beleggia, Luisa del Piano, Tommaso Enotrio, Serafino Suriano, Francesco Raimo and Daniela Trono

Plants 2025, 14(10), 1519; https://doi.org/10.3390/plants14101519 - 19 May 2025

Abstract

The feasibility of using a combination of organic fertilizer with a reduced rate of chemical nitrogen fertilizer as an alternative to conventional inorganic fertilization was tested on the growth and biomass accumulation of hemp plants and the phytochemical accumulation in their inflorescences. To [...] Read more.

The feasibility of using a combination of organic fertilizer with a reduced rate of chemical nitrogen fertilizer as an alternative to conventional inorganic fertilization was tested on the growth and biomass accumulation of hemp plants and the phytochemical accumulation in their inflorescences. To achieve this goal, a field experiment was set up with the following nine treatments: F0, no fertilizer; NPK, mineral fertilizer with 100 kg ha⁻¹ nitrogen; C1, compost from solid digestate (50%) + cardoon-based spent mushroom substrate (50%); C2, compost from solid digestate (50%) + straw-based spent mushroom substrate (50%); C3, C4, C5, and C6, composts from solid digestate (50%, 67%, 75%, and 84%, respectively) and cardoon waste (50%, 33%, 25%, and 16%, respectively); SD, non-composted solid digestate. C1–C6 and SD were added to the soil, along with half the rate (50 kg ha⁻¹) of chemical nitrogen fertilizer. Taking F0 as a reference, all fertilized treatments, except C6 and SD, showed a notable increase in plant growth and biomass accumulation in the stem, inflorescence, and whole plant. Among the organic treatments, the best growth performances were detected in C1 and C5, which reached, or even exceeded, that of NPK. Compared to F0, all fertilized treatments had high phenolic acid and flavonoid yields, while high carotenoid, tocopherol, terpene, and cannabinoid (mainly CBD) yields were detected in all fertilized treatments except C6 and SD. Among the organic treatments, C1 and C5 stood out for their highest phenolic acid, flavonoid, carotenoid, and tocopherol yields, while C1, C2, and C3 stood out for their highest terpene and cannabinoid yields, which, in both cases, reached, or even exceeded, those of NPK. Overall, our findings show that 50% replacement of inorganic nitrogen fertilizer with C1 to C5 composts may represent a cost-effective and environmentally safe alternative to conventional inorganic fertilization that can sustain the growth of hemp plant and the phytochemical accumulation in its inflorescences, thus promoting the use of this crop for fiber and bioenergy production, as well as for applications in food, nutraceutical, agrochemical, and cosmetic sectors. Full article

(This article belongs to the Special Issue Strategies for Enhancing the Production of Secondary Metabolites in Plants)

19 pages, 7245 KiB

Open AccessArticle

Nitrogen Immobilization by Wood Fiber Substrates Strongly Affects the Photosynthetic Performance of Lettuce

by Lingyi Wu, Ruohan Li, Juncheng Liu, Wenzhong Cui, Zhiyong Qi and Wanlai Zhou

Plants 2025, 14(10), 1518; https://doi.org/10.3390/plants14101518 - 19 May 2025

Abstract

Wood fiber substrates are widely used as peat substitutes in horticulture, but the impact of their high carbon-to-nitrogen ratio on nitrogen immobilization and crop photosynthetic performance remains unclear. This study systematically examined the effects of wood fiber substrates on lettuce photosynthetic performance and [...] Read more.

Wood fiber substrates are widely used as peat substitutes in horticulture, but the impact of their high carbon-to-nitrogen ratio on nitrogen immobilization and crop photosynthetic performance remains unclear. This study systematically examined the effects of wood fiber substrates on lettuce photosynthetic performance and underlying physiological mechanisms using pot experiments. Two substrate treatments—peat (control) and wood fiber—were combined with three nitrogen levels: low, medium, and high (63, 127, and 210 mg N·L⁻¹). Results indicated that wood fiber substrates significantly reduced the availability of fast-acting nitrogen, leading to a substantial decrease in lettuce biomass (39.0–56.8%), total nitrogen content (7.2–39.9%), and chlorophyll content (13.7–36.2%). Chlorophyll fluorescence kinetics analysis revealed that wood fiber substrates impair photosystem function through multiple pathways. At the early stage (15 days), key effects included structural damage to the donor side of PSII(Photosystem II), indicated by L and K peaks, and inhibited electron transfer on the PSI(Photosystem I) acceptor side (δRo decreased by 15.08–27.90%, along with a reduction in W_OI amplitude). The findings provide an important theoretical basis for optimising nitrogen management strategies for wood fibre substrates. Full article

