BBC Russian

21 pages, 16292 KiB

Open AccessArticle

Unveiling the Neem (Azadirachta indica) Effects on Biofilm Formation of Food-Borne Bacteria and the Potential Mechanism Using a Molecular Docking Approach

by Ghada Abd-Elmonsef Mahmoud, Nahed M. Rashed, Sherif M. El-Ganainy and Shimaa H. Salem

Plants 2024, 13(18), 2669; https://doi.org/10.3390/plants13182669 - 23 Sep 2024

Viewed by 364

Abstract

Biofilms currently represent the most prevalent bacterial lifestyle, enabling them to resist environmental stress and antibacterial drugs. Natural antibacterial agents could be a safe solution for controlling bacterial biofilms in food industries without affecting human health and environmental safety. A methanolic extract of [...] Read more.

Biofilms currently represent the most prevalent bacterial lifestyle, enabling them to resist environmental stress and antibacterial drugs. Natural antibacterial agents could be a safe solution for controlling bacterial biofilms in food industries without affecting human health and environmental safety. A methanolic extract of Azadirachta indica (neem) leaves was prepared and analyzed using gas chromatography–mass spectrometry for the identification of its phytochemical constituents. Four food-borne bacterial pathogens (Bacillus cereus, Novosphingobium aromaticivorans, Klebsiella pneumoniae, and Serratia marcescens) were tested for biofilm formation qualitatively and quantitatively. The antibacterial and antibiofilm properties of the extract were estimated using liquid cultures and a microtiter plate assay. The biofilm inhibition mechanisms were investigated using a light microscope and molecular docking technique. The methanolic extract contained 45 identified compounds, including fatty acids, ester, phenols, flavonoids, terpenes, steroids, and antioxidants with antimicrobial, anticancer, and anti-inflammatory properties. Substantial antibacterial activity in relation to the extract was recorded, especially at 100 μg/mL against K. pneumoniae and S. marcescens. The extract inhibited biofilm formation at 100 μg/mL by 83.83% (S. marcescens), 73.12% (K. pneumoniae), and 54.4% (N. aromaticivorans). The results indicate efficient biofilm formation by the Gram-negative bacteria S. marcescens, K. pneumoniae, and N. aromaticivorans, giving 0.74, 0.292, and 0.219 OD at 595 nm, respectively, while B. cereus was found to have a low biofilm formation potential, i.e., 0.14 OD at 595 nm. The light microscope technique shows the antibiofilm activities with the biofilm almost disappearing at 75 μg/mL and 100 μg/mL concentrations. This antibiofilm property was attributed to DNA gyrase inhibition as illustrated by the molecular docking approach. Full article

(This article belongs to the Special Issue Phytochemical and Biological Activity of Plant Extracts)

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41 pages, 5070 KiB

Open AccessReview

Insights into Chemical Diversity and Potential Health-Promoting Effects of Ferns

by Ashaimaa Y. Moussa, Jinhai Luo and Baojun Xu

Plants 2024, 13(18), 2668; https://doi.org/10.3390/plants13182668 - 23 Sep 2024

Viewed by 369

Abstract

The scientific community is focusing on how to enhance human health and immunity through functional foods, and dietary supplements are proven to have a positive as well as a protective effect against infectious and chronic diseases. Ferns act as a taxonomical linkage between [...] Read more.

The scientific community is focusing on how to enhance human health and immunity through functional foods, and dietary supplements are proven to have a positive as well as a protective effect against infectious and chronic diseases. Ferns act as a taxonomical linkage between higher and lower plants and are endowed with a wide chemical diversity not subjected to sufficient scrutinization before. Even though a wealth of traditional medicinal fern uses were recorded in Chinese medicine, robust phytochemical and biological investigations of these plants are lacking. Herein, an extensive search was conducted using the keywords ferns and compounds, ferns and NMR, ferns and toxicity, and the terms ferns and chemistry, lignans, Polypodiaceae, NMR, isolation, bioactive compounds, terpenes, phenolics, phloroglucinols, monoterpenes, alkaloids, phenolics, and fatty acids were utilized with the Boolean operators AND, OR, and NOT. Databases such as PubMed, Web of Science, Science Direct, Scopus, Google Scholar, and Reaxys were utilized to reveal a wealth of information regarding fern chemistry and their health-promoting effects. Terpenes followed by phenolics represented the largest number of isolated active compounds. Regarding the neuroprotective effects, Psilotium, Polypodium, and Dryopteris species possessed as their major phenolics component unique chemical moieties including catechins, procyanidins, and bioflavonoids. In this updated chemical review, the pharmacological and chemical aspects of ferns are compiled manifesting their chemical diversity in the last seven years (2017–2024) together with a special focus on their nutritive and potential health-promoting effects. Full article

(This article belongs to the Section Phytochemistry)

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17 pages, 4093 KiB

Open AccessArticle

Genetic Diversity of Tulipa alberti and T. greigii Populations from Kazakhstan Based on Application of Expressed Sequence Tag Simple Sequence Repeat Markers

by Moldir Yermagambetova, Shyryn Almerekova, Anna Ivashchenko, Yerlan Turuspekov and Saule Abugalieva

Plants 2024, 13(18), 2667; https://doi.org/10.3390/plants13182667 - 23 Sep 2024

Viewed by 290

Abstract

The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa [...] Read more.

The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa greigii Regel, which are critical for biodiversity yet face significant threats from human activities. This study aimed to assess these two species’ genetic diversity and population structure using 15 expressed sequence tag simple sequence repeat (EST-SSR) markers. Leaf samples from 423 individuals across 23 natural populations, including 11 populations of T. alberti and 12 populations of T. greigii, were collected and genetically characterized using EST-SSR markers. The results revealed relatively high levels of genetic variation in T. greigii compared to T. alberti. The average number of alleles per locus was 1.9 for T. alberti and 2.8 for T. greigii. AMOVA indicated substantial genetic variation within populations (75% for T. alberti and 77% for T. greigii). The Bayesian analysis of the population structure of the two species indicated an optimal value of K = 3 for both species, splitting all sampled populations into three distinct genetic clusters. Populations with the highest level of genetic diversity were identified in both species. The results underscore the importance of conserving the genetic diversity of Tulipa populations, which can help develop strategies for their preservation in stressed ecological conditions. Full article

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

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19 pages, 3319 KiB

Open AccessReview

Prion–like Proteins in Plants: Key Regulators of Development and Environmental Adaptation via Phase Separation

by Peisong Wu and Yihao Li

Plants 2024, 13(18), 2666; https://doi.org/10.3390/plants13182666 - 23 Sep 2024

Viewed by 429

Abstract

Prion–like domains (PrLDs), a unique type of low–complexity domain (LCD) or intrinsically disordered region (IDR), have been shown to mediate protein liquid–liquid phase separation (LLPS). Recent research has increasingly focused on how prion–like proteins (PrLPs) regulate plant growth, development, and stress responses. This [...] Read more.

