Plants

16 pages, 1023 KiB

Open AccessArticle

Variation in Leaf Functional Traits of Populus laurifolia Ldb and Ulmus pumila L. across Five Contrasting Urban Sites in Ulaanbaatar, Mongolia

by Otgonsaikhan Byambasuren, Anujin Bat-Amgalan, Ser-Oddamba Byambadorj, Jonathan O. Hernandez, Tuguldur Nyam-Osor and Batkhuu Nyam-Osor

Plants 2024, 13(19), 2709; https://doi.org/10.3390/plants13192709 (registering DOI) - 27 Sep 2024

Abstract

Amid urbanization, studying leaf functional traits of woody plants in urban environments is essential for understanding how urban green spaces function and how they can be effectively managed sustainably. In this study, we investigated the effects of different growing conditions on the morpho-physiological [...] Read more.

Amid urbanization, studying leaf functional traits of woody plants in urban environments is essential for understanding how urban green spaces function and how they can be effectively managed sustainably. In this study, we investigated the effects of different growing conditions on the morpho-physiological traits of Populus laurifolia and Ulmus pumila across five contrasting urban sites. The leaf area (LA), leaf length (LL), leaf width (LW), leaf biomass (LB), specific leaf area (SLA), leaf chlorophyll concentration, chlorophyll fluorescence parameters, leaf water potential at predawn (Ψ_pd) and midday (Ψ_md), leaf performance index (PI_abs), and phenotypic plasticity index (PPI) were compared across five contrasting urban sites. The soil chemical and physical properties were also compared between sites. There were significant differences in soil physicochemical characteristics between sites. We found significant effects of site on most of the morpho-physiological traits measured, except for Ψ_md. The leaf chlorophyll concentration of P. laurifolia and U. pumila varied significantly between sites. The Ψ_pd was significantly different between years and sites. In U. pumila, the mean PPI for morphological traits (0.20) was lower than that for physiological traits (0.21). In conclusion, we revealed significant variations in the morpho-physiological traits of P. laurifolia and U. pumila across the five urban sites. Hence, long-term, large-scale studies are recommended to examine how diverse species respond to different urban growing conditions and to include other ecologically important plant traits for a better understanding of urban trees in a changing environment. Full article

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

17 pages, 3975 KiB

Open AccessArticle

Identification of Genomic Regions Associated with Powdery Mildew Resistance in Watermelon through Genome-Wide Association Study

by Oak-Jin Lee, Koeun Han, Hye-Eun Lee, Hyo-Bong Jeong, Nari Yu and Wonbyoung Chae

Plants 2024, 13(19), 2708; https://doi.org/10.3390/plants13192708 - 27 Sep 2024

Abstract

Watermelon (Citrullus spp.) is an economically important crop globally, but it is susceptible to various diseases, including powdery mildew. Previous studies have identified genetic factors associated with powdery mildew resistance. However, further research using diverse genetic approaches is necessary to elucidate the [...] Read more.

Watermelon (Citrullus spp.) is an economically important crop globally, but it is susceptible to various diseases, including powdery mildew. Previous studies have identified genetic factors associated with powdery mildew resistance. However, further research using diverse genetic approaches is necessary to elucidate the underlying genetic mechanisms of this resistance. In this study, the germplasm collection comprising highly homozygous inbred lines was employed, which enabled the accumulation of consistent data and improved the reliability of the genome-wide association study (GWAS) findings. Our investigation identified two significant single-nucleotide polymorphisms (SNPs), pm2.1 and pm3.1, which were strongly associated with disease resistance. Moreover, several candidate genes were revealed within the linkage disequilibrium (LD) blocks surrounding the significant SNPs. In conclusion, the identification of significant SNPs and their additive effects, combined with the discovery of relevant candidate genes, expanded our understanding of the genetic basis of disease resistance and can pave the way for the development of more resilient watermelon cultivars through marker-assisted selection. Full article

► Show Figures

Figure 1

15 pages, 1874 KiB

Open AccessArticle

Azolla as a Safe Food: Suppression of Cyanotoxin-Related Genes and Cyanotoxin Production in Its Symbiont, Nostoc azollae

by Jonathan P. Bujak, Ana L. Pereira, Joana Azevedo, Alexandra A. Bujak, Victor Leshyk, Minh Pham Gia, Timo Stadtlander, Vitor Vasconcelos and Daniel J. Winstead

Plants 2024, 13(19), 2707; https://doi.org/10.3390/plants13192707 - 27 Sep 2024

Abstract

The floating freshwater fern Azolla is the only plant that retains an endocyanobiont, Nostoc azollae (aka Anabaena azollae), during its sexual and asexual reproduction. The increased interest in Azolla as a potential source of food and its unique evolutionary history have raised [...] Read more.

The floating freshwater fern Azolla is the only plant that retains an endocyanobiont, Nostoc azollae (aka Anabaena azollae), during its sexual and asexual reproduction. The increased interest in Azolla as a potential source of food and its unique evolutionary history have raised questions about its cyanotoxin content and genome. Cyanotoxins are potent toxins synthesized by cyanobacteria which have an anti-herbivore effect but have also been linked to neurodegenerative disorders including Alzheimer’s and Parkinson’s diseases, liver and kidney failure, muscle paralysis, and other severe health issues. In this study, we investigated 48 accessions of Azolla–Nostoc symbiosis for the presence of genes coding microcystin, nodularin, cylindrospermopsin and saxitoxin, and BLAST analysis for anatoxin-a. We also investigated the presence of the neurotoxin β-N-methylamino-L-alanine (BMAA) in Azolla and N. azollae through LC-MS/MS. The PCR amplification of saxitoxin, cylindrospermospin, microcystin, and nodularin genes showed that Azolla and its cyanobiont N. azollae do not have the genes to synthesize these cyanotoxins. Additionally, the matching of the anatoxin-a gene to the sequenced N. azollae genome does not indicate the presence of the anatoxin-a gene. The LC-MS/MS analysis showed that BMAA and its isomers AEG and DAB are absent from Azolla and Nostoc azollae. Azolla therefore has the potential to safely feed millions of people due to its rapid growth while free-floating on shallow fresh water without the need for nitrogen fertilizers. Full article

(This article belongs to the Section Plant Ecology)

► Show Figures

Figure 1

35 pages, 4666 KiB

Open AccessArticle

Ecogeographic Study of Ipomoea Species in Mauritius, Indian Ocean

by Yakshini Boyjnath, Mohammad Ehsan Dulloo, Vishwakalyan Bhoyroo and Vijayanti Mala Ranghoo-Sanmukhiya

Plants 2024, 13(19), 2706; https://doi.org/10.3390/plants13192706 - 27 Sep 2024

Abstract

The wild relatives of crops play a critical role in enhancing agricultural resilience and sustainability by contributing valuable traits for crop improvement. Shifts in climatic conditions and human activities threaten plant genetic resources for food and agriculture (PGRFA), jeopardizing contributions to future food [...] Read more.

The wild relatives of crops play a critical role in enhancing agricultural resilience and sustainability by contributing valuable traits for crop improvement. Shifts in climatic conditions and human activities threaten plant genetic resources for food and agriculture (PGRFA), jeopardizing contributions to future food production and security. Studies and inventories of the extant agrobiodiversity, in terms of numbers and distribution patterns of species and their genetic diversity, are primordial for developing effective and comprehensive conservation strategies. We conducted an ecogeographic study on Ipomoea species and assessed their diversity, distribution, and ecological preferences across different topographic, altitudinal, geographical, and climatic gradients, at a total of 450 sites across Mauritius. Species distribution maps overlaid with climatic data highlighted specific ecological distribution. Principal Component Analysis (PCA) revealed species distribution was influenced by geographical factors. Regional richness analyses indicated varying densities, with some species exhibiting localized distributions and specific ecological preferences while the other species showed diverse distribution patterns. Field surveys identified 14 species and 2 subspecies out of 21 species and 2 subspecies of Ipomoea reported in Mauritius. A gap in ex situ germplasm collections was observed and several species were identified as threatened. Further investigations and a more long-term monitoring effort to better guide conservation decisions are proposed. Full article

► Show Figures

Figure 1

16 pages, 9124 KiB

Open AccessArticle

Photosynthetic Performance of Oil Palm Genotypes under Drought Stress

by Carmenza Montoya, Edison Daza, Fernan Santiago Mejía-Alvarado, Arley Fernando Caicedo-Zambrano, Iván Ayala-Díaz, Rodrigo Ruiz-Romero and Hernán Mauricio Romero

Plants 2024, 13(19), 2705; https://doi.org/10.3390/plants13192705 - 27 Sep 2024

Abstract

Water deficiency and potential drought periods could be important ecological factors influencing cultivation areas and productivity once different crops are established. The principal supply of vegetable oil for oil crops is oil palm, and new challenges are emerging in the face of climatic [...] Read more.