(This article belongs to the Special Issue Driving Sustainability: Innovations in Producing Eco-Friendly Substrates for Soilless Culture Systems)

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16 pages, 2345 KiB

Open AccessArticle

More than Just a Shell: Indehiscent Fruits Drive Drought-Tolerant Germination in Invasive Lepidium Species

by Said Mohammed and Klaus Mummenhoff

Plants 2025, 14(10), 1517; https://doi.org/10.3390/plants14101517 - 19 May 2025

Abstract

This study aims to assess the drought stress tolerance of germinating seeds of the invasive indehiscent fruit-producing Lepidium species, specifically Lepidium appelianum, Lepidium draba, and the invasive dehiscent fruit-producing L. campestre. Drought stress tolerance experiments were conducted using various concentrations [...] Read more.

This study aims to assess the drought stress tolerance of germinating seeds of the invasive indehiscent fruit-producing Lepidium species, specifically Lepidium appelianum, Lepidium draba, and the invasive dehiscent fruit-producing L. campestre. Drought stress tolerance experiments were conducted using various concentrations of polyethylene glycol (PEG) following standard protocols. The results revealed that seeds/fruits of L. appelianum and L. draba exhibited significantly higher drought stress tolerance compared to seeds of L. campestre. Fresh seeds and fruits of L. appelianum were capable of germinating under various drought stress treatments, while fresh and after-ripened seeds and fruits of L. draba germinated in every condition except for −0.8 MPa. Conversely, L. campestre fresh seeds did not germinate under the most severe drought stress conditions (−0.6 and −0.8 MPa). It is crucial to note that fresh fruits of L. draba displayed pericarp-mediated chemical dormancy, while fresh seeds of L. campestre demonstrated physiological dormancy. However, fresh seeds and fruits of L. appelianum did not exhibit any dormancy. This study suggests that germinating seeds and fruits of L. appelianum demonstrate the strongest tolerance to drought stress, while L. draba exhibits moderate tolerance. On the contrary, L. campestre seeds display the least tolerance to drought stress. The differences in drought stress tolerance among the studied Lepidium species reflect the climatic facets in their native distribution areas. Given the potential high invasiveness associated with the drought stress tolerance of L. appelianum and L. draba, it is imperative to develop special control strategies to manage these invasive species in the face of future climate change. Full article

(This article belongs to the Special Issue Plant Invasions across Scales)

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22 pages, 3897 KiB

Open AccessArticle

Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean

by Qianli Dong, Lu Niu, Xiyu Gong, Qianlong Xing, Jie Liang, Jun Lang, Tianya Wang and Xiangdong Yang

Plants 2025, 14(10), 1516; https://doi.org/10.3390/plants14101516 - 19 May 2025

Abstract

As a globally important leguminous crop, soybean (Glycine max L.) serves as a vital source of edible oils and proteins for humans and livestock. Oils in leaves can help crops combat fungal infections, adapt to temperature changes via fatty acid modulation, and [...] Read more.

