Plants

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 (registering DOI) - 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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17 pages, 6207 KiB

Open AccessArticle

Identification and Expression Analysis of NAC Transcription Factors Related to Rust Resistance in Foxtail Millet

by Keke Gong, Jia Liu, Mengya Zhang, Zhiping Dong, Jifang Ma, Peixue Xuan, Hui Bai and Zhiyong Li

Plants 2025, 14(10), 1507; https://doi.org/10.3390/plants14101507 (registering DOI) - 17 May 2025

Abstract

Foxtail millet (Setaria italica), a vital cereal crop in China, serves as both a staple food and forage source but is threatened by rust disease caused by Uromyces setariae-italicae (Usi), leading to severe yield and quality losses. The NAM, [...] Read more.

Foxtail millet (Setaria italica), a vital cereal crop in China, serves as both a staple food and forage source but is threatened by rust disease caused by Uromyces setariae-italicae (Usi), leading to severe yield and quality losses. The NAM, ATAF1/2, and CUC2 (NAC) transcription factor family represents one of the largest plant-specific regulatory gene families, playing pivotal roles in development and stress responses. However, the functional relevance of NAC genes in foxtail millet’s defense against this pathogen remains unexplored. Here, we systematically analyzed 33 SiNAC genes from the foxtail millet genome. Phylogenetic analysis classified these genes into 11 subgroups, while chromosomal mapping localized them to nine chromosomes unevenly. Promoter analysis identified stress- and plant hormone-related cis-elements, suggesting functional diversity. Expression profiling analysis showed that most SiNAC genes exhibit tissue-specific expression patterns. Quantitative real-time PCR (qRT-PCR) results indicated that 30 genes responded to Usi infection, with 17 showing a strong association with rust resistance. Three resistance-associated genes demonstrated transactivation activity and nuclear localization, indicating their regulatory function in defense responses. This study provides both mechanistic insights into SiNAC-mediated rust resistance and potential targets for molecular breeding in foxtail millet. Full article

(This article belongs to the Section Plant Molecular Biology)

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14 pages, 1487 KiB

Open AccessArticle

Genome-Wide Association Analysis of Sweet Pepper (Capsicum annuum) Based on Agronomic Traits Using PepperSNP50K

by Yaolong Wang, Entong Li, Jiawei Lu, Jing Wang, Qiaolu Zang, Yanping Liang, Ruxia Tian, Changwei Zhang, Fangling Jiang and Yan Cheng

Plants 2025, 14(10), 1506; https://doi.org/10.3390/plants14101506 (registering DOI) - 17 May 2025

Abstract

As one of the most important vegetables globally, peppers have garnered significant attention from breeders due to their diverse agronomic traits, including plant type, leaf shape, and maturity. Understanding the genetic mechanisms underlying these traits is crucial for systematic advancements in sweet pepper [...] Read more.

As one of the most important vegetables globally, peppers have garnered significant attention from breeders due to their diverse agronomic traits, including plant type, leaf shape, and maturity. Understanding the genetic mechanisms underlying these traits is crucial for systematic advancements in sweet pepper breeding. In this study, leveraging the PepperSNP50K liquid breeding chip, we conducted a comprehensive analysis of horticultural traits and genetic diversity using sweet pepper germplasm samples. Initially, the sweet pepper populations were analyzed using SNP-based liquid chip technology. Subsequently, phenotypic surveys were performed on 217 sweet pepper samples, and the collected phenotypic data were integrated with SNP markers to conduct a genome-wide association study (GWAS) of key agronomic traits. Among the 25 horticultural traits evaluated, 11 exhibited significant associations with 54 SNP polymerization regions and 193 candidate genes. These findings provide a robust foundation for the utilization of sweet pepper germplasm resources and the development of new, improved varieties. Furthermore, in this study, we identified Caz06g05770 (Lycopene beta-cyclase) as a candidate gene responsible for the color of mature ripe fruits. This research not only enhances our understanding of the genetic basis of sweet pepper traits but also offers a practical roadmap for advancing breeding programs and boosting agricultural productivity. By bridging the gap between genetic research and practical breeding applications, this study paves the way for the development of high-yield, high-quality sweet pepper varieties tailored to meet the growing demands of global agriculture. Full article

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

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16 pages, 3933 KiB

Open AccessArticle

Resistance to Amino Acid Biosynthesis Inhibiting-Herbicides in Amaranthus palmeri Populations from Aragon (Spain)

by Eneko Trebol-Aizpurua, Mikel V. Eceiza, Clara Jimenez-Martinez, Ana I. Marí, Mercedes Royuela, Ana Zabalza and Miriam Gil-Monreal

Plants 2025, 14(10), 1505; https://doi.org/10.3390/plants14101505 (registering DOI) - 17 May 2025

Abstract

Amaranthus palmeri is a highly problematic agricultural weed due to its rapid growth, high seed production, and strong tendency to develop herbicide resistance. In Spain, the initial colonization of A. palmeri began in 2007, when populations were detected at various locations in the [...] Read more.