Water deficiency and potential drought periods could be important ecological factors influencing cultivation areas and productivity once different crops are established. The principal supply of vegetable oil for oil crops is oil palm, and new challenges are emerging in the face of climatic changes. This study investigated the photosynthetic performance of 12 genotypes of Elaeis exposed to drought stress under controlled conditions. The assay included genotypes of Elaeis guineensis, Elaeis oleifera, and the interspecific O×G hybrid (E. oleifera × E. guineensis). The principal results showed that the E. guineensis genotype was the most efficient at achieving photosynthesis under drought stress conditions, followed by the hybrid and E. oleifera genotypes. The physiological parameters showed good prospects for vegetal breeding with different O×G hybrids, mainly because of their ability to maintain the equilibrium between CO₂ assimilation and stomatal aperture. We validated 11 genes associated with drought tolerance, but no differences were detected. These results indicate that no allelic variants were represented in the RNA during sampling for the validated genotypes. In conclusion, this study helps to define genotypes that can be used as parental lines for oil palm improvement. The gas exchange data showed that drought stress tolerance could define guidelines to incorporate the available genetic resources in breeding programs across the early selection in nursery stages. Full article

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

► Show Figures

Figure 1

14 pages, 4987 KiB

Open AccessArticle

FtMYB163 Gene Encodes SG7 R2R3-MYB Transcription Factor from Tartary Buckwheat (Fagopyrum tataricum Gaertn.) to Promote Flavonol Accumulation in Transgenic Arabidopsis thaliana

by Hanmei Du, Jin Ke, Xiaoqian Sun, Lu Tan, Qiuzhu Yu, Changhe Wei, Peter R. Ryan, An’hu Wang and Hongyou Li

Plants 2024, 13(19), 2704; https://doi.org/10.3390/plants13192704 - 27 Sep 2024

Abstract

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a coarse grain crop rich in flavonoids that are beneficial to human health because they function as anti-inflammatories and provide protection against cardiovascular disease and diabetes. Flavonoid biosynthesis is a complex process, and relatively little is [...] Read more.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a coarse grain crop rich in flavonoids that are beneficial to human health because they function as anti-inflammatories and provide protection against cardiovascular disease and diabetes. Flavonoid biosynthesis is a complex process, and relatively little is known about the regulatory pathways involved in Tartary buckwheat. Here, we cloned and characterized the FtMYB163 gene from Tartary buckwheat, which encodes a member of the R2R3-MYB transcription factor family. Amino acid sequence and phylogenetic analysis indicate that FtMYB163 is a member of subgroup 7 (SG7) and closely related to FeMYBF1, which regulates flavonol synthesis in common buckwheat (F. esculentum). We demonstrated that FtMYB163 localizes to the nucleus and has transcriptional activity. Expression levels of FtMYB163 in the roots, stems, leaves, flowers, and seeds of F. tataricum were positively correlated with the total flavonoid contents of these tissues. Overexpression of FtMYB163 in transgenic Arabidopsis enhanced the expression of several genes involved in early flavonoid biosynthesis (AtCHS, AtCHI, AtF3H, and AtFLS) and significantly increased the accumulation of several flavonoids, including naringenin chalcone, naringenin-7-O-glucoside, eriodictyol, and eight flavonol compounds. Our findings demonstrate that FtMYB163 positively regulates flavonol biosynthesis by changing the expression of several key genes in flavonoid biosynthetic pathways. Full article

(This article belongs to the Section Plant Molecular Biology)

► Show Figures

Figure 1

Figure 1
Multiple sequence alignment of FtMYB163. The transcription factors were FeMYBF1 (LC369592) from common buckwheat, FtMYB6 (QPC96978) from Tartary buckwheat, AtMYB12 (AEC10843) from Arabidopsis, VvMYBF1 (FJ948477) from grape, and CsMYBF1 (KT727073) from citrus. Identical (100%), conservative (75–99%), and blocks (50–74%) of similar amino acid residues are shaded in deep blue, cherry red, and cyan, respectively. The R2/R3 SANT domain and SG7 motif1/2 are indicated in the red line and red box, respectively. Full article ">Figure 2
Phylogenetic analysis of FtMYB163. GeneBack accession numbers are listed as follows: AtMYB58 (NP_173098), AtMYB63 (NP_001321204), LlMYB1 (ADY38393), ZmMYB31 (NP_001105949), ZmMYB42 (NP_001106009), MdMYB3 (AEX08668), AtMYB7 (NP_179263), AtMYB4 (AAC83582), AtMYB8 (NP_849749), AtMYB32 (NP_195225), AtMYB3 (NP_564176), FtMYB2 (AEC32976), FaMYB11 (USN17649), FaMYB9 (USN17648), MdMYB9 (NP_001280749), PtMYB134 (ACR83705), VvMYBPA1 (NP_001268160), VvMYBPA2 (NP_001267953), PpMYB10 (ADK73605), AN2 (BAP28593), ANT1 (WDP81135), IbMYB1 (BAG68211), AtMYB113 (NP_176811), AtMYB114 (NP_176812), GtMYBP3 (AB733016), MdMYB22 (DQ074470), AtMYB111 (AAK97396), AtMYB11 (NP_191820), MsMYB (AQR58379), CcMYB12 (AXF92691), AtMYB90 (AAG42002), AtPAP1 (NP_172830), AtMYB75 (NP_176057), AtMYB43 (NP_197163), AtMYB20 (NP_176797), FtMYB1 (AEC32973), FtMYB31 (AIZ97491). FtMYB163 is highlighted with a red dot. Full article ">Figure 3
Subcellular localization and transcription activation activities of FtMYB163. (A) Subcellular localization of FtMYB163-GFP fusion protein in Nicotiana benthamiana leaves. GFP: Green fluorescent protein; DAPI: 4′,6-diamidino-2-phenylindole stain; 16318-hGFP was used as the control. Scale bar: 20 μm. (B) Transcription activation analysis of FtMYB163 in yeast AH109 cells. The transformed cells were plated on an (a) SD/-Leu/-Trp, (b) SD/-Ade/-His/-Leu/-Trp, and (c) SD/-Ade/-His/-Leu/-Trp/x-α-gal medium and incubated in an incubator at 30 °C for 3~5 d. pGBKT7, negative control; pGBKT7-53, positive control. Full article ">Figure 4
Expression pattern of FtMYB163 and the total flavonoid content in Tartary buckwheat. The expression of FtMYB163 in (A) R (roots), ST (stems), L (leaves), and F (flowers) at sprouts, six-leaf stage, and maturation stage and (B) in seeds at different developmental stages. (C) Gene expression clustering heat map of FtMYB163 and Tartary buckwheat flavonoid biosynthesis structure. (D) FtMYB163 expression analysis and (E) the total flavonoid content detection in each tissue at the corresponding period (as in (C)). (F) The correlation between the FtMYB163 expression in different tissues and the content of total flavonoids. D4~D30, the seeds 4~30 days after flowering; L1, top one leaf of adult plants; L2, top three leaves of adult plants; S1, seeds before grouting; S2, seeds at filling stage; S3, mature seeds. Blue asterisks indicated the structural genes co-expressed with FtMYB163 during the three seed development periods. The expression levels were evaluated by the 2−ΔΔCT method, and FtActin7 was used as a reference gene. The values are represented as mean ± SD (n = 5) and marked with different letters to indicate statistically significant differences at p < 0.05 (Tukey’s test). Full article ">Figure 5
Characterization of T3 transgenic Arabidopsis lines expressing FtMYB163. (A) Relative expression levels of FtMYB163 in independent homozygous T3 lines using qRT-PCR. AtACT2 was used as a reference gene. Data show the mean ± SD of three biological replicates. Different letters indicate significant differences at p < 0.05 (Student’s t-test). (B) Total flavonoid content of WT Arabidopsis and three transgenic T3 lines expressing FtMYB163 (OE-2, OE-5, and OE-7). Values are mean ± SD (n = 10), and different letters indicate significant differences at p < 0.01 (Tukey’s test). Full article ">Figure 6
Assessing how the expression of FtMYB163 in Arabidopsis leaves affects the expression of endogenous genes in the flavonoid synthesis pathway. The relative expression of Arabidopsis genes (A) flavonol synthase (AtFLS), (B) chalcone synthase (AtCHS), (C) chalcone isomerase (AtCHI), (D) flavonoid 3-hydroxylase (AtF3H), (E) flavonoid 3′-hydroxylase (AtF3′H), (F) dihydroflavonol 4-reductase (AtDFR), and (G) anthocyanidin reductase (AtANS) were measured in WT and transgenic lines (OE-2, OE-5, and OE-7). Gene expression in the WT was set to 1.0 to provide fold changes in expression. The AtACT2 gene was used as a reference. Values represent mean ± SD (n = 5), and different letters indicate significant differences (p < 0.01) (Tukey’s test). Full article ">

13 pages, 3720 KiB

Open AccessArticle

Isolation and Plant Growth Promotion Effect of Endophytic Siderophore-Producing Bacteria: A Study on Halophyte Sesuvium portulacastrum

by Xinyi Cen, Hua Li, Yanhua Zhang, Lingfeng Huang and Yuanrong Luo

Plants 2024, 13(19), 2703; https://doi.org/10.3390/plants13192703 - 27 Sep 2024

Abstract

The objective of the present study was to isolate endophytes from the roots of the halophyte Sesuvium portulacastrum, which is applied for aquatic phytoremediation. From these endophytes, siderophore-producing bacteria were specifically isolated for their potential capacity to promote plant growth. The siderophore [...] Read more.