As a globally important leguminous crop, soybean (Glycine max L.) serves as a vital source of edible oils and proteins for humans and livestock. Oils in leaves can help crops combat fungal infections, adapt to temperature changes via fatty acid modulation, and support resource recycling during leaf senescence. However, accumulating oils in leaves is a fundamental challenge due to the need to balance the inherently competing photosynthesis and fatty acid biosynthesis processes within chloroplasts. RETICULATA-RELATED (RER), known to regulate chloroplast function and plastid metabolism in Arabidopsis, plays an essential role in leaf development. Here, 14 non-redundant GmRER genes were identified in soybean and phylogenetically classified into four subclades. Most Arabidopsis RER genes were evolutionarily preserved as gene duplicates in soybean, except for GmRER5 and GmRER6. RNA secondary structures spanning the coding sequences (CDSs), the 5′- and 3′- untranslated regions (UTRs) of GmRERs, displayed exceptional structural plasticity in CDSs, while exhibiting limited conservation in UTRs. In contrast, protein structures retained conserved folds, underscoring evolutionary constraints on functional domains despite transcriptional plasticity. Notably, GmRER4a and GmRER4b represented an exceptional case of high similarity in both protein and RNA structures. Expression profiling across fourteen tissues and three abiotic stress conditions revealed a dynamic shift in expression levels between leaf-predominant and root-enriched GmRER paralogs after stress treatments. A comparative transcriptome analysis of six soybean landraces further revealed transcriptional polymorphism in the GmRER family, which was associated with the expression patterns of lipid biosynthesis regulators. Our comprehensive characterization of GmRERs may offer potential targets for soybean breeding optimization in overall plant oil production. Full article

(This article belongs to the Special Issue Advances in Oil Regulation in Seeds and Vegetative Tissues)

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17 pages, 2221 KiB

Open AccessArticle

Role of Tyrosine Phosphorylation in PEP1 Receptor 1(PEPR1) in Arabidopsis thaliana

by Jae-Han Choi and Man-Ho Oh

Plants 2025, 14(10), 1515; https://doi.org/10.3390/plants14101515 - 19 May 2025

Abstract

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have evolved to perceive environmental changes. Among LRR-RLKs, PEPR1 perceives the pep1 peptide and triggers defense signal transduction in Arabidopsis thaliana. In the present study, we focused on PEPR1 and PEPR2, which are the receptors of pep1, [...] Read more.

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have evolved to perceive environmental changes. Among LRR-RLKs, PEPR1 perceives the pep1 peptide and triggers defense signal transduction in Arabidopsis thaliana. In the present study, we focused on PEPR1 and PEPR2, which are the receptors of pep1, to understand the role of tyrosine phosphorylation. PEPR1-CD (cytoplasmic domain) recombinant protein exhibited strong tyrosine autophosphorylation, including threonine autophosphorylation. We subjected all tyrosine residues in PEPR1-CD to site-directed mutagenesis. The recombinant proteins were purified along with PEPR1-CD, and Western blotting was performed using a tyrosine-specific antibody. Among the 13 tyrosine residues in PEPR1-CD, the PEPR1(Y995F)-CD recombinant protein showed significantly reduced tyrosine autophosphorylation intensity compared to PEPR1-CD and other tyrosine mutants, despite little change in threonine autophosphorylation. To confirm the autophosphorylation site, we generated a phospho-specific peptide Ab, pY995. As a result, Tyr-995 of PEPR1-CD was a major tyrosine autophosphorylation site in vitro. To understand the function of tyrosine phosphorylation in vivo, we generated transgenic plants, expressing PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag in a pepr1/2 double mutant background. Interestingly, the root growths of PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag were not inhibited by pep1 peptide treatment, compared to Col-0 and PEPR1-Flag (pepr1/2) transgenic plants. Also, we analyzed downstream components, which included PROPEP1, MPK3, WRKY33, and RBOHD gene expressions in four different genotypes (Col-0, PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag) of plants in the presence of the pep1 peptide. Interestingly, the expressions of PROPEP1, MPK3, WRKY33, and RBOHD were not regulated by pep1 peptide treatment in PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag transgenic plants, in contrast to Col-0 and PEPR1-Flag. These results suggest that specific tyrosine residues play an important role in vivo in the plant receptor function. Full article

(This article belongs to the Special Issue Mechanisms of Plant Defense Against Abiotic Stresses)

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15 pages, 7086 KiB

Open AccessArticle

AtPADRE13 Negatively Regulates Salt Stress Tolerance in Arabidopsis thaliana

by Ziru Chang, Xiaona Tian, Xiaocui Niu, Meiting Bai, Wei Bai, Ruigang Wang, Guojing Li and Qi Yang

Plants 2025, 14(10), 1514; https://doi.org/10.3390/plants14101514 - 19 May 2025

Abstract

The PADRE (Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing) family of genes, which contains the structural DUF4228 domain of unknown function (DUF), has been reported to be associated with plant responses to abiotic stresses. However, the specific functions of this family [...] Read more.