Amaranthus palmeri is a highly problematic agricultural weed due to its rapid growth, high seed production, and strong tendency to develop herbicide resistance. In Spain, the initial colonization of A. palmeri began in 2007, when populations were detected at various locations in the province of Lleida (Catalonia). Since then, new infestations have been reported in other regions of the country, primarily infesting maize fields. Although resistance to glyphosate or to acetolactate synthase (ALS) inhibitors has been documented in several populations from Catalonia and Extremadura, little is known about the resistance profile of populations from Aragon. The main objective of this study was to characterize the putative resistance of five populations from Aragon to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibitors (glyphosate) and ALS inhibitors (nicosulfuron and imazamox). Sensitivity to both mechanisms of action was measured by root growth in vertical plates and shikimate accumulation for glyphosate. Target-site resistance was evaluated by analyzing EPSPS and ALS gene copy numbers and ALS gene mutations. The populations showed high variability, with no multiple resistance detected. The Bujaraloz population showed moderate resistance to glyphosate due to EPSPS gene amplification. In three populations, mutations in the ALS gene conferring resistance were detected. The Trp574Leu mutation was detected in approximately half of the individuals from the Albelda, Tamarite de Litera, and Caspe populations. In the latter, the Pro197Thr mutation was also present. This study reveals significant genetic variability within each population and provides evidence for the spread of herbicide resistance across different regions of Spain. Full article

(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)

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21 pages, 2620 KiB

Open AccessArticle

Sugar and Free Amino Acid Contents in Winter Wheat Flour Under Fusarium Head Blight Treatment and Natural Infection

by Valentina Španić, Beka Sarić, Katarina Šunić Budimir, Jurica Duvnjak and Slađana Žilić

Plants 2025, 14(10), 1504; https://doi.org/10.3390/plants14101504 (registering DOI) - 16 May 2025

Abstract

Fusarium head blight (FHB) is one of the most devastating diseases in wheat. Besides its negative impact on grain yield, FHB also negatively influences quality. Changes in sugar and free amino acid content were analyzed in flour from Fusarium-infected and non-infected grains [...] Read more.

Fusarium head blight (FHB) is one of the most devastating diseases in wheat. Besides its negative impact on grain yield, FHB also negatively influences quality. Changes in sugar and free amino acid content were analyzed in flour from Fusarium-infected and non-infected grains of six wheat varieties differing in Fusarium resistance. The concentrations of sugars and free amino acids were determined using a high-performance liquid chromatography device. In flour from FHB-infected grains, the average total amount of fructose, glucose, maltose, total sugars, and total reducing sugars was significantly increased, compared to non-treated flour from the Tika Taka variety, which was the most FHB-susceptible. The total content of free amino acids in flour from FHB-infected varieties increased in proportion to their susceptibility. In Tika Taka, there was a significant increase in free amino acid content of about 46%, while a significant decrease of 16% was observed in the highly resistant Vulkan variety. A highly significant correlation was established between the degree of FHB susceptibility and the content of aspartic acid, glutamic acid, glutamine and histidine, glycine, alanine, methionine, valine, tryptophan, phenylalanine, leucine, and threonine. Most amino acids had strong positive correlations with each other, but among the sugars, only fructose and glucose content showed a strong positive correlation with specific amino acids that were induced by Fusarium infection. Overall, it can be concluded that FHB-susceptible varieties have a high risk of FHB infection, which results in the hydrolysis of sucrose into fructose and glucose, together with an increase in free amino acids, which deteriorates the quality of wheat. Full article

(This article belongs to the Section Plant Molecular Biology)

21 pages, 2813 KiB

Open AccessArticle

Fall and Winter Temperatures, Together with Spring Temperatures, Determine the First Flowering Date of Prunus armeniaca L

by Di Tang, Brady K. Quinn, Yunfeng Yang, Liang Guo, David A. Ratkowsky and Peijian Shi

Plants 2025, 14(10), 1503; https://doi.org/10.3390/plants14101503 (registering DOI) - 16 May 2025

Abstract

Chilling and spring temperature accumulation are both considered key factors determining the timing of the spring bloom in many flowering plants. The accumulated developmental progress (ADP) method predicted the first flowering date (FFD) of a species of Rosaceae well in a previous study. [...] Read more.