Prion–like domains (PrLDs), a unique type of low–complexity domain (LCD) or intrinsically disordered region (IDR), have been shown to mediate protein liquid–liquid phase separation (LLPS). Recent research has increasingly focused on how prion–like proteins (PrLPs) regulate plant growth, development, and stress responses. This review provides a comprehensive overview of plant PrLPs. We analyze the structural features of PrLPs and the mechanisms by which PrLPs undergo LLPS. Through gene ontology (GO) analysis, we highlight the diverse molecular functions of PrLPs and explore how PrLPs influence plant development and stress responses via phase separation. Finally, we address unresolved questions about PrLP regulatory mechanisms, offering prospects for future research. Full article

(This article belongs to the Special Issue Responses of Plant Molecular Physiology to Environments)

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16 pages, 4638 KiB

Open AccessEssay

Effects of Fertilization and Planting Modes on Soil Organic Carbon and Microbial Community Formation of Tree Seedlings

by Sutong Fan, Yao Tang, Hongzhi Yang, Yuda Hu, Yelin Zeng, Yonghong Wang, Yunlin Zhao, Xiaoyong Chen, Yaohui Wu and Guangjun Wang

Plants 2024, 13(18), 2665; https://doi.org/10.3390/plants13182665 - 23 Sep 2024

Viewed by 625

Abstract

Biochar and organic fertilizer can significantly increase soil organic carbon (SOC) and promote agricultural production, but it is still unclear how they affect forest SOC after. Here, low-quality plantation soil was subjected to four distinct fertilization treatments: (CK, without fertilization; BC, tea seed [...] Read more.

Biochar and organic fertilizer can significantly increase soil organic carbon (SOC) and promote agricultural production, but it is still unclear how they affect forest SOC after. Here, low-quality plantation soil was subjected to four distinct fertilization treatments: (CK, without fertilization; BC, tea seed shell biochar alone; OF, tea meal organic fertilizer alone; BCF, tea seed shell biochar plus tea meal organic fertilizer). Cunninghamia lanceolata (Lamb.) Hook and Cyclobalanopsis glauca (Thunb.) Oersted seedlings were then planted in pots at the ratios of 2:0, 1:1, and 0:2 (SS, SQ, QQ) and grown for one year. The results showed that the BCF treatment had the best effect on promoting seedling growth and increasing SOC content. BCF changed soil pH and available nutrient content, resulting in the downregulation of certain oligotrophic groups (Acidobacteria and Basidiomycetes) and the upregulation of eutrophic groups (Ascomycota and Proteobacteria). Key bacterial groups, which were identified by Line Discriminant Analysis Effect Size analysis, were closely associated with microbial biomass carbon (MBC) and SOC. Pearson correlation analysis showed that bacterial community composition exhibited a positive correlation with SOC, MBC, available phosphorus, seedling biomass, and plant height, whereas fungal community composition was predominantly positively correlated with seedling underground biomass. It suggested that environmental differences arising from fertilization and planting patterns selectively promote microbial communities that contribute to organic carbon formation. In summary, the combination of biochar and organic fertilizers would enhance the improvement and adaptation of soil microbial communities, playing a crucial role in increasing forest soil organic carbon and promoting tree growth. Full article

(This article belongs to the Special Issue Mechanisms Regulating C, N, and P Storage, Cycle, and Stoichiometry in Plant Ecosystems under Climate Change)

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24 pages, 5391 KiB

Open AccessArticle

Viromes of Monocotyledonous Weeds Growing in Crop Fields Reveal Infection by Several Viruses Suggesting Their Virus Reservoir Role

by Zsuzsanna N. Galbács, Evans Duah Agyemang, György Pásztor, András Péter Takács and Éva Várallyay

Plants 2024, 13(18), 2664; https://doi.org/10.3390/plants13182664 - 23 Sep 2024

Viewed by 524

Abstract

In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, [...] Read more.

In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants in the same locations and determined their viromes using small RNA high-throughput sequencing (HTS). As a result, we have identified the presence of wheat streak mosaic virus (WSMV), barley yellow striate mosaic virus (BYSMV), barley virus G (BVG), and two additional viruses, namely Aphis glycines virus 1 (ApGlV1) and Ljubljana dicistrovirus 1 (LDV1), which are described for the first time in Hungary. New hosts of the viruses were identified: Cynodon dactylon is a new host of BYSMV and LDV1, Echinocloa crus-galli is a new host of BVG, ApGlV1 and LDV1, Sorghum halepense is a new host of ApGlV1, and Panicum miliaceum is a new host of LDV1. At the same time, Zea mays is a new host of ApGlV1 and LDV1. Small RNA HTS diagnosed acute infections but failed to detect persistent ones, which could be revealed using RT-PCR. The infection rates at the different locations and plant species were different. The phylogenetic analyses of the sequenced virus variants suggest that the tested monocotyledonous weeds can host different viruses and play a virus reservoir role. Viral spread from the reservoir species relies on the activity of insect vectors, which is why their management requires an active role in plant protection strategies, which need careful planning in the changing environment. Full article

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

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16 pages, 5278 KiB

Open AccessArticle

A Flowering Morphological Investigation, Fruit Fatty Acids, and Mineral Elements Dynamic Changes of Idesia polycarpa Maxim

by Yanpeng Wang, Cuiyu Liu, Jiasong Hu, Kaiyun Wu, Bangchu Gong and Yang Xu

Plants 2024, 13(18), 2663; https://doi.org/10.3390/plants13182663 - 23 Sep 2024

Viewed by 341

Abstract

Idesia polycarpa Maxim is a high-value species of fruit oil with edible, abundant linoleic acid and polyphenols. Idesia polycarpa is described as a dioecious species, and the flowers are male; female and bisexual flowers are produced on separate plants. In order to explore [...] Read more.

Idesia polycarpa Maxim is a high-value species of fruit oil with edible, abundant linoleic acid and polyphenols. Idesia polycarpa is described as a dioecious species, and the flowers are male; female and bisexual flowers are produced on separate plants. In order to explore the flower types of Idesia polycarpa, the morphology of its flowers and inflorescence were investigated in this study. The flower and inflorescence types, the diameter, and the flowering sequencing in male and female inflorescence were determined. We also detected the length, width, and fresh weight of leaves, shoots, and female inflorescence, as well as the length and fresh weight of the petiole during the development. Additionally, we compared the length, width, the length/width ratio, and the flowering density between 5- and 7-year-old female trees. The phenological period observation of Idesia polycarpa showed that the development process can be roughly divided into 12 stages, including bud burst, leaf expansion, inflorescence growth, initial flowering, full flowering, flower decline, initial fruiting, fruit enlargement, fruit color change, fruit ripening, post-ripening of fruit, and leaf fall periods. Furthermore, four elites’ fruit determined the oil content and the composition of fatty acid content during the development. The dynamic of fatty acids contents, the palrnitic acid, palmitoleic acid, stearic acid, oleic acid, and linolenic acid contents were detected during the fruit development of four elites. Moreover, the mineral elements content of fruit of four elites during development were determined. The patterns of vegetative and reproductive growth in young dioecious trees of Idesia polycarpa provided the theoretical basis for artificial pruning and training. Full article

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

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20 pages, 1768 KiB

Open AccessReview

Sesame, an Underutilized Oil Seed Crop: Breeding Achievements and Future Challenges

by Saeed Rauf, Taiyyibah Basharat, Adane Gebeyehu, Mohammed Elsafy, Mahbubjon Rahmatov, Rodomiro Ortiz and Yalcin Kaya

Plants 2024, 13(18), 2662; https://doi.org/10.3390/plants13182662 - 23 Sep 2024

Viewed by 702

Abstract

Sesame seeds and their edible oil are highly nutritious and rich in mono- and polyunsaturated fatty acids. Bioactive compounds such as sterols, tocopherols, and sesamol provide significant medicinal benefits. The high oil content (50%) and favorable mono- and polyunsaturated fatty acid balance, as [...] Read more.