The objective of the present study was to isolate endophytes from the roots of the halophyte Sesuvium portulacastrum, which is applied for aquatic phytoremediation. From these endophytes, siderophore-producing bacteria were specifically isolated for their potential capacity to promote plant growth. The siderophore production capacity of the isolated bacteria was quantified, and a high-yield siderophore-producing strain was selected for further investigation. A total of 33 endophytic bacteria were successfully isolated and identified using a culturable approach. Of these, 10 siderophore-producing bacteria were identified using the selective agar assay, displaying siderophore unit (SU) values ranging from 11.90% to 80.39%. It is noteworthy that Erwinia sp. QZ-E9 exhibited the highest siderophore production capacity, achieving an SU of 80.39%. A microcosm co-cultivation experiment was conducted with the strain QZ-E9 in iron-deficient conditions (2 μmol/L Fe³⁺). The results demonstrated that strain QZ-E9 significantly enhanced the growth of S. portulacastrum, by increases in both fresh weight (1.41 g) and root length (18.7 cm). Furthermore, fluorescence in situ hybridization (FISH) was utilized to ascertain the colonization pattern of strain QZ-E9 within the plant roots. The analysis demonstrated that strain QZ-E9 exhibited extensive colonization of the epidermal and outer cortical cells of S. portulacastrum roots, as well as the intercellular spaces and vascular tissues. This colonization indicated that Erwinia sp. QZ-E9 plays a crucial role in promoting the growth of S. portulacastrum, presumably through its siderophore-mediated iron acquisition mechanism. Full article

(This article belongs to the Special Issue Plant Growth Promoting Bacteria and Mycorrhizas as Biocontrol and Biostimulants Agents)

► Show Figures

Figure 1

Figure 1
Phylogenetic analysis of isolated bacteria based on 16S rRNA gene sequences. Full article ">Figure 2
Siderophore-producing bacteria determined by CAS agar plate. ((A): Strain QZ-E9; (B): Strain QZ-E23). Full article ">Figure 3
OD600 and SU values of Erwinia sp. QZ-E9 in different iron ion concentrations. The solid line is the change in the OD600 value of the strain under different addition groups, and the dotted line is the change in SU value under different addition groups. Full article ">Figure 4
Fresh weight variations of S. portulacastrum under different treatments. Full article ">Figure 5
Root length variations of S. portulacastrum under different treatments. Full article ">Figure 6
S. portulacastrum inoculated with Erwinia sp. QZ-E9 in 0 μmol/L iron ion. Full article ">Figure 7
FISH images inside the roots of S. portulacastrum under different treatments ((A) shows the excited image of the EUB338 probe labeled with Cy3 only in group P; (B) shows the excited image of the EUB338 probe labeled with red fluorescent Cy3 in group P + B; and (C) shows the excited image of the probe labeled with Cy3 and the probe labeled with green fluorescent FITC at the same time in group P + B. The magnification is 10× and all the lengths of the scales in the figure are 50 μmol/L). Full article ">

20 pages, 5610 KiB

Open AccessArticle

Biochemical and Proteomic Analyses in Drought-Tolerant Wheat Mutants Obtained by Gamma Irradiation

by Ayşe Şen, Tamer Gümüş, Aslıhan Temel, İrfan Öztürk and Özge Çelik

Plants 2024, 13(19), 2702; https://doi.org/10.3390/plants13192702 - 27 Sep 2024

Abstract

The bread wheat cultivar (Triticum aestivum L. cv. Sagittario) as a parental line and its mutant, drought-tolerant lines (Mutant lines 4 and 5) were subjected to polyethylene glycol (PEG)-induced drought. Drought stress resulted in decreased chlorophyll levels and the accumulation of proline [...] Read more.

The bread wheat cultivar (Triticum aestivum L. cv. Sagittario) as a parental line and its mutant, drought-tolerant lines (Mutant lines 4 and 5) were subjected to polyethylene glycol (PEG)-induced drought. Drought stress resulted in decreased chlorophyll levels and the accumulation of proline and TBARS, despite increases in activities of catalase, peroxidase, and superoxide dismutase enzymes. Transcription of the genes encoding these enzymes and delta-1-pyrroline 5-carboxylase synthetase was induced by drought. 2-DE gel electrophoresis analysis identified differentially expressed proteins (DEPs) in the mutant lines, which are distinguished by “chloroplast”, “mitochondrion”, “pyruvate dehydrogenase complex”, and “homeostatic process” terms. The drought tolerance of the mutant lines might be attributed to improved photosynthesis, efficient ATP synthesis, and modified antioxidant capacity. In addition to proteomics data, the drought tolerance of wheat genotypes might also be assessed by chlorophyll content and TaPOX gene expression. To our knowledge, this is the first proteomic analysis of gamma-induced mutants of bread wheat. These findings are expected to be utilized in plant breeding studies. Full article

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

► Show Figures

Figure 1

Figure 1
Effects of PEG-induced osmotic stress on chlorophyll content (A), proline content (B), and TBARS content (C) of the parental line (commercial cultivar) and its mutant lines 4 and 5. Values are the arithmetic means of biological pentaplicates (n = 5), and the error bars correspond to the standard deviations (SD). Significant differences were determined according to Tukey’s HSD test performed after a 2-way ANOVA. The letters on the columns represent the statistical significance among the genotypes under the same conditions (control or PEG). Columns indicated by different letters are statistically different (p < 0.05). Asterisks represent the statistical significance of a genotype between different conditions as follows: * p < 0.05, *** p < 0.001, and ns (not significant). Full article ">Figure 2
Effects of PEG-induced osmotic stress on the activities of the enzymes CAT (A), POX (B), and SOD (C) of the parental line (commercial cultivar) and its mutant lines 4 and 5. Values are the arithmetic means of biological pentaplicates (n = 5), and the error bars correspond to the standard deviations (SD). Significant differences were determined according to Tukey’s HSD test performed after a 2-way ANOVA. The letters on the columns represent the statistical significance among the genotypes under the same conditions (control or PEG). Columns indicated by different letters are statistically different (p < 0.05). Asterisks represent the statistical significance of a genotype between different conditions as follows: *** p < 0.001. Full article ">Figure 3
Effects of PEG-induced osmotic stress on the expression of the genes TaCAT (A), TaP5CS (B), TaPOX (C), and TaSOD2 (D) of the parental line (commercial cultivar) and its mutant lines 4 and 5. Values are the arithmetic means of biological triplicates (n = 3), and the error bars correspond to the standard deviations (sd). Columns indicated by different letters are statistically different (p < 0.05) at the same conditions (control or PEG). Significant differences were determined according to Tukey’s HSD test at *** p < 0.001. Full article ">Figure 4
Gene ontology (GO) analyses. Pie charts show the PEG-induced GO terms of cellular component (A,D), molecular function (B,E) and biological process (C,F) in the parental line (A–C) and in the mutant lines (D–F). Full article ">Figure 5
Gene ontology (GO) analyses. Pie charts show the PEG-repressed GO terms of cellular component (A,D), molecular function (B,E) and biological process (C,F) in the parental line (A–C) and in the mutant lines (D–F). Full article ">

21 pages, 2695 KiB

Open AccessArticle

Establishment of a Sensitive and Reliable Droplet Digital PCR Assay for the Detection of Bursaphelenchus xylophilus

by Yu Su, Xuedong Zhu, Haozheng Jing, Haiying Yu and Huai Liu

Plants 2024, 13(19), 2701; https://doi.org/10.3390/plants13192701 - 26 Sep 2024

Abstract

Pine wilt disease (PWD), which poses a significant risk to pine plantations across the globe, is caused by the pathogenic agent Bursaphelenchus xylophilus, also referred to as the pine wood nematode (PWN). A droplet digital PCR (ddPCR) assay was developed for the [...] Read more.