Chilling and spring temperature accumulation are both considered key factors determining the timing of the spring bloom in many flowering plants. The accumulated developmental progress (ADP) method predicted the first flowering date (FFD) of a species of Rosaceae well in a previous study. However, whether this approach can be applied to other species, and whether the prediction errors in FFD based on the ADP method can be further accounted for by fall and winter temperatures (FWTs), remains unknown. The ADP method and two others were tested using a 39-year apricot FFD data series. The goodness of fit obtained with each method was assessed using the root mean square error (RMSE) between the observed and predicted FFDs. We used the residuals obtained using the ADP method as a response variable to fit generalized additive models (GAMs) including six FWTs as predictors. The GAMs generated based on different combinations of predictors were compared using Akaike’s information criterion (AIC) to test whether using FWTs can reduce prediction error. The ADP method had the lowest RMSE, which equaled 3.0904 days. Together, the number of cold days, the number of chilling hours, the mean value of the daily maximum temperatures, and the mean value of the daily mean temperatures from 1 November of the preceding year to the starting date accounted for 96% of the deviance in the residuals obtained using the ADP method. Including these predictors reduced the RMSE to 0.6162 days. The ADP method is a valid technique to quantify the effect of spring temperatures from a given starting date on the FFD. The FWTs and the number of cold days can also influence the FFD. The present work provides evidence that FWTs including daily maximum temperatures and spring mean temperatures together determine the FFD of apricot. Full article

(This article belongs to the Section Plant Modeling)

17 pages, 3526 KiB

Open AccessArticle

Indole-3-Butyric Acid Enhances Root Formation and Alleviates Low-Temperature Stress in Sugarcane: Molecular Insights and Identification of Candidate Genes

by Xiao-Qiu Zhang, Yong-Jian Liang, Xiu-Peng Song, Mei-Xin Yan, Li-Qiu Tang, Zhen-Qiang Qin, Yu-Xin Huang, De-Wei Li, Dong-Mei Huang, Ze-Sheng Shi, Bao-Qing Zhang and Dong-Liang Huang

Plants 2025, 14(10), 1502; https://doi.org/10.3390/plants14101502 (registering DOI) - 16 May 2025

Abstract

Sugarcane (Saccharum officinarum L.) faces significant challenges in China, including labor-intensive cultivation, low yields, and environmental stresses. Enhancing root development and stress tolerance through phytohormones and molecular breeding is a promising approach to boosting productivity. Indole-3-butyric acid is a phytohormone known for [...] Read more.

Sugarcane (Saccharum officinarum L.) faces significant challenges in China, including labor-intensive cultivation, low yields, and environmental stresses. Enhancing root development and stress tolerance through phytohormones and molecular breeding is a promising approach to boosting productivity. Indole-3-butyric acid is a phytohormone known for promoting root development and stress resistance. However, its effects on sugarcane root development under low temperature remain poorly understood. This study demonstrated that IBA markedly promoted root initiation, elongation, and biomass under low temperature, and significantly increased the levels of phytohormones, including GA₃, ABA, JA, IAA, and ZT, suggesting the activation of multiple signaling pathways. Transcriptome analysis revealed numerous differentially expressed genes related to metabolic pathways such as glycolysis, the tricarboxylic acid cycle, and glutathione metabolism. Weighted gene co-expression network analysis identified core gene modules correlated with phytohormone activities, highlighting their role in the IBA-mediated stress response. Eleven core genes, including GSTU6, FAR1, and BCAT3, and nine hub genes, such as Ub-CEP52-1 and ACS1, were identified as critical components for IBA-induced root development and stress mitigation. These findings provide insights into the molecular mechanisms underlying IBA-induced root development and stress tolerance in sugarcane, offering candidate genes for breeding high-yield, stress-tolerant varieties and demonstrating IBA’s potential as a strategy to enhance productivity under challenging conditions. Full article

(This article belongs to the Special Issue Sugarcane Breeding and Biotechnology for Sustainable Agriculture)

21 pages, 14511 KiB

Open AccessArticle

Identification of a Specific Role of Dihydrozeatin in the Regulation of the Cell Differentiation Activity in Arabidopsis Roots

by Federico Vinciarelli, Mirko De Vivo, Alessio Terenzi, Francesca Cazzaniga, Samuele Amati, Pierpaolo Damato, Elena Salvi, Marta Del Bianco, Riccardo Di Mambro, Paolo Costantino, Sabrina Sabatini and Raffaele Dello Ioio

Plants 2025, 14(10), 1501; https://doi.org/10.3390/plants14101501 - 16 May 2025

Abstract

The plant hormones cytokinins are a class of heterogeneous active compounds that control multiple aspects of development and physiology. Among cytokinins, trans-zeatin (tZ), the most abundant cytokinin, has been extensively studied in relation to its effects on development, and it plays [...] Read more.