Sesame seeds and their edible oil are highly nutritious and rich in mono- and polyunsaturated fatty acids. Bioactive compounds such as sterols, tocopherols, and sesamol provide significant medicinal benefits. The high oil content (50%) and favorable mono- and polyunsaturated fatty acid balance, as well as resilience to water stress, make sesame a promising candidate crop for global agricultural expansion. However, sesame production faces challenges such as low yields, poor response to agricultural inputs, and losses due to capsule dehiscence. To enhance yield, traits like determinate growth, dwarfism, a high harvest index, non-shattering capsules, disease resistance, and photoperiod sensitivity are needed. These traits can be achieved through variation or induced mutation breeding. Crossbreeding methods often result in unwanted genetic changes. The gene editing CRISPR/Cas9 technology has the potential to suppress detrimental alleles and improve the fatty acid profile by inhibiting polyunsaturated fatty acid biosynthesis. Even though sesame is an orphan crop, it has entered the genomic era, with available sequences assisting molecular breeding efforts. This progress aids in associating single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR) with key economic traits, as well as identifying genes related to adaptability, oil production, fatty acid synthesis, and photosynthesis. Additionally, transcriptomic research can reveal genes involved in abiotic stress responses and adaptation to diverse climates. The mapping of quantitative trait loci (QTL) can identify loci linked to key traits such as capsule size, seed count per capsule, and capsule number per plant. This article reviews recent advances in sesame breeding, discusses ongoing challenges, and explores potential strategies for future improvement. Hence, integrating advanced genomic tools and breeding strategies provides promising ways to enhance sesame production to meet global demands. Full article

(This article belongs to the Section Plant Genetic Resources)

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22 pages, 12133 KiB

Open AccessArticle

Abiotic Stress Effect on Agastache mexicana subsp. mexicana Yield: Cultivated in Two Contrasting Environments with Organic Nutrition and Artificial Shading

by Judith Morales-Barrera, Juan Reséndiz-Muñoz, Blas Cruz-Lagunas, José Luis Fernández-Muñoz, Flaviano Godínez-Jaimes, Tania de Jesús Adame-Zambrano, Mirna Vázquez-Villamar, Teollincacihuatl Romero-Rosales, María Teresa Zagaceta-Álvarez, Karen Alicia Aguilar-Cruz, Jorge Estrada-Martínez and Miguel Angel Gruintal-Santos

Plants 2024, 13(18), 2661; https://doi.org/10.3390/plants13182661 - 23 Sep 2024

Viewed by 295

Abstract

Research on medicinal plants is essential for their conservation, propagation, resistance to environmental stress, and domestication. The use of organic nutrition has been demonstrated to improve soil fertility and plant quality. It is also important to study the effects of the Basic Cation [...] Read more.

Research on medicinal plants is essential for their conservation, propagation, resistance to environmental stress, and domestication. The use of organic nutrition has been demonstrated to improve soil fertility and plant quality. It is also important to study the effects of the Basic Cation Saturation Ratio (BCSR) approach, which is a topic where there is currently controversy and limited scientific information. Evaluating the growth and yields of Agastache mexicana subsp. mexicana (Amm) in different environments is crucial for developing effective propagation and domestication strategies. This includes examining warm and subhumid environments with rain in summer in comparison to mild environments with summer rain. Significant differences were observed in the effects of cold, waterlogging, and heat stresses on the plant’s biomass yield and the morphometric-quantitative modeling by means of isolines. The biomass yield was 56% higher in environment one compared to environment two, 19% higher in environment one with organic nutrition, and 48% higher in environment two with organic nutrition compared to using only BCSR nutrition. In the second harvesting cycle, the plants in environment one did not survive, while the plants in environment two managed to survive without needing additional nutrition. Statistical and mathematical analyses provided information about the population or sample. Additionally, further analysis using isolines as a new approach revealed new insights into understanding phenology and growth issues. Full article

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

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17 pages, 4491 KiB

Open AccessArticle

Comparative Analysis of Water Stress Regimes in Avocado Plants during the Early Development Stage

by Tatiana Rondon, Manuel Guzmán-Hernández, Maria C. Torres-Madronero, Maria Casamitjana, Lucas Cano, July Galeano and Manuel Goez

Plants 2024, 13(18), 2660; https://doi.org/10.3390/plants13182660 - 23 Sep 2024

Viewed by 415

Abstract

The avocado cv. Hass requires a suitable rootstock for optimal development under water stress. This study evaluated the performance of two avocado rootstocks (ANRR88 and ANGI52) grafted onto cv. Hass under four water stress conditions, 50% and 25% deficit, and 50% and 25% [...] Read more.

The avocado cv. Hass requires a suitable rootstock for optimal development under water stress. This study evaluated the performance of two avocado rootstocks (ANRR88 and ANGI52) grafted onto cv. Hass under four water stress conditions, 50% and 25% deficit, and 50% and 25% excess during the nursery stage. Plant height, leaf area (LA), dry matter (DM), and Carbon (OC) content in the roots, stems, and leaves were measured. Root traits were evaluated using digital imaging, and three vegetation indices (NDVI, CI_RE, and MTCI) were used to quantify stress. The results showed that genotype significantly influenced the response to water stress. ANRR88 exhibited adaptation to moderate to high water deficits. ANGI52 adapted better to both water deficit and excess, and showed greater root exploration. LA and DM reductions of up to 60% were observed in ANRR88, suggesting a higher sensitivity to extreme changes in water availability. More than 90% of the total OC accumulation was observed in the stem and roots. The NDVI and the MTCI quantified the presence and levels of stress applied, and the 720 nm band provided high precision and speed for detecting stress. These insights are crucial for selecting rootstocks that ensure optimal performance under varying water availability, enhancing productivity and sustainability. Full article

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

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17 pages, 2969 KiB

Open AccessArticle

Characterization of Plant-Growth-Promoting Rhizobacteria for Tea Plant (Camellia sinensis) Development and Soil Nutrient Enrichment

by Mengjiao Wang, Haiyan Sun, Huiping Dai and Zhimin Xu

Plants 2024, 13(18), 2659; https://doi.org/10.3390/plants13182659 - 23 Sep 2024

Viewed by 283

Abstract

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties [...] Read more.

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants. Full article

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12 pages, 1456 KiB

Open AccessArticle

Advancements in Cold-Region Rice Breeding: The 4S Phenotypic-Design Breeding System and Its Applications in Heilongjiang

by Baohai Liu, Shoujun Nie, Shiwei Gao, Qing Liu, Yuqiang Liu, Fengchen Mu, Bo Zhang, Beiping Zhao, Hongru Gao, Licheng Wu, Minggang Xiao and Kun Li

Plants 2024, 13(18), 2658; https://doi.org/10.3390/plants13182658 - 23 Sep 2024

Viewed by 366

Abstract

Heilongjiang, located in the cold region, is China’s largest rice-producing and commercializing province. The variety selection of rice in cold regions (RCR) is indispensable in promoting the rice industry’s development, and technological innovation in breeding theory plays a significant role in breeding breakthrough. Based [...] Read more.