Pine wilt disease (PWD), which poses a significant risk to pine plantations across the globe, is caused by the pathogenic agent Bursaphelenchus xylophilus, also referred to as the pine wood nematode (PWN). A droplet digital PCR (ddPCR) assay was developed for the quick identification of the PWN in order to improve detection sensitivity. The research findings indicate that the ddPCR assay demonstrated significantly higher analysis sensitivity and detection sensitivity in comparison to traditional quantitative PCR (qPCR). However, it had a more limited dynamic range. High specificity was shown by both the ddPCR and qPCR techniques in the diagnosis of the PWN. Assessments of reproducibility revealed that ddPCR had lower coefficients of variation at every template concentration. Inhibition tests showed that ddPCR was less susceptible to inhibitors. There was a strong linear association between standard template measurements obtained using ddPCR and qPCR (Pearson correlation = 0.9317; p < 0.001). Likewise, there was strong agreement (Pearson correlation = 0.9348; p < 0.001) between ddPCR and qPCR measurements in the evaluation of pine wood samples. Additionally, wood samples from symptomatic (100% versus 86.67%) and asymptomatic (31.43% versus 2.9%) pine trees were diagnosed with greater detection rates using ddPCR. This study’s conclusions highlight the advantages of the ddPCR assay over qPCR for the quantitative detection of the PWN. This method has a lot of potential for ecological research on PWD and use in quarantines. Full article

(This article belongs to the Special Issue New Strategies for the Control of Plant-Parasitic Nematodes)

27 pages, 2419 KiB

Open AccessReview

Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms

by Ming Yin, Shanwen Wang, Yanfang Wang, Ronghua Wei, Yawei Liang, Liying Zuo, Mingyue Huo, Zekai Huang, Jie Lang, Xiuqin Zhao, Fan Zhang, Jianlong Xu, Binying Fu, Zichao Li and Wensheng Wang

Plants 2024, 13(19), 2700; https://doi.org/10.3390/plants13192700 - 26 Sep 2024

Abstract

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice [...] Read more.

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice and the associated epigenetic responses (DNA methylation). Abiotic stress factors, including high temperature, drought, cold, heavy metal pollution, and high salinity, have a negative impact on crop productivity. Epigenetic changes are key regulatory factors in plant stress responses, and DNA methylation is one of the earliest discovered and thoroughly studied mechanisms in these epigenetic regulatory mechanisms. The normal growth of rice is highly dependent on the environment, and changes in the environment can lead to rice sterility and severe yield loss. Changes in the regulation of the DNA methylation pathway are involved in rice’s response to stress. Various DNA methylation-regulating protein complexes that function during rice development have been identified. Significant changes in DNA methylation occur in numerous stress-responsive genes, particularly those in the abscisic acid signaling pathway. These findings underscore the complex mechanisms of the abiotic stress response in rice. We propose the effective improvement of tolerance traits by regulating the epigenetic status of rice and emphasize the role of DNA methylation in abiotic stress tolerance, thereby addressing global climate change and ensuring food security. Full article

(This article belongs to the Special Issue Mechanisms of Plant Regulation against Environmental Stress)

► Show Figures

Figure 1

19 pages, 1840 KiB

Open AccessArticle

Pomological and Molecular Characterization of Apple Cultivars in the German Fruit Genebank

by Lea Broschewitz, Stefanie Reim, Henryk Flachowsky and Monika Höfer

Plants 2024, 13(19), 2699; https://doi.org/10.3390/plants13192699 - 26 Sep 2024

Abstract

Traditional varieties are a valuable tool in modern apple breeding. However, the use of synonyms and missing source documentation hinder an effective identification and conservation of relevant cultivars. During several projects, the authenticity and diversity of the apple cultivar collection of the German [...] Read more.

Traditional varieties are a valuable tool in modern apple breeding. However, the use of synonyms and missing source documentation hinder an effective identification and conservation of relevant cultivars. During several projects, the authenticity and diversity of the apple cultivar collection of the German Fruit Genebank (GFG) was evaluated extensively. The trueness-to-type of 7890 apple trees was assessed on a pomological and molecular level. Pomological evaluations were performed by at least two experienced experts to identify the original cultivar names. On the molecular level, a set of 17 SSR markers was used to determine a unique genetic profile for each apple cultivar. The pomological and molecular characterization was expressed in terms of a comprehensive trueness-to-type criterion and the results were previously published as a well-curated dataset. In this study, the published dataset was analyzed to evaluate the quality and diversity of the apple collection of the GFG and highlight new findings based on phylogenetic and parentage analysis. The dataset contains 1404 unique genetic profiles corresponding to unambiguous cultivar names. Of these 1404 cultivars, 74% were assessed as true-to-type. The collection of diploid apple cultivars showed a high degree of expected heterozygosity (H_exp = 0.84). Genetic diversity in terms of year and location of origin was investigated with a STRUCTURE analysis. It was hypothesized that genetic diversity might decline overtime due to restrictive breeding programs. The results showed a shift dynamic between older and newer cultivars in one specific cluster, but no significant decrease in genetic diversity was observed in this study. Lastly, a parentage analysis was performed to check parental relationships based on historical research. Out of 128 parent–child trios, 110 trios resulted in significant relationships and reconfirmed the information from the literature. In some cases, the information from the literature was disproven. This analysis also allowed for readjusting the trueness-to-type criteria for previously undetermined cultivars. Overall, the importance of authenticity evaluations for gene bank cultivars was highlighted. Furthermore, the direct use of the dataset was shown by relevant investigations on the genetic diversity and structure of the apple cultivar collections of the GFG. Full article

(This article belongs to the Section Plant Genetic Resources)

► Show Figures

Figure 1

Figure 1
Representation of 1404 apple genotypes corresponding to cultivars in the German Fruit Genebank (GFG) sectioned by authenticity of cultivar identification (trueness-to-type) given in percentage and count. Full article ">Figure 2
Combined effect of discrimination power of 17 SSR markers represented by average non-exclusion probability of identity of two unrelated individuals (PID) and average non-exclusion probability of identity of two siblings (PIDsib). The markers required for near 100% discrimination of the apple genotypes are marked in yellow. Full article ">Figure 3
Genetic structure of 569 apple genotypes based on STRUCTURE analysis of 17 SSR markers at predefined K = 4. Each genotype is represented by a vertical bar that is partitioned in color according to the inferred membership fraction to clusters 1 to 4 (C1 to C4). The data are sorted by Q-value per age group. The expected heterozygosity (Hexp) per age group is given. Age groups refer to the respective age range of the cultivars. Full article ">Figure 4
Phylogenetic tree of the genetic structure analysis results. Genetic data of 17 SSR markers of 569 apple cultivars were used for tree construction using the neighbor-joining method. Cultivars are marked according to their respective dominant cluster (C1 to C4; Clusters 1 to 4) based on the inferred membership fraction. In each cluster, the cultivar with the highest inferred membership fraction is marked with red font color and additional labels. A high-resolution image is provided in <a href="#app1-plants-13-02699" class="html-app">Supplementary Figure S2</a>. Full article ">

17 pages, 12872 KiB

Open AccessArticle

Altitude-Dependent Morphophysiological, Anatomical, and Metabolomic Adaptations in Rhodiola linearifolia Boriss.

by Nina V. Terletskaya, Malika Erbay, Aigerim Mamirova, Kazhybek Ashimuly, Nazym K. Korbozova, Aigerim N. Zorbekova, Nataliya O. Kudrina and Matthias H. Hoffmann

Plants 2024, 13(19), 2698; https://doi.org/10.3390/plants13192698 - 26 Sep 2024

Abstract

Rhodiola linearifolia Boriss., a perennial alpine plant from the Crassulaceae family, is renowned for its unique medicinal properties. However, existing research on this species is limited, particularly regarding the impact of altitude on its physiological and medicinal compounds. The current study employed morphophysiological [...] Read more.

Rhodiola linearifolia Boriss., a perennial alpine plant from the Crassulaceae family, is renowned for its unique medicinal properties. However, existing research on this species is limited, particularly regarding the impact of altitude on its physiological and medicinal compounds. The current study employed morphophysiological and anatomical methods to explore the adaptive mechanisms of R. linearifolia across different altitudinal gradients, while also examining photosynthetic pigments and metabolomic changes. Our results indicate that despite the simultaneous effects of various mountain abiotic factors, significant correlations can be identified between altitude and trait variation. An optimal growth altitude of 2687 m above sea level was identified, which is pivotal for sustainable ecosystem management and potential species introduction strategies. It is noted that increasing altitude stress enhances the synthesis of secondary antioxidant metabolites in R. linearifolia, enhancing its pharmaceutical potential. Full article

(This article belongs to the Special Issue Responses of Plants and Plant Communities to Environmental Changes in Mountain Areas)

► Show Figures

Figure 1

21 pages, 14187 KiB

Open AccessArticle

Functional Analysis of the PoSERK-Interacting Protein PorbcL in the Embryogenic Callus Formation of Tree Peony (Paeonia ostii T. Hong et J. X. Zhang)

by Yinglong Song, Jiange Wang, Jiale Zhu, Wenqian Shang, Wenqing Jia, Yuke Sun, Songlin He, Xitian Yang and Zheng Wang

Plants 2024, 13(19), 2697; https://doi.org/10.3390/plants13192697 - 26 Sep 2024

Abstract

SERK is a marker gene for early somatic embryogenesis. We screened and functionally verified a SERK-interacting protein to gain insights into tree-peony somatic embryogenesis. Using PoSERK as bait, we identified PorbcL (i.e., the large subunit of Rubisco) as a SERK-interacting protein from a [...] Read more.