The PADRE (Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing) family of genes, which contains the structural DUF4228 domain of unknown function (DUF), has been reported to be associated with plant responses to abiotic stresses. However, the specific functions of this family in the salt stress response remain unknown. AtPADRE13 is induced by salt stress and ABA (abscisic acid). After the overexpression of AtPADRE13 in Arabidopsis, seeds were found to be insensitive to ABA treatment. After salt treatment, the overexpression lines presented a significantly lower survival rate, increased MDA (Malondialdehyde) content, and reduced antioxidant enzyme activities compared with the wild-type, and were more sensitive to salt stress. Transcriptome data analysis further revealed that AtPADRE13 overexpression resulted in different degrees of down-regulation for a series of positive regulators related to ABA catabolism, transport, and their mediated plant responses to salt stress. In addition, the expression of genes related to ROS (reactive oxygen species) scavenging was down-regulated. In conclusion, AtPADRE13 plays a negative regulatory role in the response to salt stress in Arabidopsis. Full article

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

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15 pages, 3619 KiB

Open AccessArticle

Effects of Stumping on Ecological Stoichiometry and Allometric Growth in Leaf, Absorptive Root, and Rhizosphere Soil of Hippophae rhamnoides

by Lu Liu, Yuefeng Guo, Wangsuo Liu, Darifu Ba and Fei Feng

Plants 2025, 14(10), 1513; https://doi.org/10.3390/plants14101513 - 19 May 2025

Abstract

To clarify the effects of stumping on the C, N, and P allocation strategy of Hippophae rhamnoides L. artificial forests at the decaying stage in feldspathic sandstone areas, we tested stumping heights of 0, 10, 15, and 20 cm from the ground (denoted [...] Read more.

To clarify the effects of stumping on the C, N, and P allocation strategy of Hippophae rhamnoides L. artificial forests at the decaying stage in feldspathic sandstone areas, we tested stumping heights of 0, 10, 15, and 20 cm from the ground (denoted H1, H2, H3, and H4, respectively) with non-stumped trees as a control (CK). The N (LN, RN), P (LP, RP), and N:P (LN:LP, RN:RP) in the leaves and absorptive roots and the C, N, C:N, C:P, and N:P in rhizosphere soils after different treatments all manifested in the order H3 > H2 > H1 > H4 > CK. Among them, the LN and RN of H3 presented the largest amplitudes of increase (31% and 263%, respectively) compared with those of CK. There were very significant allometric relationships between LC and RC (−0.57, trade-off relationship), between LN and RN, and between LP and RP (0.32, 2.01; synergistic relationship) in stumped H. rhamnoides, and the accumulation rates of LC and LN were slower than those of RC and RN. After the stumping, certain correlations were present between the characteristics, except that neither LC nor RC significantly differed across the different treatments. The growth of H. rhamnoides after the different treatments was mainly regulated by P. The stumped H. rhamnoides grew at a faster rate, and the optimal stumping height was 15 cm. These findings are valuable for revegetation and for the prevention and control of soil erosion in feldspathic sandstone areas. Full article

(This article belongs to the Section Plant Ecology)

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14 pages, 1407 KiB

Open AccessArticle

Phenotypic Genetic Analysis of Fruit Branch Angle in Upland Cotton

by Yanping Tan, Yilei Long, Yinan Yang, Yin Wang, Shen Jin and Xiantao Ai

Plants 2025, 14(10), 1512; https://doi.org/10.3390/plants14101512 - 18 May 2025

Abstract

This study aims to reveal the genetic variation of fruit branch angle (FBA) in upland cotton, thereby providing a scientific basis and practical guidance for cotton architecture breeding. We explored the genetic variation pattern of FBA in 300 upland cottons from different regions [...] Read more.