Heilongjiang, located in the cold region, is China’s largest rice-producing and commercializing province. The variety selection of rice in cold regions (RCR) is indispensable in promoting the rice industry’s development, and technological innovation in breeding theory plays a significant role in breeding breakthrough. Based primarily on long-term research, contemplation, and breeding practices, the 4S (selected topic, selected breeding, selected progenies, and selected promotion) phenotypic-design breeding technical system for RCR, which has revolutionized the theoretical basis and deepened the conceptual model, has been developed through systematic analyses and generalization. The system covers several key aspects such as scientific question formulation, breeding objective optimization, parental taxa hybridization, progeny population selection, and innovation dissemination, aiming to improve the foresight, precision, and efficiency of breeding. Furthermore, the system has demonstrated successful cases of rice variety breeding over the past 20 years, such as for Suijing 3, Suijing 4, Suijing 18, and a series of other rice varieties, providing theoretical and technical supports for cold-region rice breeding. Full article

(This article belongs to the Collection OMICs, Epigenetics and Genome Editing Techniques for Food and Nutritional Security)

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15 pages, 18012 KiB

Open AccessArticle

Impact of Quorum Sensing on the Virulence and Survival Traits of Burkholderia plantarii

by Minhee Kang, Duyoung Lee, Mohamed Mannaa, Gil Han, Haeun Choi, Seungchul Lee, Gah-Hyun Lim, Sang-Woo Kim, Tae-Jin Kim and Young-Su Seo

Plants 2024, 13(18), 2657; https://doi.org/10.3390/plants13182657 - 23 Sep 2024

Viewed by 326

Abstract

Quorum sensing (QS) is a mechanism by which bacteria detect and respond to cell density, regulating collective behaviors. Burkholderia plantarii, the causal agent of rice seedling blight, employs the LuxIR-type QS system, common among Gram-negative bacteria, where LuxI-type synthase produces QS signals [...] Read more.

Quorum sensing (QS) is a mechanism by which bacteria detect and respond to cell density, regulating collective behaviors. Burkholderia plantarii, the causal agent of rice seedling blight, employs the LuxIR-type QS system, common among Gram-negative bacteria, where LuxI-type synthase produces QS signals recognized by LuxR-type regulators to control gene expression. This study aimed to elucidate the QS mechanism in B. plantarii KACC18965. Through whole-genome analysis and autoinducer assays, the plaI gene, responsible for QS signal production, was identified. Motility assays confirmed that C8-homoserine lactone (C8-HSL) serves as the QS signal. Physiological experiments revealed that the QS-defective mutant exhibited reduced virulence, impaired swarming motility, and delayed biofilm formation compared to the wild type. Additionally, the QS mutant demonstrated weakened antibacterial activity against Escherichia coli and decreased phosphate solubilization. These findings indicate that QS in B. plantarii significantly influences various pathogenicity and survival traits, including motility, biofilm formation, antibacterial activity, and nutrient acquisition, highlighting the critical role of QS in pathogen virulence and adaptability. Full article

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

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30 pages, 4060 KiB

Open AccessArticle

Growth, Biochemical Traits, Antioxidant Enzymes, and Essential Oils of Four Aromatic and Medicinal Plants Cultivated in Phosphate-Mine Residues

by Khadija Ait Elallem, Widad Ben Bakrim, Abdelaziz Yasri and Ali Boularbah

Plants 2024, 13(18), 2656; https://doi.org/10.3390/plants13182656 - 22 Sep 2024

Viewed by 676

Abstract

Revegetation emerges as a promising approach to alleviate the adverse impacts of mining residues. However, it is essential to evaluate the characteristics of these materials and select suitable plant species to ensure successful ecosystem restoration. This study aimed to investigate the effects of [...] Read more.

Revegetation emerges as a promising approach to alleviate the adverse impacts of mining residues. However, it is essential to evaluate the characteristics of these materials and select suitable plant species to ensure successful ecosystem restoration. This study aimed to investigate the effects of phosphate-mine residues (MR) on the growth, biochemical properties, and essential oil concentration of Rosmarinus officinalis L., Salvia Officinalis L., Lavandula dentata L., and Origanum majorana L. The results showed that R. officinalis L. appeared to be particularly well-suited to thriving in MR soil. Our finding also revealed that L. dentata L., O. majorana L., and S. officinalis L. grown in MR exhibited significantly lower growth performance (lower shoot length, smaller leaves, and altered root structure) and higher antioxidant activities, with an alterations of photosynthetic pigment composition. They showed a decrease in total chlorophylls when grown on MR (0.295, 0.453, and 0.562 mg g⁻¹ FW, respectively) compared to the control (0.465, 0.807, and 0.808 mg g⁻¹ FW, respectively); however, they produced higher essential oil content (1.8%, 3.06%, and 2.88%, respectively). The outcomes of this study could offer valuable insights for the advancement of revegetation technologies and the utilization of plant products derived from phosphate-mine residues. Full article

(This article belongs to the Section Plant Ecology)

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18 pages, 11034 KiB

Open AccessArticle

Dual-Stream Architecture Enhanced by Soft-Attention Mechanism for Plant Species Classification

by Imran Ullah Khan, Haseeb Ali Khan and Jong Weon Lee

Plants 2024, 13(18), 2655; https://doi.org/10.3390/plants13182655 - 22 Sep 2024

Viewed by 347

Abstract

Plants play a vital role in numerous domains, including medicine, agriculture, and environmental balance. Furthermore, they contribute to the production of oxygen and the retention of carbon dioxide, both of which are necessary for living beings. Numerous researchers have conducted thorough research in [...] Read more.

Plants play a vital role in numerous domains, including medicine, agriculture, and environmental balance. Furthermore, they contribute to the production of oxygen and the retention of carbon dioxide, both of which are necessary for living beings. Numerous researchers have conducted thorough research in the classification of plant species where certain studies have focused on limited numbers of classes, while others have employed conventional machine-learning and deep-learning models to classify them. To address these limitations, this paper introduces a novel dual-stream neural architecture embedded with a soft-attention mechanism specifically developed for accurately classifying plant species. The proposed model utilizes residual and inception blocks enhanced with dilated convolutional layers for acquiring both local and global information. Following the extraction of features, both streams are combined, and a soft-attention technique is used to improve the distinct characteristics. The efficacy of the model is shown via extensive experimentation on varied datasets, including several plant species. Moreover, we have contributed a novel dataset that comprises 48 classes of different plant species. The results demonstrate a higher level of performance when compared to current models, emphasizing the capability of the dual-stream design in improving accuracy and model generalization. The integration of a dual-stream architecture, dilated convolutions, and soft attention provides a strong and reliable foundation for the botanical community, supporting advancement in the field of plant species classification. Full article

(This article belongs to the Section Plant Modeling)

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16 pages, 1741 KiB

Open AccessArticle

Water-Light Interaction and Its Effect on the Morphophysiology of Cedrela fissilis Vell. Seedlings

by Juliana Milene Silverio, Silvana de Paula Quintão Scalon, Cleberton Correia Santos, Jéssica Aline Linné, Anderson dos Santos Dias, Rodrigo da Silva Bernardes and Thaise Dantas

Plants 2024, 13(18), 2654; https://doi.org/10.3390/plants13182654 - 22 Sep 2024

Viewed by 314

Abstract

Plant responses to different light and water availability are variable among species and their respective phenotypic plasticity, and the combination between these two abiotic factors can alleviate or intensify stressful effects. This study aimed to evaluate the impacts of exposure time of Cedrela [...] Read more.