SERK is a marker gene for early somatic embryogenesis. We screened and functionally verified a SERK-interacting protein to gain insights into tree-peony somatic embryogenesis. Using PoSERK as bait, we identified PorbcL (i.e., the large subunit of Rubisco) as a SERK-interacting protein from a yeast two-hybrid (Y2H) library of cDNA from developing tree-peony somatic embryos. The interaction between PorbcL and PoSERK was verified by Y2H and bimolecular fluorescence complementation analyses. PorbcL encodes a 586-amino-acid acidic non-secreted hydrophobic non-transmembrane protein that is mainly localized in the chloroplast and plasma membrane. PorbcL was highly expressed in tree-peony roots and flowers and was up-regulated during zygotic embryo development. PorbcL overexpression caused the up-regulation of PoSERK (encoding somatic embryogenesis receptor-like kinase), PoAGL15 (encoding agamous-like 15), and PoGPT1 (encoding glucose-6-phosphate translocator), while it caused the down-regulation of PoLEC1 (encoding leafy cotyledon 1) in tree-peony callus. PorbcL overexpression led to increased indole-3-acetic acid (IAA) content but decreasing contents of abscisic acid (ABA) and 6-benzyladenosine (BAPR). The changes in gene expression, high IAA levels, and increased ratio of IAA to ABA, BAPR, 1-Aminocyclopropanecarboxylic acid (ACC), 5-Deoxystrigol (5DS), and brassinolide (BL) promoted embryogenesis. These results provide a foundation for establishing a tree-peony embryogenic callus system. Full article

(This article belongs to the Special Issue Molecular Mechanisms Involved in Somatic Embryogenesis and Organogenesis of Plants)

► Show Figures

Figure 1

22 pages, 13024 KiB

Open AccessArticle

Developmental Morphology, Physiology, and Molecular Basis of the Pentagram Fruit of Averrhoa carambola

by Wanli Tuo, Chunmei Wu, Xuexuan Wang, Zirui Yang, Lianhuan Xu, Siyuan Shen, Junwen Zhai and Shasha Wu

Plants 2024, 13(19), 2696; https://doi.org/10.3390/plants13192696 - 26 Sep 2024

Abstract

Averrhoa carambola, a key tropical and subtropical economic tree in the Oxalidaceae family, is distinguished by its unique pentagram-shaped fruit. This study investigates the developmental processes shaping the polarity of A. carambola fruit and their underlying hormonal and genetic mechanisms. By analyzing [...] Read more.

Averrhoa carambola, a key tropical and subtropical economic tree in the Oxalidaceae family, is distinguished by its unique pentagram-shaped fruit. This study investigates the developmental processes shaping the polarity of A. carambola fruit and their underlying hormonal and genetic mechanisms. By analyzing the Y1, Y2, and Y3 developmental stages—defined by the fruit diameters of 3–4 mm, 4–6 mm, and 6–12 mm, respectively—we observed that both cell number and cell size contribute to fruit development. Our findings suggest that the characteristic pentagram shape is established before flowering and is maintained throughout development. A hormonal analysis revealed that indole-3-acetic acid (IAA) and abscisic acid (ABA) show differential distribution between the convex and concave regions of the fruit across the developmental stages, with IAA playing a crucial role in polar auxin transport and shaping fruit morphology. A transcriptomic analysis identified several key genes, including AcaGH3.8, AcaIAA20, AcaYAB2, AcaXTH6, AcaYAB3, and AcaEXP13, which potentially regulate fruit polarity and growth. This study advances our comprehension of the molecular mechanisms governing fruit shape, offering insights for improving fruit quality through targeted breeding strategies. Full article

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

► Show Figures

Figure 1

21 pages, 3266 KiB

Open AccessReview

Finally Freed—Cannabis in South Africa: A Review Contextualised within Global History, Diversity, and Chemical Profiles

by Valencia V. Ndlangamandla, Adeola Salawu-Rotimi, Vuyiswa S. Bushula-Njah, Nompilo L. Hlongwane, Gugu F. Sibandze, Fikisiwe C. Gebashe and Nokuthula P. Mchunu

Plants 2024, 13(19), 2695; https://doi.org/10.3390/plants13192695 - 26 Sep 2024

Abstract

Cannabis sativa L. is a monotypic genus belonging to the family Cannabaceae. It is one of the oldest species cultivated by humans, believed to have originated in Central Asia. In pivotal judgements in 2016 and 2018, the South African Constitutional Court legalised the [...] Read more.

Cannabis sativa L. is a monotypic genus belonging to the family Cannabaceae. It is one of the oldest species cultivated by humans, believed to have originated in Central Asia. In pivotal judgements in 2016 and 2018, the South African Constitutional Court legalised the use of Cannabis within the country for medicinal and recreational purposes, respectively. These decrees opened opportunities for in-depth research where previously there had been varying sentiments for research to be conducted on the plant. This review seeks to examine the history, genetic diversity, and chemical profile of Cannabis. The cultivation of Cannabis by indigenous people of southern Africa dates back to the eighteenth century. Indigenous rural communities have been supporting their livelihoods through Cannabis farming even before its legalisation. However, there are limited studies on the plant’s diversity, both morphologically and genetically, and its chemical composition. Also, there is a lack of proper documentation of Cannabis varieties in southern Africa. Currently, the National Centre for Biotechnology Information (NCBI) has 15 genome assemblies of Cannabis obtained from hemp and drug cultivars; however, none of these are representatives of African samples. More studies are needed to explore the species’ knowledge gaps on genetic diversity and chemical profiles to develop the Cannabis sector in southern Africa. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)

► Show Figures

Figure 1

Figure 1
The brief history and movement of Cannabis (illustration adapted from [<a href="#B4-plants-13-02695" class="html-bibr">4</a>,<a href="#B10-plants-13-02695" class="html-bibr">10</a>,<a href="#B12-plants-13-02695" class="html-bibr">12</a>]). Full article ">Figure 2
Morphological differences between 2 (A) female, 2 (B) male plants, and 2 (C) hermaphrodite plants of Cannabis (illustration by V.V Ndlangamandla). Full article ">Figure 3
The morphological variation of C. sativa subsp. sativa, C. sativa. subsp. Indica, and C. sativa subsp. ruderalis (illustration from [<a href="#B55-plants-13-02695" class="html-bibr">55</a>]). Full article ">Figure 4
Glandular trichomes on the surface of the female flower, stem, and leaf of Cannabis, adapted from [<a href="#B77-plants-13-02695" class="html-bibr">77</a>]. Full article ">Figure 5
The biosynthesis pathway leading to the synthesis of cannabinoids, the adapted form from the previous studies [<a href="#B28-plants-13-02695" class="html-bibr">28</a>,<a href="#B67-plants-13-02695" class="html-bibr">67</a>]. Full article ">

18 pages, 5856 KiB

Open AccessArticle

Alleviating Effects of Methyl Jasmonate on Pepper (Capsicum annuum L.) Seedlings under Low-Temperature Combined with Low-Light Stress

by Kaiguo Pu, Nenghui Li, Yanqiang Gao, Miao Zhang, Tiantian Wang, Jianming Xie and Jing Li

Plants 2024, 13(19), 2694; https://doi.org/10.3390/plants13192694 - 26 Sep 2024

Abstract

Low temperature combined with low light (LL) is an important factor limiting pepper quality and yield. ‘Hang Jiao No. 2′ were used as experimental materials, and different concentrations of MeJA (T1 (0 μM), T2 (100 μM), T3 (150 μM), T4 (200 μM), T5 [...] Read more.

Low temperature combined with low light (LL) is an important factor limiting pepper quality and yield. ‘Hang Jiao No. 2′ were used as experimental materials, and different concentrations of MeJA (T1 (0 μM), T2 (100 μM), T3 (150 μM), T4 (200 μM), T5 (250 μM) and T6 (300 μM)) were sprayed under LL stress to explore the positive effect of exogenous methyl jasmonate (MeJA) on peppers under LL stress. The photosynthetic properties, osmoregulatory substance, reactive oxygen species, antioxidant enzyme activities, and related gene expressions of the peppers were measured. Our results demonstrated that 200 μM MeJA treatment significantly increased chlorophyll content, light quantum flux per active RC electron transfer (Eto/RC), maximum captured photonic flux per active RC (TRo/RC), energy flux for electron transfer in the excitation cross section (Eto/CSm), energy flux captured by absorption in the excitation cross section (TRo/CSm), soluble protein, and soluble sugar content. Moreover, it significantly improved the maximum photochemical efficiency of PSII (Fv/Fm) and performance index based on absorbed light energy (PI (abs)) by 56.77% and 67.00%, respectively, and significantly decreased malondialdehyde (MDA) content and relative conductivity by 30.55% and 28.17%, respectively. Additionally, antioxidant enzyme activities were elevated, and the expression of the related genes was activated in pepper seedlings under stress, leading to a significant reduction in reactive oxygen species content. In conclusion, our findings confirmed that 200 μM MeJA could reduce the injury of LL to pepper leaves to the photosynthetic organs of pepper leaves, protect the integrity of the cell membrane, and further improve the tolerance of pepper seedlings to LL. Full article