The plant hormones cytokinins are a class of heterogeneous active compounds that control multiple aspects of development and physiology. Among cytokinins, trans-zeatin (tZ), the most abundant cytokinin, has been extensively studied in relation to its effects on development, and it plays a key role in promoting cell differentiation. In analogy with tZ, here we demonstrate that dihydrozeatin (DHZ) controls (root) development by promoting cell differentiation. By means of pharmacological and genetic analysis, we demonstrate that DHZ is specifically and uniquely perceived by the histidine kinase (HK) receptor AHK3, and that this interaction is sufficient to promote cell differentiation in the root meristem via activation of the transcription factors ARABIDOPSIS RESPONSE REGULATOR 1, 12, and 11. We also show that DHZ and tZ activity might be conserved among plants. Our results support the idea that different types of cytokinins act via specific receptors to exert their roles and suggest new approaches to study their activity in differentiation. Full article

(This article belongs to the Special Issue The Molecular Basis of Plant Developmental Diversity)

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18 pages, 942 KiB

Open AccessReview

Analysis of Electrome as a Tool for Plant Monitoring: Progress and Perspectives

by Elizaveta Kozlova, Lyubov Yudina, Ekaterina Sukhova and Vladimir Sukhov

Plants 2025, 14(10), 1500; https://doi.org/10.3390/plants14101500 - 16 May 2025

Abstract

In recent years, the electromic approach, which is based on the ‘electrome’ concept, to the analysis of electrical activity in plants has become increasingly relevant, as it can allow the detection of early signs of stress and the classification of external factors on [...] Read more.

In recent years, the electromic approach, which is based on the ‘electrome’ concept, to the analysis of electrical activity in plants has become increasingly relevant, as it can allow the detection of early signs of stress and the classification of external factors on the basis of complex, systemic changes in electrical parameters. However, the mechanisms underlying the observed complex effects remain unresolved. This review describes the main electrical signals in plants and their influence on physiological processes and tolerance to abiotic stressors, discusses limitations of traditional methods of investigation of electrical activity, summarizes modern strategies for electrome analysis, and considers the prospect of applying mathematical modeling to interpret the electromic data. We suggest that the integration of the electromic approach and mathematical modeling can greatly enhance the ability to investigate plant electrical signaling, opening new ways for fundamental and applied research in plant electrophysiology. Full article

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

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Graphical abstract

13 pages, 2134 KiB

Open AccessArticle

Digitally Quantifying Growth and Verdancy of Lolium Plants In Vitro

by Mara B. Depetris, Adam M. Dimech and Kathryn M. Guthridge

Plants 2025, 14(10), 1499; https://doi.org/10.3390/plants14101499 - 16 May 2025

Abstract

The image analysis of plants provides an opportunity to measure changes in growth and physiology quantitatively, and non-destructively, over time providing significant advantages over traditional methods of assessment which often rely on qualitative and subjective measures to distinguish between different treatments or genotypes [...] Read more.

The image analysis of plants provides an opportunity to measure changes in growth and physiology quantitatively, and non-destructively, over time providing significant advantages over traditional methods of assessment which often rely on qualitative and subjective measures to distinguish between different treatments or genotypes in an experiment. Image analysis techniques are commonly deployed for the analysis of plants in the field or glasshouse, but few studies have demonstrated the use of image analysis to phenotype plants grown under aseptic conditions in culture media. Lolium × hybridum Hausskn ‘Shogun’ plants were germinated in vitro and cultured on media containing combinations of thidiazuron [1-phenyl-3-(1,2,3-thiadiazol-5-yl) urea] (TDZ), N6-benzylaminopurine (BA) and gibberellic acid (GA3) or on phytohormone-free control media. RGB images were taken of the plants throughout the experiment and morphological image analysis techniques were used to quantify changes in plant development. A novel approach to quantitatively measure ’greenness‘ in plants using the CIELAB colour model (L*a*b) colour space from RGB images was developed. This methodology could be utilised to develop improved in vitro growth protocols for Lolium and grass species with similar morphology. Full article

(This article belongs to the Special Issue Modeling of Plants Phenotyping and Biomass)

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21 pages, 1788 KiB

Open AccessArticle

Microstructure and Microorganisms Alternation of Paddy Soil: Interplay of Biochar and Water-Saving Irrigation

by Jiazhen Hu, Shihong Yang, Wim M. Cornelis, Mairan Zhang, Qian Huang, Haonan Qiu, Suting Qi, Zewei Jiang, Yi Xu and Lili Zhu

Plants 2025, 14(10), 1498; https://doi.org/10.3390/plants14101498 - 16 May 2025

Abstract

Biochar application and controlled irrigation (CI) enhance water conservation, lower emissions, and increase crop yields. However, the synergistic effects on the relationship between paddy soil microstructure and microbiome remain poorly understood. This study investigates the impact of different irrigation regimes and biochar applications [...] Read more.