Plant responses to different light and water availability are variable among species and their respective phenotypic plasticity, and the combination between these two abiotic factors can alleviate or intensify stressful effects. This study aimed to evaluate the impacts of exposure time of Cedrela fissilis Vell. seedlings to different water and light availability considering natural radiation variations and the interaction of these factors. Seedlings were submitted to combinations of three shading levels—SH (0, 30 and 70%) and three water regimes based on the water holding capacity (WHC) in the substrate, constituting nine cultivation conditions: T1—0% SH + 40% WHC; T2—0% SH + 70% WHC; T3—0% SH + 100% WHC; T4—30% SH + 40% WHC; T5—30% SH + 70% WHC; T6—30% SH + 100% WHC; T7—70% SH + 40% WHC; T8—70% SH + 70% WHC; T9—70% SH + 100% WHC. C. fissilis seedlings are sensitive to water deficit, here represented by 40% WHC, regardless of exposure time, and when cultivated in full sun even though there are variations in radiation, the stressful effects were enhanced, acting in a synergistic manner. The condition that provided better gas exchange performance and greater total dry mass accumulation for C. fissilis seedlings was 30% shading combined with 100% WHC. C. fissilis seedlings have physiological plasticity and resilience to survive under different water and light conditions. Full article

(This article belongs to the Special Issue Physiology and Seedling Production of Plants)

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14 pages, 5392 KiB

Open AccessArticle

Phenotypic Analysis and Gene Cloning of Rice Floury Endosperm Mutant wcr (White-Core Rice)

by Yihao Yang, Xiaoyi Yang, Lingjun Wu, Zixing Sun, Yi Zhang, Ziyan Shen, Juan Zhou, Min Guo and Changjie Yan

Plants 2024, 13(18), 2653; https://doi.org/10.3390/plants13182653 - 22 Sep 2024

Viewed by 259

Abstract

The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting [...] Read more.

The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting in reduced grain weight. The total starch and amylose content remained unchanged, but the levels of the four component proteins in the mutant brown rice significantly decreased. Additionally, the milled rice (inner endosperm) showed a significant decrease in total starch and amylose content, accompanied by a nearly threefold increase in albumin content. The swelling capacity of mutant starch was reduced, and its chain length distribution was altered. The target gene was mapped on chromosome 5 within a 65 kb region. A frameshift mutation occurred due to an insertion of an extra C base in the second exon of the cyOsPPDKB gene, which encodes pyruvate phosphate dikinase. Expression analysis revealed that wcr not only affected genes involved in starch metabolism but also downregulated expression levels of genes associated with storage protein synthesis. Overall, wcr plays a crucial role as a regulator factor influencing protein synthesis and starch metabolism in rice grains. Full article

(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding)

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15 pages, 6972 KiB

Open AccessArticle

Metabolomics Revealed the Tolerance and Growth Dynamics of Arbuscular Mycorrhizal Fungi (AMF) to Soil Salinity in Licorice

by Li Fan, Chen Zhang, Jiafeng Li, Zhongtao Zhao and Yan Liu

Plants 2024, 13(18), 2652; https://doi.org/10.3390/plants13182652 - 22 Sep 2024

Viewed by 238

Abstract

Several studies have been devoted to seeking some beneficial plant-related microorganisms for a long time, and on this basis, it has been found that arbuscular mycorrhizal fungi (AMF) have a considerable positive impact on plant health as a biological fungal agent. In this [...] Read more.

Several studies have been devoted to seeking some beneficial plant-related microorganisms for a long time, and on this basis, it has been found that arbuscular mycorrhizal fungi (AMF) have a considerable positive impact on plant health as a biological fungal agent. In this study, we focused on the effects of different AMF on the growth dynamics and root configuration of licorice under saline and alkali conditions. The metabolites of licorice under different AMF were assessed using liquid chromatography–tandem mass spectrometry (LC-MS/MS). Funneliformis mosseae (Fm) and Rhizophagus intraradices (Ri) were added as different AMF treatments, while the sterilized saline–alkali soil was treated as a control. Samples were taken in the R1 period (15 d after AMF treatment) and the R2 period (45 d after AMF treatment). The results showed that the application of AMF significantly increased the root growth of licorice and significantly increased the biomass of both shoot and root. A total of 978 metabolites were detected and divided into 12 groups including lipids, which accounted for 15.44%; organic acids and their derivatives, at 5.83%; benzene compounds and organic heterocyclic compounds, at 5.42%; organic oxides, at 3.78%; and ketones, accounting for 3.17%. Compared with the control, there were significant changes in the differential metabolites with treatment inoculated with AMF; the metabolic pathways and biosynthesis of secondary metabolites were the main differential metabolite enrichment pathways in the R1 period, and those in the R2 period were microbial metabolism in diverse environments and the degradation of aromatic compounds. In conclusion, the use of AMF as biofertilizer can effectively improve the growth of licorice, especially in terms of the root development and metabolites, in saline–alkali soil conditions. Full article

(This article belongs to the Special Issue Role of Microbes in Alleviating Abiotic Stress in Plants)

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21 pages, 3338 KiB

Open AccessArticle

Biochemical and Epigenetic Regulation of Glutamate Metabolism in Maize (Zea mays L.) Leaves under Salt Stress

by Alexander T. Eprintsev, Galina B. Anokhina, Polina S. Selivanova, Polina P. Moskvina and Abir U. Igamberdiev

Plants 2024, 13(18), 2651; https://doi.org/10.3390/plants13182651 - 21 Sep 2024

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Abstract

The effect of salt stress (150 mM NaCl) on the expression of genes, methylation of their promoters, and enzymatic activity of glutamate dehydrogenase (GDH), glutamate decarboxylase (GAD), and the 2-oxoglutarate (2-OG)–dehydrogenase (2-OGDH) complex was studied in maize (Zea mays L.). GDH activity [...] Read more.

The effect of salt stress (150 mM NaCl) on the expression of genes, methylation of their promoters, and enzymatic activity of glutamate dehydrogenase (GDH), glutamate decarboxylase (GAD), and the 2-oxoglutarate (2-OG)–dehydrogenase (2-OGDH) complex was studied in maize (Zea mays L.). GDH activity increased continuously under salt stress, being 3-fold higher after 24 h. This was accompanied by the appearance of a second isoform with lower electrophoretic mobility. The expression of the Gdh1 gene strongly increased after 6–12 h of incubation, which corresponded to the demethylation of its promoter, while Gdh2 gene expression slightly increased after 2–6 h and then decreased. GAD activity gradually increased in the first 12 h, and then returned to the control level. This corresponded to the increase of Gad expression and its demethylation. Salt stress led to a 2-fold increase in the activity of 2-OGDH during the first 6 h of NaCl treatment, then the activity returned to the control level. Expression of the genes Ogdh1 and Ogdh3 peaked after 1–2 h of incubation. After 6–8 h with NaCl, the expression of these genes declined below the control levels, which correlated with the higher methylation of their promoters. We conclude that salt stress causes a redirection of the 2-OG flux to the γ-aminobutyric acid shunt via its amination to glutamate, by altering the expression of the Gdh1 and Gdh2 genes, which likely promotes the assembly of the native GDH molecule having a different subunit composition and greater affinity for 2-OG. Full article

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

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17 pages, 10109 KiB

Open AccessArticle

Virus-Induced galactinol-sucrose galactosyltransferase 2 Silencing Delays Tomato Fruit Ripening

by Pengcheng Zhang, Jingjing Wang, Yajie Yang, Jingjing Pan, Xuelian Bai, Ting Zhou and Tongfei Lai

Plants 2024, 13(18), 2650; https://doi.org/10.3390/plants13182650 - 21 Sep 2024

Viewed by 391

Abstract

Tomato fruit ripening is an elaborate genetic trait correlating with significant changes at physiological and biochemical levels. Sugar metabolism plays an important role in this highly orchestrated process and ultimately determines the quality and nutritional value of fruit. However, the mode of molecular [...] Read more.