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

► Show Figures

Figure 1

Figure 1
Effect of different concentrations of MeJA on stem height and stem thickness of pepper seedlings under LL stress. T1, 0 μM MeJA. T2, 100 μM MeJA. T3, 150 μM MeJA. T4, 200 μM MeJA. T5, 250 μM MeJA. T6, 300 μM MeJA. The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) Stem height and stem thickness. (B) Fresh weight. (C) Dry weight. Full article ">Figure 2
Effects of different concentrations of MeJA on MDA and relative conductivity of pepper seedlings under low temperature combined with low-light stress. The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) MDA content. (B) Relative electrical conductivity. Full article ">Figure 3
Effect of different concentrations of MeJA on the superoxide anion content of pepper seedlings under low temperature combined with low-light stress: The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) NBT histochemical staining. (B) O2− content. Full article ">Figure 4
Effect of different concentrations of MeJA on chlorophyll content of pepper seedlings under low temperature combined with low-light stress. The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) Chlorophyll a content. (B) Chlorophyll b content. (C) Chlorophyll a+b content. Full article ">Figure 5
Visual analysis of chlorophyll fluorescence parameters of low temperature combined with low light pepper seedlings treated with different concentrations of MeJA. Images of Fv/Fm, Y(II), qP and qN. Full article ">Figure 6
Effects of different concentrations of MeJA on chlorophyll fluorescence kinetics (OJIP curves), JIP-test parameters of pepper seedlings, energy allocation to individual active reaction centers, and energy allocation per unit cross section in pepper seedlings under low temperature combined with low-light stress: The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) OJIP curves. (B) JIP-test parameters. (C) Electron absorption, capture, transfer, and dissipation energy per unit active reaction center. (D) Electron absorption, capture, transfer, and dissipation energies per unit cross section. Full article ">Figure 7
Effects of different concentrations of MeJA on soluble proteins and soluble sugars in pepper seedlings at low temperature combined with low-light stress. The results are expressed as the mean ± SE of five replicates, and the different letters denote the significant difference among treatments (p < 0.05), according to Duncan’s multiple tests. (A) Soluble protein content. (B) Soluble sugar content. Full article ">Figure 8
Effects of different concentrations of MeJA on antioxidant enzyme activities and expression of related genes in pepper seedlings under low temperature combined with low-light stress: (A–C) SOD, POD, CAT activity. (D–F) CaSOD, CaPOD, CaCAT relative expression. Full article ">

24 pages, 14977 KiB

Open AccessArticle

Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in Sinopodophyllum hexandrum Seeds

by Rongchun Ning, Caixia Li, Tingting Fan, Tingting Ji and Wenhua Xu

Plants 2024, 13(19), 2693; https://doi.org/10.3390/plants13192693 - 26 Sep 2024

Abstract

Sinopodophyllum hexandrum (Royle) Ying, an endangered perennial medicinal herb, exhibits morpho-physiological dormancy in its seeds, requiring cold stratification for germination. However, the precise molecular mechanisms underlying this transition from dormancy to germination remain unclear. This study integrates transcriptome and plant hormone-targeted metabolomics techniques [...] Read more.

Sinopodophyllum hexandrum (Royle) Ying, an endangered perennial medicinal herb, exhibits morpho-physiological dormancy in its seeds, requiring cold stratification for germination. However, the precise molecular mechanisms underlying this transition from dormancy to germination remain unclear. This study integrates transcriptome and plant hormone-targeted metabolomics techniques to unravel these intricate molecular regulatory mechanisms during cold stratification in S. hexandrum seeds. Significant alterations in the physicochemical properties (starch, soluble sugars, soluble proteins) and enzyme activities (PK, SDH, G-6-PDH) within the seeds occur during stratification. To characterize and monitor the formation and transformation of plant hormones throughout this process, extracts from S. hexandrum seeds at five stratification stages of 0 days (S0), 30 days (S1), 60 days (S2), 90 days (S3), and 120 days (S4) were analyzed using UPLC-MS/MS, revealing a total of 37 differential metabolites belonging to seven major classes of plant hormones. To investigate the biosynthetic and conversion processes of plant hormones related to seed dormancy and germination, the transcriptome of S. hexandrum seeds was monitored via RNA-seq, revealing 65,372 differentially expressed genes associated with plant hormone synthesis and signaling. Notably, cytokinins (CKs) and gibberellins (GAs) exhibited synergistic effects, while abscisic acid (ABA) displayed antagonistic effects. Furthermore, key hub genes were identified through integrated network analysis. In this rigorous scientific study, we systematically elucidate the intricate dynamic molecular regulatory mechanisms that govern the transition from dormancy to germination in S. hexandrum seeds during stratification. By meticulously examining these mechanisms, we establish a solid foundation of knowledge that serves as a scientific basis for facilitating large-scale breeding programs and advancing the artificial cultivation of this highly valued medicinal plant. Full article

(This article belongs to the Special Issue Metabolomics in Medicinal Plants and Agricultural Research)

► Show Figures

Figure 1

18 pages, 2783 KiB

Open AccessArticle

The Ectopic Expression of the MpDIR1(t) Gene Enhances the Response of Plants from Arabidopsis thaliana to Biotic Stress by Regulating the Defense Genes and Antioxidant Flavonoids

by Mingzheng Duan, Liuyuan Bao, Momina Eman, Duo Han, Yongzhi Zhang, Bingsong Zheng, Shunqiang Yang and Muhammad Junaid Rao

Plants 2024, 13(19), 2692; https://doi.org/10.3390/plants13192692 - 25 Sep 2024

Abstract

The Defective in Induced Resistance 1 (DIR1) gene, a member of the lipid transferase proteins (LTPs), plays a crucial role in plant defense against pathogens. While previous transcriptomic studies have highlighted the significant expression of citrus LTPs during biotic stress, functional [...] Read more.

The Defective in Induced Resistance 1 (DIR1) gene, a member of the lipid transferase proteins (LTPs), plays a crucial role in plant defense against pathogens. While previous transcriptomic studies have highlighted the significant expression of citrus LTPs during biotic stress, functional annotations of LTPs in the Citrus genera remain limited. In this study, we cloned the Murraya paniculata DIR1 (MpDIR1(t)) gene and overexpressed it in Arabidopsis thaliana to evaluate its stress response mechanisms against biotic stress. The transgenic Arabidopsis lines showed fewer disease symptoms in response to Pseudomonas syringae (Pst DC3000) compared to wild-type Arabidopsis. Defense and pathogenesis-responsive genes such as PR1, PR4, PR5, and WRKY12 were significantly induced, showing a 2- to 12-fold increase in all transgenic lines compared to the wild type. In addition, the Pst DC3000-infected transgenic Arabidopsis lines demonstrated elevated levels of flavonoids and salicylic acid (SA), along with higher expression of SA-related genes, compared to the wild type. Moreover, all transgenic lines possessed lower reactive oxygen species levels and higher activity of antioxidant defense enzymes such as superoxide dismutase, peroxidase, and catalase under Pst DC3000 stress compared to the wild type. The up-regulation of defense genes, activation of the SA pathway, accumulation of flavonoids, and reinforcement of antioxidant defense mechanisms in transgenic Arabidopsis lines in response to Pst DC3000 underscore the critical role of MpDIR1(t) in fortifying plant immunity. Thus, MpDIR1(t) constitutes a promising candidate gene for improving bacterial disease resistance in commercial citrus cultivars. Full article

(This article belongs to the Special Issue Plant Defense against Pathogens: Micro- to Molecular Insights)

► Show Figures

Figure 1

24 pages, 3840 KiB

Open AccessArticle

Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes

by Furrukh Mehmood, Mingai Li, Alessio Bertolli, Filippo Prosser and Claudio Varotto

Plants 2024, 13(19), 2691; https://doi.org/10.3390/plants13192691 - 25 Sep 2024

Abstract

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications [...] Read more.

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species’ adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products. Full article

(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)

► Show Figures

Figure 1

12 pages, 3410 KiB

Open AccessArticle

Genome-Wide Identification of the COMT Gene Family in Juglans regia L. and Response to Drought Stress

by Xiaolan Ma, Hongjia Luo, Jianhong Li, Zhiyue Wei, Yanlong Gao, Zhongxing Zhang and Yanxiu Wang

Plants 2024, 13(19), 2690; https://doi.org/10.3390/plants13192690 - 25 Sep 2024

Abstract

Caffeic acid O-methyltransferase (COMT), as a multifunctional enzyme involved in various physiological and biochemical processes in lignin metabolism, plays an important role in a plant’s response to stress. In this study, we isolated COMT family members from the walnut genome by [...] Read more.