Biochar application and controlled irrigation (CI) enhance water conservation, lower emissions, and increase crop yields. However, the synergistic effects on the relationship between paddy soil microstructure and microbiome remain poorly understood. This study investigates the impact of different irrigation regimes and biochar applications on soil physicochemical properties, soil microstructure, and the composition and functions of soil microorganisms in paddy soil. The CA treatment (CI with 60 t/hm² biochar) showed higher abundances of Mycobacteriaceae, Streptomycetaceae, Comamonadaceae, and Nocardioidaceae than the CK treatment (CI without biochar), which was attributed to two main factors. First, CA increased the pore throat equivalent radius (EqR), throat surface area (SAR), total throat number (TTN), volume fraction (VF), and connected porosity (CP) by 1.47–9.61%, 7.50–25.21%, 41.55–45.99%, 61.12–73.04%, and 46.36–93.75%, respectively, thereby expanding microbial habitats and providing refuges for microorganisms. Second, CA increased the cation exchange capacity (CEC), mean weight diameter (MWD), soil organic carbon (SOC), and total nitrogen (TN) by 22.14–25.06%, 42.24–56.61%, 22.98–56.5%, and 9.41–87.83%, respectively, reinforcing soil structural stability and carbon storage, which promoted microbial community diversity. FK (flood irrigation without biochar) showed no significant correlations with these environmental factors. Compared to CK soil metabolites at Level 2 and Level 3, FK exhibited higher levels of the citrate cycle, indicating that changes in water and oxygen environments due to CI reduced soil organic matter decomposition and carbon cycle. CA and CK strongly correlated with the soil microstructure (VF, CP, TTN, SAR, EqR), and CA notably enhanced soil metabolites related to the synthesis and degradation of ketone bodies, suggesting that biochar can mitigate the adverse metabolomic effects of CI. These results indicate that biochar application in CI paddy fields highlights the critical role of soil microstructure in microbial composition and function and better supports soil sustainability. Full article

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

15 pages, 13242 KiB

Open AccessArticle

Genetic Diversity and Connectivity of Reef-Building Halimeda macroloba in the Indo-Pacific Region

by Xiaohan Song, Jianting Yao, Michael Y. Roleda, Yanshuo Liang, Rui Xu, Yude Lin, Shienna Mae C. Gonzaga, Yuqun Du and Delin Duan

Plants 2025, 14(10), 1497; https://doi.org/10.3390/plants14101497 - 16 May 2025

Abstract

Understanding population genetic connectivity is crucial for the sustainability and persistence of marine biodiversity. As a fundamental reef-building macroalga of the coastal ecosystem, Halimeda macroloba Decaisne is one of the dominant intertidal seaweeds in the Indo-Pacific region. However, its genetic structure and population [...] Read more.

Understanding population genetic connectivity is crucial for the sustainability and persistence of marine biodiversity. As a fundamental reef-building macroalga of the coastal ecosystem, Halimeda macroloba Decaisne is one of the dominant intertidal seaweeds in the Indo-Pacific region. However, its genetic structure and population connectivity have been poorly recognized. Here, we explored the population genetic structure and genetic connectivity of H. macroloba using chloroplast tufA, rps3-rpl14, and rbcL. Our results indicated low genetic diversity and shallow population genetic structure at the intraspecific level, uncovering five genetic groups with six subdivided lineages in tufA and two genetic clusters in rps3-rpl14. We detected demographic expansion in the last glacial period of the Pleistocene and significantly asymmetric gene flow among different geographical units. We suggest that the southwestward ocean currents under the influence of northeast monsoon in the Indo-Pacific region are the main factor in shaping the present genetic structure, and the asexual reproduction of H. macroloba also plays an important role of the low genetic diversity pattern; in addition, the divergence between genetic clusters might be related to the historical isolation led by the paleoclimate oscillation in the Pleistocene. The Xisha Islands in the northern South China Sea might serve as a potential refugium of H. macroloba, which needs extra attention to conservation management. Given the limitation of sample size, we need to conduct more field work and carry out further research at a larger scale in the future. Our study provided new insights into the theory of population connectivity in the Indo-Pacific region and provided scientific basis for tropical costal seaweed conservation. Full article

(This article belongs to the Special Issue Epigenetics, Ecology and Evolution in Algae)

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14 pages, 7203 KiB

Open AccessArticle

Is Self-Incompatibility Related to Nectar Presence in Dendrobium?

by Karolina Zielińska, Kamil Kisło, Piotr Dobrzyński, Kevin L. Davies and Małgorzata Stpiczyńska

Plants 2025, 14(10), 1496; https://doi.org/10.3390/plants14101496 - 16 May 2025

Abstract

Studies on the gain or loss of nectar during the course of evolution in Dendrobium Sw. (Orchidaceae) are able to provide important information concerning the reproductive biology of this enormous orchid genus and highlight reproductive barriers—in particular, changes to compatibility. By employing a [...] Read more.