Tomato fruit ripening is an elaborate genetic trait correlating with significant changes at physiological and biochemical levels. Sugar metabolism plays an important role in this highly orchestrated process and ultimately determines the quality and nutritional value of fruit. However, the mode of molecular regulation is not well understood. Galactinoal-sucrose galactosyltransferase (GSGT), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), can transfer the galactose unit from 1-α-D-galactosyl-myo-inositol to sucrose and yield raffinose, or catalyze the reverse reaction. In the present study, the expression of SlGSGT2 was decreased by Potato Virus X (PVX)-mediated gene silencing, which led to an unripe phenotype in tomato fruit. The physiological and biochemical changes induced by SlGSGT2 silencing suggested that the process of fruit ripening was delayed as well. SlGSGT2 silencing also led to significant changes in gene expression levels associated with ethylene production, pigment accumulation, and ripening-associated transcription factors (TFs). In addition, the interaction between SlGSGT2 and SlSPL-CNR indicated a possible regulatory mechanism via ripening-related TFs. These findings would contribute to illustrating the biological functions of GSGT2 in tomato fruit ripening and quality forming. Full article

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

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19 pages, 4364 KiB

Open AccessArticle

Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species

by Zhenxiu Xu, Haikun Wei, Mingyue Li, Yingjie Qiu, Lei Li, Ke-Wang Xu and Zhonglong Guo

Plants 2024, 13(18), 2649; https://doi.org/10.3390/plants13182649 - 21 Sep 2024

Viewed by 400

Abstract

The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex [...] Read more.

The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species. Full article

(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)

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16 pages, 3963 KiB

Open AccessArticle

Effect of Delayed Irrigation at the Jointing Stage on Nitrogen, Silicon Nutrition and Grain Yield of Winter Wheat in the North China Plain

by Hao Zheng, Jinyang Sun, Yueping Liang, Caiyun Cao, Yang Gao, Junpeng Zhang, Hongkai Dang and Chunlian Zheng

Plants 2024, 13(18), 2648; https://doi.org/10.3390/plants13182648 - 21 Sep 2024

Viewed by 475

Abstract

Water scarcity is a key limitation to winter wheat production in the North China Plain, and it is essential to explore the optimal timing of spring irrigation to optimize N and Si uptake as well as to safeguard yields. The aim of this [...] Read more.

Water scarcity is a key limitation to winter wheat production in the North China Plain, and it is essential to explore the optimal timing of spring irrigation to optimize N and Si uptake as well as to safeguard yields. The aim of this study was to systematically study the effect mechanism of nitrogen and silicon absorption of winter wheat on yield under spring irrigation and to provide a scientific basis for optimizing irrigation strategy during the growth period of winter wheat. In this experiment, the winter wheat ‘Heng 4399’ was used. Five irrigation periods, i.e., 0 d (CK), 5 d (AJ5), 10 d (AJ10), 15 d (AJ15), and 20 d (AJ20) after the jointing stage, were set up to evaluate the nitrogen (N) and silicon (Si) absorption and grain yield (GY). The results showed that delayed irrigation for 5–10 days at the jointing stage had increased the GY. With the delay of irrigation time, the N/Si content of the entire plant at the maturity period increased first and then decreased; among that, the maximum N contents appeared in AJ15 and AJ5 in 2015 and 2020, respectively, while the Si concentrations appeared in AJ5 and AJ10 in sequence. Compared with AJ15 and AJ20, the N accumulation of vegetative organs in AJ5 increased by 3.05~23.13% at the flowering stage, 14.12~40.12% after the flowering stage, and a 1.76~6.45% increase in the N distribution rate at maturity stage. A correlation analysis revealed that the GY was significantly and positively correlated with the N/Si accumulation at the anthesis and N translocation after the anthesis stage. In conclusion, under limited irrigation conditions, delaying watering for 5 to 10 days at the jointing stage can improve the nitrogen and silicon absorption and nutrient status of wheat plants and increase wheat yield. Full article

(This article belongs to the Special Issue Strategies to Improve Water-Use Efficiency in Plant Production)

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21 pages, 5341 KiB

Open AccessArticle

Functional Identification and Regulatory Active Site Screening of the DfDXS Gene of Dryopteris fragrans

by Hanxu Zhao, Jiameng Su, Zhaoxuan Zhong, Tongyou Xiong, Weicong Dai, Dongrui Zhang and Ying Chang

Plants 2024, 13(18), 2647; https://doi.org/10.3390/plants13182647 - 21 Sep 2024

Viewed by 322

Abstract

Dryopteris fragrans (L.) Schott has anti-inflammatory and antioxidant properties, and terpenoids are important components of its active constituents. The methyl-D-erythritol 4-phosphate (MEP) pathway is one of the major pathways for the synthesis of terpene precursors in plants, and 1-deoxy-D-xylulose-5-phosphate synthase (DXS) is the [...] Read more.

Dryopteris fragrans (L.) Schott has anti-inflammatory and antioxidant properties, and terpenoids are important components of its active constituents. The methyl-D-erythritol 4-phosphate (MEP) pathway is one of the major pathways for the synthesis of terpene precursors in plants, and 1-deoxy-D-xylulose-5-phosphate synthase (DXS) is the first rate-limiting enzyme in this pathway. DXS has been shown to be associated with increased stress tolerance in plants. In this experiment, two DXS genes were extracted from the D. fragrans transcriptome and named DfDXS1 and DfDXS2. Based on phylogenetic tree and conserved motif analyses, DXS was shown to be highly conserved evolutionarily and its localization to chloroplasts was determined by subcellular localization. Prokaryotic expression results showed that the number and growth status of recombinant colonies were better than the control under 400 mM NaCl salt stress and 800 mM mannitol-simulated drought stress. In addition, the DfDXS1 and DfDXS2 transgenic tobacco plants showed improved resistance to drought and salt stress. DfDXS1 and DfDXS2 responded strongly to methyl jasmonate (MeJA) and PEG-mimicked drought stress following exogenous hormone and abiotic stress treatments of D. fragrans. The transcriptional active sites were investigated by dual luciferase and GUS staining assays, and the results showed that the STRE element (AGGGG), the ABRE element (ACGTGGC), and the MYC element (CATTTG) were the important transcriptional active sites in the promoters of the two DXS genes, which were closely associated with hormone response and abiotic stress. These results suggest that the DfDXS gene of D. fragrans plays an important role in hormone signaling and response to stress. This study provides a reference for analyzing the molecular mechanisms of stress tolerance in D. fragrans. Full article

(This article belongs to the Special Issue Isoprenoids: Metabolic Mechanisms, Bioactivity and Application)

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20 pages, 15914 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the HMGR Gene Family in Taraxacum kok-saghyz Provide Insights into Its Regulation in Response to Ethylene and Methyl Jsamonate Treatments

by Pingping Du, Huan He, Jiayin Wang, Lili Wang, Zhuang Meng, Xiang Jin, Liyu Zhang, Fei Wang, Hongbin Li and Quanliang Xie

Plants 2024, 13(18), 2646; https://doi.org/10.3390/plants13182646 - 21 Sep 2024

Viewed by 429

Abstract

HMGR (3-hydroxy-3-methylglutaryl-CoA reductase) plays a crucial role as the first rate-limiting enzyme in the mevalonate (MVA) pathway, which is the upstream pathway of natural rubber biosynthesis. In this study, we carried out whole-genome identification of Taraxacum kok-saghyz (TKS), a novel rubber-producing alternative plant, [...] Read more.