This study aims to reveal the genetic variation of fruit branch angle (FBA) in upland cotton, thereby providing a scientific basis and practical guidance for cotton architecture breeding. We explored the genetic variation pattern of FBA in 300 upland cottons from different regions and different periods, respectively. Cluster analysis and principal component analysis were used to comprehensively evaluate the plant architecture traits and yield traits in 300 upland cottons. The results demonstrated that the range of variation of FBA in cotton was 43.59–69.32°, the coefficient of variation ranged from 6.06% to 7.42%, and the broad-sense heritability was 75.50%. The order of FBA in different regions was as follows: Foreign Germplasm (FG; 56.77°) > Yellow River Region (YRR; 56.24°) > Yangtze River Region (YZRR; 56.16°) > Liaoning Special Maturing Region (LSMR; 55.35°) > Northwest Inland Region (NIR; 55.25), which is rich in genetic diversity. FBA in cotton in different periods had obvious differences. FBA was the largest before 1960, and as the period progressed, FBA showed an overall fluctuating decrease, whose coefficient of variation and genetic diversity index tended to increase. In this study, it was found that when the range of FBA was 50.46–55.31°, cotton had the best overall performance, with compact architecture, fewer empty fruit branches, more bells, and higher yield, which can be further developed and utilized as an excellent cotton germplasm resource. Full article

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

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16 pages, 3815 KiB

Open AccessArticle

Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan

by Aruzhan Mendybayeva, Alibek Makhambetov, Kirill Yanin, Aisha Taskuzhina, Marina Khusnitdinova and Dilyara Gritsenko

Plants 2025, 14(10), 1511; https://doi.org/10.3390/plants14101511 - 18 May 2025

Abstract

Kazakhstan’s rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, [...] Read more.

Kazakhstan’s rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host—microbe relationships that can inform apple breeding and ecological preservation efforts. Full article

(This article belongs to the Special Issue Evolution and Genetics of Plant–Microbe Interactions)

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16 pages, 1585 KiB

Open AccessReview

Smart Chip Technology for the Control and Management of Invasive Plant Species: A Review

by Qaiser Javed, Mohammed Bouhadi, Smiljana Goreta Ban, Dean Ban, David Heath, Babar Iqbal, Jianfan Sun and Marko Černe

Plants 2025, 14(10), 1510; https://doi.org/10.3390/plants14101510 - 18 May 2025

Abstract

Invasive plant species threaten biodiversity, disrupt ecosystems, and are costly to manage. Standard control methods, such as mechanical and chemical (herbicides), are usually ineffective and time-consuming and negatively affect the environment, especially in the latter case. This review explores the potential of smart [...] Read more.

Invasive plant species threaten biodiversity, disrupt ecosystems, and are costly to manage. Standard control methods, such as mechanical and chemical (herbicides), are usually ineffective and time-consuming and negatively affect the environment, especially in the latter case. This review explores the potential of smart chip technology (SCT) as a sustainable, precision approach tool for invasive species management. Integrating microchip sensors with artificial intelligence (AI) into the Internet of Things (IoT) and remote sensing technology allows for real-time monitoring, predictive modelling, and focused action, significantly improving management effectiveness. As one of many examples discussed herein, AI-driven decision-making systems can process real-time data from IoT-enabled environmental sensors to optimize invasive species detection. Smart chip technology also offers real-time monitoring of invasive species’ life processes, spread, and environmental effects, enabling artificial intelligence-powered eco-friendly control strategies that minimize herbicide usage and lessen collateral ecosystem damage. Despite the potential of SCT, challenges remain, including cost, biodegradability, and regulatory constraints. However, recent advances in biodegradable electronics and AI-driven automation offer promising solutions to many identified obstacles. Future research should focus on scalable deployment, improved predictive analytics, and interdisciplinary collaboration to drive innovation. Using SCT can help make invasive species control more sustainable while supporting biodiversity and strengthening agricultural systems. Full article

(This article belongs to the Special Issue Ecology and Management of Invasive Plants—2nd Edition)

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15 pages, 1788 KiB

Open AccessArticle

Nutritional Efficiency of Coffea canephora: The Role of Genetic Variability and Nutrient Accumulation

by Cleidson Alves da Silva, Jéssica Rodrigues Dalazen, Weverton Pereira Rodrigues, Rodrigo Barros Rocha and Fábio Luiz Partelli

Plants 2025, 14(10), 1509; https://doi.org/10.3390/plants14101509 - 17 May 2025

Abstract

The genetic variability of Coffea canephora is essential for the identification of genotypes with enhanced nutritional traits. This study aimed to characterize C. canephora genotypes based on nutrient accumulation in fruits, evaluated over two consecutive harvests. The experiment followed a randomized block design [...] Read more.