Studies on the gain or loss of nectar during the course of evolution in Dendrobium Sw. (Orchidaceae) are able to provide important information concerning the reproductive biology of this enormous orchid genus and highlight reproductive barriers—in particular, changes to compatibility. By employing a literature search on the compatibility system of Dendrobium, supplemented by new experimental data of 13 taxa investigated by means of microscopy, histochemistry, and phylogenetic analysis, we aimed to ascertain whether there is, in this genus, a relationship between self-compatibility (SC) and the presence of nectar. Nectariferous plant species are thought to be visited more frequently by pollinators, resulting in geitonogamy or selfing; therefore, the presence of nectar in some Dendrobium species may promote self-incompatibility (SI), whereas a lack of nectar may increase cross-pollination. Our investigations confirmed that the capacity for nectar secretion was gained and lost several times in this genus, and that similarly organized nectar spurs were present in all species investigated, regardless of their ability to produce nectar. SI, SC, and the presence or absence of nectar have all evolved independently, but, of the 42 taxa investigated whose status both relating to nectar presence and compatibility was known, nectar was more frequent in self-incompatible taxa. Full article

(This article belongs to the Section Plant Systematics, Taxonomy, Nomenclature and Classification)

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16 pages, 1526 KiB

Open AccessArticle

Combination of Nanobioproduct and Chemical Ethylene Synthesis Inhibitor with Entomopathogenic Fungi: A Novel Management Strategy for Coffee Berry Borer in Arabica Coffee

by Lilian F. Sousa, Ana P. A. Antunes, Maísa M. Moreira, Érika H. Arantes, Ezequiel G. Souza, Bruno H. S. Souza, Tatiana Cardoso e Bufalo, Camila G. Freitas, Caroline Dambroz and Joyce Dória

Plants 2025, 14(10), 1495; https://doi.org/10.3390/plants14101495 - 16 May 2025

Abstract

Brazil is the leading producer and exporter of coffee, accounting for more than one-third of global production. However, the coffee berry borer (CBB), Hypothenemus hampei, poses a significant threat to coffee yield and quality. Its control has been primarily based on the [...] Read more.

Brazil is the leading producer and exporter of coffee, accounting for more than one-third of global production. However, the coffee berry borer (CBB), Hypothenemus hampei, poses a significant threat to coffee yield and quality. Its control has been primarily based on the use of chemical insecticides, which entail risks to human health and the environment. We evaluated the efficacy of an ethylene synthesis inhibitor and a Bacillus subtilis-based nanobioproduct combined with entomopathogenic fungi against the CBB. The treatments included combinations of potassium phosphate-based and nanobioproduct-based bioregulators, bioinsecticide comprising Beauveria bassiana + Metarhizium anisopliae, and chemical insecticides (acetamiprid + bifenthrin). The experiment included an in vitro assay assessing the reproduction of CBB females on treated coffee berries and a field trial evaluating the impact of the treatments on coffee bean quality, beverage sensory attributes, and antioxidant enzyme activities. All insecticide treatments, except the bioregulator at 6 L ha⁻¹ + insecticides, significantly reduced larvae production. The 6 L ha⁻¹ bioregulator treatment reduced bean defects. The fungi + insecticide treatment increased superoxide dismutase activity, while ascorbate peroxidase activity was highest in the control, followed by the fungi + nanobioproduct treatment group. The nanobioproduct bioregulator combined with entomopathogenic fungi proved to be an efficient strategy for managing the CBB. Full article

(This article belongs to the Special Issue Biosynthesis of Nanoparticles: A New Approach Between Nanotechnology and Plant Bioinputs)

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17 pages, 1473 KiB

Open AccessArticle

Phosphite Compounds Suppress Anthracnose in Soybean Seeds Infected by Colletotrichum truncatum and Stimulate Growth and Defense Mechanisms

by Manoel Batista da Silva Júnior, Mário Lúcio Vilela de Resende, Edson Ampélio Pozza, Alexandre Ribeiro Maia de Resende, Gustavo César Dias Silveira, Jayne Deboni da Veiga, Júlia Marques Oliveira and André Costa da Silva

Plants 2025, 14(10), 1494; https://doi.org/10.3390/plants14101494 - 16 May 2025

Abstract

Soybean is one of the main agricultural commodities, and its productivity is limited by several diseases, such as anthracnose, which is caused by a complex of fungal species, with Colletotrichum truncatum being the most prevalent. Management is mainly carried out through chemical seed [...] Read more.

Soybean is one of the main agricultural commodities, and its productivity is limited by several diseases, such as anthracnose, which is caused by a complex of fungal species, with Colletotrichum truncatum being the most prevalent. Management is mainly carried out through chemical seed treatment. However, a reduction in the sensitivity of C. truncatum to fungicides was observed. Therefore, it is extremely important to search for products that are effective in controlling the disease. The objectives of this study were to evaluate the efficacy of commercial formulations of copper, potassium, manganese, and zinc phosphites in the treatment of soybean seeds infected by C. truncatum, as well as their direct fungitoxicity and ability to induce soybean defense mechanisms. For this purpose, seeds inoculated with C. truncatum were subjected to phosphites and a fungicide (carbendazim + thiram). The seeds were exposed to germination, health, and vigor tests. Fungal toxicity and the ability of phosphites to induce defense through the activities of catalase, peroxidase, and superoxide dismutase enzymes, as well as the levels of lignin and total soluble phenols, were also evaluated. Mn and Zn phosphites showed direct toxicity to C. truncatum and were as effective as the fungicide (carbendazim + thiram) in treating soybean seeds infected by the fungus. Mn phosphite induced the production of catalase (CAT), peroxidase (POX) and lignin, while Zn phosphite increased the production of CAT and POX. These results demonstrate the efficacy of Mn and Zn phosphites in controlling C. truncatum in infected soybean seeds, their direct toxic action, and their ability to induce resistance. Full article