HMGR (3-hydroxy-3-methylglutaryl-CoA reductase) plays a crucial role as the first rate-limiting enzyme in the mevalonate (MVA) pathway, which is the upstream pathway of natural rubber biosynthesis. In this study, we carried out whole-genome identification of Taraxacum kok-saghyz (TKS), a novel rubber-producing alternative plant, and obtained six members of the TkHMGR genes. Bioinformatic analyses were performed including gene structure, protein properties, chromosomal localization, evolutionary relationships, and cis-acting element analyses. The results showed that HMGR genes were highly conserved during evolution with a complete HMG-CoA reductase conserved domain and were closely related to Asteraceae plants during the evolutionary process. The α-helix is the most prominent feature of the secondary structure of the TkHMGR proteins. Collinearity analyses demonstrated that a whole-genome duplication (WGD) event and tandem duplication event play a key role in the expansion of this family and TkHMGR1 and TkHMGR6 have more homologous gene between other species. Cis-acting element analysis revealed that the TkHMGR gene family had a higher number of MYB-related, light-responsive, hormone-responsive elements. In addition, we investigated the expression patterns of family members induced by ethylene (ETH) and methyl jasmonate (MeJA), and their expression levels at different stages of T. kok-saghyz root development. Finally, subcellular localization results showed that six TkHMGR members were all located in the endoplasmic reticulum. In conclusion, the results of our study lay a certain theoretical basis for the subsequent improvement of rubber yield, molecular breeding of rubber-producing plants, and genetic improvement of T. kok-saghyz. Full article

(This article belongs to the Special Issue Bioinformatics and Functional Genomics in Modern Plant Science)

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16 pages, 5598 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of MYB Transcription Factors in Sudan Grass under Drought Stress

by Qiuxu Liu, Yalin Xu, Xiangyan Li, Tiangang Qi, Bo Li, Hong Wang and Yongqun Zhu

Plants 2024, 13(18), 2645; https://doi.org/10.3390/plants13182645 - 21 Sep 2024

Viewed by 577

Abstract

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families [...] Read more.

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass. Full article

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

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14 pages, 715 KiB

Open AccessArticle

Effects of Acmella radicans Invasion on Soil Seed Bank Community Characteristics in Different Habitats

by Xiaohan Wu, Kexin Yang, Fengping Zheng, Gaofeng Xu, Zewen Fan, David Roy Clements, Yunhai Yang, Shaosong Yang, Guimei Jin, Fudou Zhang and Shicai Shen

Plants 2024, 13(18), 2644; https://doi.org/10.3390/plants13182644 - 21 Sep 2024

Viewed by 375

Abstract

To examine the effects of the recent Acmella radicans invasion on plant community and diversity in invaded habitats, the composition, density, species richness, diversity indices, and evenness index of the soil seed bank community of two different habitats (wasteland and cultivated land) in [...] Read more.

To examine the effects of the recent Acmella radicans invasion on plant community and diversity in invaded habitats, the composition, density, species richness, diversity indices, and evenness index of the soil seed bank community of two different habitats (wasteland and cultivated land) in Yunnan Province, China, were analyzed through field sampling and greenhouse germination tests. A total of 28 species of plants belonging to 15 families and 28 genera, all annual herbs, were found in the soil seed bank. Seed densities and species number in the seed bank tended to be greater in April than in October; cultivated land also featured higher seed densities and species numbers compared to wasteland. With increased A. radicans cover, the seed bank population of A. radicans also significantly increased, but the seed bank populations of many other dominant species (e.g., Ageratum conyzoides and Gamochaeta pensylvanica) and native species (e.g., Laggera crispata and Poa annua) clearly declined. The germination of A. radicans seeds was concentrated during the period from the 4th to the 5th weeks. Vertically, the seed number of A. radicans was significantly different among the 0–5 cm, 5–10 cm and 10–20 cm layers that accounted for 80.7–90.6%, 9.4–16.1% and 0.0–3.2% of the total seed density in wasteland, respectively; and in cultivated land, A. radicans accounted for 56.8–64.9%, 26.7–31.8% and 8.1–13.5% of the total seed density, respectively. With reduced A. radicans cover, the species richness, Simpson index, Shannon–Wiener index, and Pielou indices of the weed community generally increased, and most diversity indices of weed communities in cultivated land were lower than in wasteland under the same cover of A. radicans. The results indicate that the invasion of A. radicans has negatively affected local weed community composition and reduced weed community diversity, and that these negative impacts in cultivated land may be enhanced by human disturbance. Our study was the first to elucidate the influence of A. radicans invasion on soil seed bank community characteristics in invaded habitats, providing a better understanding of its invasion and spread mechanisms in order to aid in developing a scientific basis for the prevention and control of this invader. Full article

(This article belongs to the Special Issue Plant Invasion 2023)

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20 pages, 6666 KiB

Open AccessArticle

Rhizofungus Aspergillus terreus Mitigates Heavy Metal Stress-Associated Damage in Triticum aestivum L.

by Naveen Dilawar, Muhammad Hamayun, Amjad Iqbal, Bokyung Lee, Sajid Ali, Ayaz Ahmad, Abdulwahed Fahad Alrefaei, Turki Kh. Faraj, Ho-Youn Kim and Anwar Hussain

Plants 2024, 13(18), 2643; https://doi.org/10.3390/plants13182643 - 21 Sep 2024

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Abstract

Industrial waste and sewage deposit heavy metals into the soil, where they can remain for long periods. Although there are several methods to manage heavy metals in agricultural soil, microorganisms present a promising and effective solution for their detoxification. We isolated a rhizofungus, [...] Read more.

Industrial waste and sewage deposit heavy metals into the soil, where they can remain for long periods. Although there are several methods to manage heavy metals in agricultural soil, microorganisms present a promising and effective solution for their detoxification. We isolated a rhizofungus, Aspergillus terreus (GenBank Acc. No. KT310979.1), from Parthenium hysterophorus L., and investigated its growth-promoting and metal detoxification capabilities. The isolated fungus was evaluated for its ability to mitigate lead (25 and 75 ppm) and copper (100 and 200 ppm) toxicity in Triticum aestivum L. seedlings. The experiment utilized a completely randomized design with three replicates for each treatment. A. terreus successfully colonized the roots of wheat seedlings, even in the presence of heavy metals, and significantly enhanced plant growth. The isolate effectively alleviates lead and copper stress in wheat seedlings, as evidenced by increases in shoot length (142%), root length (98%), fresh weight (24%), dry weight (73%), protein content (31%), and sugar content (40%). It was observed that wheat seedlings possess a basic defense system against stress, but it was insufficient to support normal growth. Fungal inoculation strengthened the host’s defense system and reduced its exposure to toxic heavy metals. In treated seedlings, exposure to heavy metals significantly upregulated MT1 gene expression, which aided in metal detoxification, enhanced antioxidant defenses, and maintained metal homeostasis. A reduction in metal exposure was observed in several areas, including normalizing the activities of antioxidant enzymes that had been elevated by up to 67% following exposure to Pb (75 mg/kg) and Cu (200 mg/kg). Heavy metal exposure elevated antioxidant levels but also increased ROS levels by 86%. However, with Aspergillus terreus colonization, ROS levels stayed within normal ranges. This decrease in ROS was associated with reduced malondialdehyde (MDA) levels, enhanced membrane stability, and restored root architecture. In conclusion, rhizofungal colonization improved metal tolerance in seedlings by decreasing metal uptake and increasing the levels of metal-binding metallothionein proteins. Full article

(This article belongs to the Special Issue Role of Microbial Plant Biostimulants in Abiotic Stress Mitigation)

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12 pages, 2436 KiB

Open AccessArticle

Identification of Salt-Stress-Responding Genes by Weighted Gene Correlation Network Analysis and Association Analysis in Wheat Leaves

by Linyi Qiao, Yijuan Li, Liujie Wang, Chunxia Gu, Shiyin Luo, Xin Li, Jinlong Yan, Chengda Lu, Zhijian Chang, Wei Gao and Xiaojun Zhang

Plants 2024, 13(18), 2642; https://doi.org/10.3390/plants13182642 - 21 Sep 2024

Viewed by 264

Abstract

The leaf is not only the main site of photosynthesis, but also an important organ reflecting plant salt tolerance. Discovery of salt-stress-responding genes in the leaf is of great significance for the molecular improvement of salt tolerance in wheat varieties. In this study, [...] Read more.