Caffeic acid O-methyltransferase (COMT), as a multifunctional enzyme involved in various physiological and biochemical processes in lignin metabolism, plays an important role in a plant’s response to stress. In this study, we isolated COMT family members from the walnut genome by bioinformatics and analyzed their physicochemical properties and their expression under drought stress to provide gene resources for drought resistance in walnut. The results showed that 33 COMT genes were identified from walnuts and distributed on different chromosomes. The molecular weight of proteins varies greatly. According to the phylogenetic tree, the family can be divided into seven subgroups, which are relatively conservative in evolution and closely related to Arabidopsis thaliana. Promoter analysis showed that the promoter of the walnut COMT gene contains rich cis-elements of plant hormone response and stress response, and the real-time fluorescence scale name can be significantly induced by drought stress. Compared with wild-type Arabidopsis, overexpression JrCOMT19 significantly increased the enzyme activity (SOD, POD, and CAT) and proline content. Meanwhile, overexpression of JrCOMT19 significantly increased the lignin content and expression of related genes. Therefore, JrCOMT plays an important role in responding to drought in walnuts, and overexpression JrCOMT19 can improve the resistance to drought stress by increasing lignin content, antioxidant enzyme activity, and osmotic substance content. Full article

(This article belongs to the Special Issue Crop Stress Tolerance and Green Production: Celebrating the 90th Anniversary of the Founding of Northwest A&F University)

► Show Figures

Figure 1

Figure 1
Bioinformatics analysis of JrCOMT gene family. (a) Domain specific to the COMT family. (b) Chromosome mapping of JrCOMT family genes. (c) Evolutionary tree analysis of JrCOMT and AtCOMT genes. The phylogenetic tree was generated using MEGA. The different colors in the figure represent the evolutionary tree groups (A–G) of JrCOMT and AtCOMT; the green dots represent the JrCOMTs gene, and the red five-pointed stars represent the AtCOMTs gene. (d) Cis-acting element analysis of JrCOMT family genes. Two kb 5′ upstream regions of all the identified JrCOMT genes were retrieved and analyzed through the PlantCARE database to identify the presence. The different cis-regulatory elements on each of the promoters were represented with different colors. (e) Intraspecific collinearity analysis of JrCOMT family genes. Sixteen chromosomes are represented in partial circles with different colors. Jrcomt genes in different chromosomes are indicated by black labels. Same colored lines connecting two chromosomal regions indicate the duplicated gene pairs in Medicago. The illustration was generated using CIRCOS-0.69-9 software. Full article ">Figure 2
Heat map of JrCOMTs expression under drought stress. The expressive level of 9 different JrCOMTs genes at 0, 6, 12, 24, 48, and 72 h. Expression data were retrieved from genevestigator (<a href="https://genevestigator.com/gv/" target="_blank">https://genevestigator.com/gv/</a>, accessed on 5 August 2024), and the heatmap was created with hierarchical clustering of Manhattan distance correlation using MeV 4.9.0 software package. A color scale is provided along with the heat map to recognize the differential pattern of expression. Full article ">Figure 3
Bioinformatics analysis of JrCOMT19 gene. (a) Secondary structure of JrCOMT. (b) Evolutionary tree analysis of JrCOMT and other species. Protein sequences for other species were downloaded from NCBI. The phylogenetic tree was generated using MEGA. (c) The tertiary structure of JrCOMT. (d) Cis-acting element of JrCOMT. Full article ">Figure 4
Amplification and expression of JrCOMT19 gene in transgenic Arabidopsis thaliana. (a) Glue map of JrCOMT19 gene clone. (b) Expression levels of JrCOMT gene in WT and transgenic Arabidopsis thaliana. “*” means that the difference between samples is significant at the level of 0.05 (p < 0.05). Data are means of three replicates with SE. Values not followed by the same letter indicate significant differences between treatments, according to Duncan method of single-factor ANOVA (p < 0.05). Full article ">Figure 5
The phenotypes of JrCOMT19-OE and wild-type (WT) A. thaliana under normal conditions (CK) and drought stress (T). (a) Phenotypes of wild and transgenic Arabidopsis thaliana under drought stress. H, S, and G represent three different types of lignin. (b) Lignin content. (c) Relative water content. (d) Relative expression level of genes resulting in lignin. “ns” means that the difference between samples is not significant, and “*” means that the difference between samples is significant at the level of 0.05 (p < 0.05). Data are means of three replicates with SE. Values not followed by the same letter indicate significant differences between treatments, according to Duncan method of single-factor ANOVA (p < 0.05). Full article ">Figure 6
Physiological indices of JrCOMT19 and wild-type (WT) A. thaliana under normal conditions (CK) and drought stress (T). (a) The Chl content. (b) The CAT activities. (c) The Pro content. (d) The POD activities. (e) The SOD activities. (f) The REC conductivity. “ns” means that the difference between samples is not significant, and “*” means that the difference between samples is significant at the level of 0.05 (p < 0.05). Data are means of three replicates with SE. Values not followed by the same letter indicate significant differences between treatments, according to Duncan method of single-factor ANOVA (p < 0.05). Full article ">

12 pages, 2892 KiB

Open AccessArticle

Enhancing Red Table Grape Coloration Using Tsikoudia: A Novel and Sustainable Approach

by Emmanouil Kontaxakis, Dimitrios Lydakis and Ioannis Fisarakis

Plants 2024, 13(19), 2689; https://doi.org/10.3390/plants13192689 - 25 Sep 2024

Abstract

Achieving optimal coloration in red table grapes, especially in warm-climate regions, presents significant challenges due to high temperatures that inhibit anthocyanin biosynthesis. Conventional methods to enhance grape coloration, including the use of abscisic acid (ABA), ethephon, foliar nutrient supplementation, and viticultural practices like [...] Read more.

Achieving optimal coloration in red table grapes, especially in warm-climate regions, presents significant challenges due to high temperatures that inhibit anthocyanin biosynthesis. Conventional methods to enhance grape coloration, including the use of abscisic acid (ABA), ethephon, foliar nutrient supplementation, and viticultural practices like cluster trimming and girdling, have limitations related to cost, regulatory restrictions, and potential adverse effects on grapes quality. This study proposes the application of tsikoudia, a traditional Greek alcoholic beverage, as a novel, sustainable, and cost-effective alternative to conventional practices. Tsikoudia, applied during the veraison stage, significantly improved the coloration of ‘Crimson Seedless’ and ‘Red Globe’ grapes by enhancing anthocyanin accumulation and altering color parameters. Specifically, lightness (L*), chroma (C*), and hue angle (h), measured using the CIE-Lab color system, were reduced, while the Color Index for Red Grapes (CIRG) was increased. Additionally, total anthocyanin content, determined through spectrophotometric analysis, also showed an increase. These changes indicate a more intense red coloration. This research highlights the effectiveness of tsikoudia in improving grape coloration and contributes to the development of more sustainable viticultural practices. Full article

(This article belongs to the Special Issue All about Viticulture and Vineyard Management: Development, Innovation and Sustainability)

► Show Figures

Figure 1

Figure 1
Effect of treatments on the coloration of ‘Crimson Seedless’ grapes, expressed as CIE-Lab color parameters lightness (L*), chroma (C*), hue angle (h), and Color Index for Red Grapes (CIRG). The different letters for each year (in italics for the 2023) indicate significant differences according to Duncan’s multiple range test (p ≤ 0.05) among the treatments. Error bars represent the standard errors of the means. Full article ">Figure 2
Effect of treatments on the coloration of ‘Red Globe’ grapes, expressed as CIE-Lab color parameters lightness (L*), chroma (C*), hue angle (h), and Color Index for Red Grapes (CIRG). The different letters for each year (in italics for the 2023) indicate significant differences according to Duncan’s multiple range test (p ≤ 0.05) among the treatments. Error bars represent the standard errors of the means. Full article ">Figure 3
Effect of treatments on the total anthocyanin content in ‘Crimson Seedless’ and ‘Red Globe’ grape skins. The different letters for each year (in italics for the 2023) indicate significant differences according to Duncan’s multiple range test (p ≤ 0.05) among the treatments. Error bars represent the standard errors of the means. Full article ">

17 pages, 6508 KiB

Open AccessArticle

RNA-Seq Analysis and Candidate Gene Mining of Gossypium hirsutum Stressed by Verticillium dahliae Cultured at Different Temperatures

by Ni Yang, Zhaolong Gong, Yajun Liang, Shiwei Geng, Fenglei Sun, Xueyuan Li, Shuaishuai Qian, Chengxia Lai, Mayila Yusuyin, Junduo Wang and Juyun Zheng

Plants 2024, 13(19), 2688; https://doi.org/10.3390/plants13192688 - 25 Sep 2024

Abstract

The occurrence and spread of Verticillium dahliae (V. dahliae) in cotton depends on the combined effects of pathogens, host plants, and the environment, among which temperature is one of the most important environmental factors. Studying how temperature impacts the occurrence of [...] Read more.