(This article belongs to the Special Issue Genetic Research on Soybean Response to Adversity Stress and Disease Stress)

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13 pages, 3321 KiB

Open AccessArticle

Molecular Genotyping by 20K Gene Arrays (Genobait) to Unravel the Genetic Structure and Genetic Diversity of the Puccinia striiformis f. sp. tritici Population in the Eastern Xizang Autonomous Region

by Mudi Sun, Wenbin Chen, Qianrong Yong, Xinyu Kong, Xue Qiu and Jie Zhao

Plants 2025, 14(10), 1493; https://doi.org/10.3390/plants14101493 - 16 May 2025

Abstract

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to wheat production in China. Previous epidemic studies have demonstrated the potential of high genetic diversity in the southwest regions of China. Among this epidemic region, [...] Read more.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to wheat production in China. Previous epidemic studies have demonstrated the potential of high genetic diversity in the southwest regions of China. Among this epidemic region, the eastern Xizang (Tibet) region holds particular significance, as both wheat and barley crops are susceptible to Pst. However, limited information exists regarding the level of population genetic diversity, reproduction model, and migration patterns of the rust in eastern Xizang. The present study seeks to address this gap by analyzing 146 Pst isolates collected from the Basu, Zuogong, and Mangkang regions, genotyping by the 20K target Gene Array (Genobait). Our results showed relatively low genotypic diversity in the Basu region, while the highest genetic diversity was observed in the Mangkang area. Structural analysis revealed the abundance of admixed groups in Mangkang, which exhibited this population occurred due to sexual recombination between two different ancestor groups. Gene flow was observed between Zuogong and Basu populations, but it almost did not occur between Mangkang and Zuogong/Basu populations. This region is the world’s highest-altitude epidemic area, thus facilitating the evolution of the rust and possessing the potential to transmit newly evolved Pst races to lower wheat-growing regions. Implementing disease management strategies in this area is of potential importance to prevent the transmission of Pst races to other parts of Xizang, even neighboring regions possibly. This study facilitates our understanding of epidemiological and population genetic knowledge and the evolution of Pst in Xizang. Full article

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

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21 pages, 2401 KiB

Open AccessReview

Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics

by Eyob Kassaye Wolella, Zhen Cheng, Mengyuan Li, Dandan Xia, Jianwei Zhang, Liu Duan, Li Liu, Zhiyong Li and Jian Zhang

Plants 2025, 14(10), 1492; https://doi.org/10.3390/plants14101492 - 16 May 2025

Abstract

Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50–80% of the daily calorie intake. The completion of rice genome sequencing marks a significant milestone in understanding functional genomics, yet the systematic identification of gene [...] Read more.

Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50–80% of the daily calorie intake. The completion of rice genome sequencing marks a significant milestone in understanding functional genomics, yet the systematic identification of gene functions remains a bottleneck for rice improvement. Large-scale mutant libraries in which the functions of genes are lost or gained (e.g., through chemical/physical treatments, T-DNA, transposons, RNAi, CRISPR/Cas9) have proven to be powerful tools for the systematic linking of genotypes to phenotypes. So far, using different mutagenesis approaches, a million mutant lines have been established and about 5–10% of the predicted rice gene functions have been identified due to the high demands of labor and low-throughput utilization. DNA-barcoding-based large-scale mutagenesis offers unprecedented precision and scalability in functional genomics. This review summarizes large-scale loss-of-function and gain-of-function mutant library development approaches and emphasizes the integration of DNA barcoding for pooled analysis. Unique DNA barcodes can be tagged to transposons/retrotransposons, DNA constructs, miRNA/siRNA, gRNA, and cDNA, allowing for pooling analysis and the assignment of functions to genes that cause phenotype alterations. In addition, the integration of high-throughput phenotyping and OMICS technologies can accelerate the identification of gene functions. Full article

(This article belongs to the Special Issue Crop Improvement by Modern Breeding Strategies)

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16 pages, 3469 KiB

Open AccessArticle

Phenotypic Characters and Inheritance Tendency of Agronomic Traits in F1 Progeny of Pear

by Xiaojie Zhang, Mengyue Tang, Jiamei Li, Yue Chi, Kexin Wang, Jianying Peng and Yuxing Zhang

Plants 2025, 14(10), 1491; https://doi.org/10.3390/plants14101491 - 16 May 2025

Abstract

Studying fruit genetic trends, heterosis, and growth traits in pear hybrid progeny provides the foundation for variety breeding. The aim of this research is to reveal the trait performance of the hybrid progeny of Chinese white pear and Western pear and provide a [...] Read more.