The leaf is not only the main site of photosynthesis, but also an important organ reflecting plant salt tolerance. Discovery of salt-stress-responding genes in the leaf is of great significance for the molecular improvement of salt tolerance in wheat varieties. In this study, transcriptome sequencing was conducted on the leaves of salt-tolerant wheat germplasm CH7034 seedlings at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on weighted gene correlation network analysis of differentially expressed genes (DEGs) under salt stress, 12 co-expression modules were obtained, of which, 9 modules containing 4029 DEGs were related to the salt stress time-course. These DEGs were submitted to the Wheat Union database, and a total of 904,588 SNPs were retrieved from 114 wheat germplasms, distributed on 21 wheat chromosomes. Using the R language package and GAPIT program, association analysis was performed between 904,588 SNPs and leaf salt injury index of 114 wheat germplasms. The results showed that 30 single nucleotide polymorphisms (SNPs) from 15 DEGs were associated with salt tolerance. Then, nine candidate genes, including four genes (TaBAM, TaPGDH, TaGluTR, and TaAAP) encoding enzymes as well as five genes (TaB12D, TaS40, TaPPR, TaJAZ, and TaWRKY) encoding functional proteins, were identified by converting salt tolerance-related SNPs into Kompetitive Allele-Specifc PCR (KASP) markers for validation. Finally, interaction network prediction was performed on TaBAM and TaAAP, both belonging to the Turquoise module. Our results will contribute to a further understanding of the salt stress response mechanism in plant leaves and provide candidate genes and molecular markers for improving salt-tolerant wheat varieties. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Salinity Stress and Tolerance—2nd Edition)

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29 pages, 7547 KiB

Open AccessArticle

Transcriptomic and Phenotypical Analysis of the Physiological Plasticity of Chamaecyparis hodginsii Roots under Different Nutrient Environments and Adjacent Plant Competition

by Bingjun Li, Wenchen Chen, Yanmei Pan, Wenxiu Wu, Ying Zhang, Jundong Rong, Tianyou He, Liguang Chen and Yushan Zheng

Plants 2024, 13(18), 2641; https://doi.org/10.3390/plants13182641 - 21 Sep 2024

Viewed by 274

Abstract

Chamaecyparis hodginsii seedlings undergo significant changes during growth due to different nutrient environments and adjacent plant competition, which is evident in the physiological plasticity changes in their roots. Therefore, in this experiment, 20 one-year-old elite C. hodginsii family seedlings were selected as the [...] Read more.

Chamaecyparis hodginsii seedlings undergo significant changes during growth due to different nutrient environments and adjacent plant competition, which is evident in the physiological plasticity changes in their roots. Therefore, in this experiment, 20 one-year-old elite C. hodginsii family seedlings were selected as the test objects, and the different nutrient environments and adjacent plant competition environments in nature were artificially simulated. Four nutrient environments (N heterogeneous nutrient environment, P heterogeneous nutrient environment, K heterogeneous nutrient environment, and homogeneous environment) and three planting patterns (single plant, conspecific neighbor, and heterospecific neighbor) were set up to determine the differences in root physiological indexes and plasticity of different family seedlings, and the families and treatment combinations with higher comprehensive evaluation were selected. The transcriptome sequencing of fine roots of C. hodginsii under different treatments was performed to analyze the differentially expressed genes. The results showed that the root activity, antioxidant enzyme activity, and nutrient element content of C. hodginsii seedlings in the N and P heterogeneous environments were higher than those in the homogeneous nutrient environment, while there was no significant difference between the K heterogeneous nutrient environment and the homogeneous environment, but MDA content was higher than that in other nutrient environments. The root activity and antioxidant enzyme activity in the competitive patterns were generally higher than those in the single plant and reached the peak in the heterospecific neighbor. The root physiological plasticity index of line 490 was the highest, but the comprehensive evaluation of root physiological indexes of lines 539 and 535 was better. The pattern with the highest comprehensive evaluation score was P heterogeneous nutrient environment × heterospecific neighbor. The effects of the N and P heterogeneous nutrient environments on root transcriptome genes were similar, which significantly increased DNA transcription and regulatory factor activity, while K heterogeneous nutrient environment focused on the regulation of root enzyme activity. The heterogeneous nutrient environment induces the conduction of hormone signals in the roots of C. hodginsii and induces the synthesis of phenylpropanone. The biosynthesis of phenylpropanone in the roots of C. hodginsii will increase significantly under competitive patterns. In summary, the N and P heterogeneous nutrient environments and the heterospecific neighbor can improve the root physiological indexes of C. hodginsii families, and the root physiological indexes of lines 539 and 535 are the best. The nutrient environment and competition pattern mainly affect the root system to transmit hormone signals to regulate enzyme activity. Full article

(This article belongs to the Section Plant Molecular Biology)

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23 pages, 10170 KiB

Open AccessArticle

Comparative Analysis of Chemical Profiles and Biological Activities of Essential Oils Derived from Torreya grandis Arils and Leaves: In Vitro and In Silico Studies

by Pengfei Deng, Huiling Wang and Xiaoniu Xu

Plants 2024, 13(18), 2640; https://doi.org/10.3390/plants13182640 - 21 Sep 2024

Viewed by 450

Abstract

Torreya grandis (T. grandis, Taxaceae) is a well-known nut tree species. Its fruit aril and leaves possess a unique aroma, making it an ideal natural raw material for extracting essential oils (EOs). This study aims to comprehensively compare the composition, biological [...] Read more.

Torreya grandis (T. grandis, Taxaceae) is a well-known nut tree species. Its fruit aril and leaves possess a unique aroma, making it an ideal natural raw material for extracting essential oils (EOs). This study aims to comprehensively compare the composition, biological activities, and pharmacological mechanism of EOs extracted from the arils (AEO) and leaves (LEO) of T. grandis. The results revealed that the chemical composition of the two EOs was highly consistent, with α-pinene and D-limonene as the main components. Both EOs significantly reduced cellular melanin production and inhibited tyrosinase activity in α-MSH-stimulated B16 cells (p < 0.05). AEO and LEO suppressed inflammatory responses in LPS-stimulated RAW 264.7 macrophages, significantly inhibiting cellular NO production and proinflammatory cytokines such as TNF-α and IL-6 (p < 0.05). A network pharmacology analysis reveals that AEO and LEO share similar molecular mechanisms and pharmacological pathways for treating skin pigmentation and inflammation. Regulating inflammatory cytokines may be a critical pathway for AEO and LEO in treating skin pigmentation. These findings suggest that AEO and LEO have potential for cosmetic applications. The leaves of T. grandis could be a valuable source of supplementary materials for producing T. grandis aril EO. Full article

(This article belongs to the Section Phytochemistry)

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