The genetic variability of Coffea canephora is essential for the identification of genotypes with enhanced nutritional traits. This study aimed to characterize C. canephora genotypes based on nutrient accumulation in fruits, evaluated over two consecutive harvests. The experiment followed a randomized block design with four replications, comprising 42 genotypes. To assess nutrient accumulation, fruit samples were collected from each genotype and oven-dried. In a plant tissue analysis laboratory, the concentrations of N, P, K, Ca, Mg, S, Fe, Mn, Cu, Zn, and B were determined. Nutrient accumulation in the fruits was calculated as dry mass × nutrient concentration, and the data were converted to kg or g of nutrients accumulated per ton of coffee beans at 12% moisture content. The results revealed significant variability among genotypes in nutrient accumulation, with the general accumulation order being N > K > Ca > Mg > S > P > Mn > Fe > B > Cu > Zn. Multivariate analysis identified seven groups, with Verdim R, Clementino, and Pirata forming distinct clusters due to their unique characteristics. Clementino exhibited the highest nutrient accumulation, while LB1 had the lowest. The study demonstrated high heritability for all traits, indicating strong genetic control, along with significant positive correlations among nutrients. These findings highlight the potential of selecting nutrient-efficient genotypes to enhance the sustainability of coffee cultivation. The nutritional data obtained can support the development of more nutritionally efficient cultivars, ensuring long-term sustainability in coffee production. Full article

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

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25 pages, 1576 KiB

Open AccessArticle

Performance, Agro-Morphological, and Quality Traits of Durum Wheat (Triticum turgidum L. ssp. durum Desf.) Germplasm: A Case Study in Jemâa Shaïm, Morocco

by Khadija Manhou, Mona Taghouti, Rachid Moussadek, Houda Elyacoubi, Sahar Bennani, Abdelmjid Zouahri, Ahmed Ghanimi, Hatim Sanad, Majda Oueld Lhaj, Driss Hmouni and Houria Dakak

Plants 2025, 14(10), 1508; https://doi.org/10.3390/plants14101508 - 17 May 2025

Abstract

The productivity and resilience of durum wheat have been enhanced through the selection of accessions, optimizing agronomic and quality traits to address environmental challenges. This study evaluates the performance of 219 durum wheat accessions, including 120 elite lines from a national breeding program [...] Read more.

The productivity and resilience of durum wheat have been enhanced through the selection of accessions, optimizing agronomic and quality traits to address environmental challenges. This study evaluates the performance of 219 durum wheat accessions, including 120 elite lines from a national breeding program (G1 to G120), 63 international lines (G121 to G183), 27 Moroccan varieties (including Faraj, Karim, Tomouh, Marzak, Amria, Chaoui, IRDEN, and others), and nine landraces (G211 to G219, from Imilchil, Rich, and Taounate regions). Trials were conducted at the Jemâa Shaïm experimental station (INRA-Morocco) with an “Alpha lattice” design and two replications. Significant correlations were observed between spike length (SL) and number of spikelets per spike (SPS) (r = 0.950; p < 0.001), and between grain yield (GY) and thousand-kernel weight (TKW) (r = 0.530; p < 0.01), while no correlation was found between quality parameters and GY (r = 0.010; p > 0.05). Principal component analysis (PCA) revealed that agronomic traits explained 77.12% of variability, while quality traits accounted for 95.54%. Elite lines exhibited a high yellow pigment index (14.90), important for technological quality. Traditional landraces performed well in spike length (8.78 cm), thousand-kernel weight (50.23 g), protein content (17.07%), and gluten content (36.90%). Moroccan varieties such as Faraj achieved a grain yield of 6.12 t/ha, while international lines showed the highest SDS value (9.39 mL). These findings highlight the potential of diverse accessions for developing high-yielding, high-quality durum wheat. Full article

(This article belongs to the Topic Abiotic Stress Responses in Wheat: Perspectives on Productivity and Sustainability)

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