Studying fruit genetic trends, heterosis, and growth traits in pear hybrid progeny provides the foundation for variety breeding. The aim of this research is to reveal the trait performance of the hybrid progeny of Chinese white pear and Western pear and provide a theoretical basis for other breeders to predict the trait performance of their hybrid progeny when selecting Eastern pear and Western pear as parents. Our research team constructed a ‘Yuluxiang’ × ‘Xianghongli’ interspecific hybrid population in 2015, and in 2023, we conducted a two-year investigation of 16 traits in 140 hybrid progeny, including 11 fruit traits and 5 growth traits, and analyzed and compared the genetic variation and heterosis of traits, as well as the correlation between various traits. The results showed that the hybrid progeny was widely segregated for single fruit weight (FW), soluble solid (SS) content, and titratable acid (TA) content and conformed to a normal distribution, with quantitative genetic traits under polygenic control. The highest two-year coefficients of variation for TA were 54.42% in 2023 and 39.17% in 2024. A genetic trend of decreasing FW was observed, which was greatly influenced by the male sex. The ratio of soft soluble flesh to crispy flesh was 1:1, and the gene controlling this trait may be a quality trait controlled by a single gene. The traits that showed transgressive heterosis for two years included fruit longitudinal diameter (FLoD), fruit shape index (FSI), and TA, and those that showed negative heterosis included FW, SS, leaf longitudinal diameter (LLoD), and leaf lateral diameter (LLaD). Correlation analysis indicated that the progeny of crosses in this combination, which had red fruit skin, may also present red early flowering color (EFC) and young leaf color (YLC), reddish brown annual branch color (ABC), and lower FSI, fruit stalk length (FSL), LLaD, and TA. Thus, at the seedling stage, individuals with red-colored fruit may be screened by observing the color of young leaves and young stems and the lateral diameter of the leaves. Principal component analysis showed that among the 16 traits included in six principal components, peel color (PC), FLoD, 2024SS, fruit tape (FT), and FSI were the main factors causing differences in fruit phenotypes. This study systematically elucidated the genetic trends of agronomic traits in pears and will provide a theoretical basis for the selection of parents and early selection of hybrid progeny in pear hybrid breeding. Full article

(This article belongs to the Special Issue Trends in Research on Plant Genetic Resources: Insects, Plant Diseases, and Genetic Diversity)

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14 pages, 1327 KiB

Open AccessArticle

Fruit and Fruit-Derived Products of Selected Sambucus Plants as a Source of Phytosterols and Triterpenoids

by Otgonbileg Onolbaatar, Soyol Dashbaldan, Cezary Pączkowski and Anna Szakiel

Plants 2025, 14(10), 1490; https://doi.org/10.3390/plants14101490 - 16 May 2025

Abstract

Plant-derived foods have gained recognition for their health-promoting values, which are largely attributed to bioactive compounds such as phytosterols and triterpenoids. This study aimed to analyze the content of these compounds in the fruit of black elder (elderberry) Sambucus nigra L. and in [...] Read more.

Plant-derived foods have gained recognition for their health-promoting values, which are largely attributed to bioactive compounds such as phytosterols and triterpenoids. This study aimed to analyze the content of these compounds in the fruit of black elder (elderberry) Sambucus nigra L. and in commercially available food products, including jam, juice, syrup and wine. An additional objective was to compare the phytosterol and triterpenoid profiles of fruits and fruit cuticular waxes from wild and cultivated elderberry (cultivar Haschberg), ornamental elderberry (S. nigra f. porphyrophylla cultivar Black lace “Eva”), and red elderberry (S. racemosa). Qualitative and quantitative determinations were performed using gas chromatography coupled with mass spectrometry (GC-MS). This study provides a detailed characterization of triterpenoids in black and red elderberries, revealing a complex composition of oleanane-, 18-oleanane-, ursane-, lupane- and taraxastane-type compounds. Elderberry fruits were found to be rich sources of phytosterols (ranging from 0.54 mg/g d.w. in cultivated elderberry cv. Haschberg to 0.96 mg/g in ornamental elderberry) and triterpenoids (from 1.41 mg/g d.w. in S. racemosa to 13.81 mg/g in ornamental elderberry). Among the processed products, jam contained the highest concentration of these compounds (a total of 340 µg/g) and wine contained the lowest (0.87 µg/mL). Furthermore, the results suggest that certain features of the triterpenoid profile in S. nigra and S. racemosa may hold chemotaxonomic significance for the Sambucus genus. Full article

(This article belongs to the Special Issue Valuable Sources of Bioactive Natural Products from Plants, 2nd Edition)

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