The occurrence and spread of Verticillium dahliae (V. dahliae) in cotton depends on the combined effects of pathogens, host plants, and the environment, among which temperature is one of the most important environmental factors. Studying how temperature impacts the occurrence of V. dahliae in cotton and the mechanisms governing host defense responses is crucial for disease prevention and control. Understanding the dual effects of temperature on both pathogens and hosts can provide valuable insights for developing effective strategies to manage this destructive fungal infection in cotton. This study was based on the deciduous V. dahliae Vd-3. Through cultivation at different temperatures, Vd-3 formed the most microsclerotia and had the largest colony diameter at 25 °C. Endospore toxins were extracted, and 48 h was determined to be the best pathogenic time point for endotoxins to infect cotton leaves through a chlorophyll fluorescence imaging system and phenotypic evaluation. Transcriptome sequencing was performed on cotton leaves infected with Vd-3 endotoxins for 48 h at different culture temperatures. A total of 34,955 differentially expressed genes (DEGs) were identified between each temperature and CK (no pathogen inoculation), including 17,422 common DEGs. The results of the enrichment analysis revealed that all the DEGs were involved mainly in photosynthesis and sugar metabolism. Among the 34,955 DEGs, genes in the biosynthesis and signal transduction pathways of jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) were identified, and their expression patterns were determined. A total of 5652 unique DEGs were clustered into six clusters using the k-means clustering algorithm, and the functions and main transcription factors (TFs) of each cluster were subsequently annotated. In addition, we constructed a gene regulatory network via weighted correlation network analysis (WGCNA) and identified twelve key genes related to cotton defense against V. dahliae at different temperatures, including four genes encoding transcription factors. These findings provide a theoretical foundation for investigating temperature regulation in V. dahliae infecting cotton and introduce novel genetic resources for enhancing resistance to this disease in cotton plants. Full article

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

► Show Figures

Figure 1

9 pages, 1844 KiB

Open AccessArticle

An Improved Sampling and Baiting Method for Phytophthora tropicalis and P. heveae Detection in Macadamia integrifolia

by Christopher M. Ference and Lisa M. Keith

Plants 2024, 13(19), 2687; https://doi.org/10.3390/plants13192687 - 25 Sep 2024

Abstract

Macadamia nuts are, economically, the second most important crop in the state of Hawai’i. A recent decline in yield and acreage has been attributed to insect damage and diseases such as Macadamia Quick Decline (MQD) caused by Phytophthora tropicalis and P. heveae. [...] Read more.

Macadamia nuts are, economically, the second most important crop in the state of Hawai’i. A recent decline in yield and acreage has been attributed to insect damage and diseases such as Macadamia Quick Decline (MQD) caused by Phytophthora tropicalis and P. heveae. To develop an improved methodology for the diagnosis and treatment of MQD, investigations were undertaken to better understand the pathosystem of the disease. These investigations included sampling from multiple locations from sectioned trees utilizing two methods of tissue collection and isolations using two baiting techniques. The collection of tissue from the cambium and phloem of trees after scraping away the bark and in locations of recent or current sap exudation using a narrow diameter steel awl proved to be an efficient means for the molecular detection of the MQD pathogens from infected trees exhibiting MQD symptoms. In addition, a more efficient and cost-effective baiting method using apple puree was developed. Full article

(This article belongs to the Special Issue Novel Methods for Detection and Control Strategies of Phytopathogens)

► Show Figures

Figure 1

14 pages, 1186 KiB

Open AccessReview

The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant–Soil Systems: A Review

by Ying Zhu, Yijing Xing, Yue Li, Jingyi Jia, Yeqing Ying and Wenhui Shi

Plants 2024, 13(19), 2686; https://doi.org/10.3390/plants13192686 - 25 Sep 2024

Abstract

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. [...] Read more.

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency. Full article

(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)

► Show Figures

Figure 1

17 pages, 3076 KiB

Open AccessArticle

Transcriptome Profiling Identifies Plant Hormone Signaling Pathway-Related Genes and Transcription Factors in the Drought and Re-Watering Response of Ginkgo biloba

by Meiling Ming, Juan Zhang, Jiamin Zhang, Jing Tang, Fangfang Fu and Fuliang Cao

Plants 2024, 13(19), 2685; https://doi.org/10.3390/plants13192685 - 25 Sep 2024

Abstract

Ginkgo biloba, usually referred to as a “living fossil,” is widely planted in many countries because of its medicinal value and beautiful appearance. Owing to ginkgo’s high resistance to drought stress, ginkgo seedlings can even survive withholding water for several days without [...] Read more.

Ginkgo biloba, usually referred to as a “living fossil,” is widely planted in many countries because of its medicinal value and beautiful appearance. Owing to ginkgo’s high resistance to drought stress, ginkgo seedlings can even survive withholding water for several days without exhibiting leaf wilting and desiccation. To assess the physiological and transcriptomic mechanisms involved in the drought stress and re-watering responses of Ginkgo biloba, ginkgo seedlings were subjected to drought treatment for 15 d (D_15 d) and 22 d (D_22 d) until they had severely wilted, followed by re-watering for 3 d (D_Re3 d) to restore normal growth. Variations in physiological characteristics (relative water content, malondialdehyde (MDA) content, stomatal aperture, and antioxidant enzyme activity) during drought and re-watering were assessed. In total, 1692, 2031, and 1038 differentially expressed genes (DEGs) were upregulated, while 1691, 2820, and 1910 were downregulated in D_15 d, D_22 d, and D_Re3 d, respectively, relative to the control. Three pathways, namely, plant hormone signal transduction, plant–pathogen interaction, and the plant MAPK signaling pathway, were enriched during drought stress and re-watering. The DEGs involved in plant hormone signal transduction pathways (those of IAA, CTK, GA, ABA, ETH, BR, SA, and JA) and the major differentially expressed transcription factors (TFs; MYB, bHLH, AP2/ERF, NAC, WRKY, and bZIP) were identified. Quantitative real-time PCR revealed six TFs as positive or negative regulators of drought stress response. These phenotype-related physiological characteristics, DEGs, pathways, and TFs provide valuable insights into the drought stress and re-watering responses in G. biloba. Full article

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

► Show Figures

Figure 1

Figure 1
Phenotypes, physiological, and biochemical characteristics of G. biloba under drought and re-watering treatments. (A) Phenotypes of G. biloba drought for 0 d, 15 d, 22 d and re-watering 3 d, compared with the control group (CK) with regular irrigation. (B) Relative water content. (C) Malondialdehyde (MDA) content. (D) Stomatal aperture. (E) Catalase (CAT) activity. (F) Superoxide dismutase (SOD) activity. (G) Peroxidase (POD) activity. All data are presented as the mean ± SDs (n ≥ 3 biological replicates). Lowercase letters above bars indicate significant differences as determined by one-way ANOVA test followed by Tukey’s multiple comparisons test (p < 0.05). Full article ">Figure 2
Identification and analysis of differentially expressed genes (DEGs) in G. biloba leaves during drought and re-watering treatments. (A) Principal component analysis of 21 samples based on transcripts per kilobase of exon model per million mapped reads (TPM). (B) Hierarchical clustering analysis of 21 samples based on Manhattan distance. (C) Number of DEGs in the drought and re-watering treatments. (D,E) Venn diagram of DEGs in the drought and re-watering treatments. (F–H) Volcano plots of DEGs at D_15 d vs. CK_15 d, D_22 d vs. CK_22 d, and D_Re3 d vs. CK_Re3 d. Red and blue dots indicate significantly upregulated and downregulated genes, respectively. The labeled genes indicate the most significantly differentially expressed genes. Full article ">Figure 3
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs in the leaves of G. biloba under drought and re-watering treatments. (A) The top 10 GO enrichment items for each group. (B) The top 10 KEGG enrichment items for each group. D: drought; CK: control with regular irrigation. Full article ">Figure 4
DEGs involved in plant hormone signal transduction during drought and re-watering treatments in G. biloba. (A) Schematic representation of the plant hormone signal transduction pathway. DEGs encoding key enzymes are shaded, and their expression is presented in the heatmap. The small, yellow five-pointed star indicates genes belonging to TFs. (B–H) Heatmap of DEGs encoding the auxin (IAA), cytokinin (CTK), gibberellin (GA), abscisic acid (ABA), ethylene (ETH), salicylic acid (SA), and brassinosteroid (BR) signal transduction pathways. Full article ">Figure 5
The major differentially expressed transcription factor families involved in the drought and re-watering treatments in G. biloba. (A) MYB. (B) AP2/ERF. (C) bHLH. (D) bZIP. (E) WRKY. (F) NAC. Genes labeled with red and blue rectangles indicate upregulation and downregulation, respectively. Full article ">Figure 6
The relative expression levels of key differentially expressed transcription factors based on qRT-PCR analysis. (A) Upregulated MYB. (B) Downregulated MYB. (C) Downregulated WRKY. (D) Downregulated bZIP. (E) Downregulated NAC. (F) Downregulated AP2/ERF. Full article ">

22 pages, 11500 KiB

Open AccessArticle

Overexpression of Auxin/Indole-3-Acetic Acid Gene TrIAA27 Enhances Biomass, Drought, and Salt Tolerance in Arabidopsis thaliana

by Muhammad Zafar Iqbal, Yuzhou Liang, Muhammad Anwar, Akash Fatima, Muhammad Jawad Hassan, Asif Ali, Qilin Tang and Yan Peng

Plants 2024, 13(19), 2684; https://doi.org/10.3390/plants13192684 - 25 Sep 2024

Abstract

White clover (Trifolium repens L.) is an important forage and aesthetic plant species, but it is susceptible to drought and heat stress. The phytohormone auxin regulates several aspects of plant development and alleviates the effects of drought stress in plants, including white [...] Read more.

White clover (Trifolium repens L.) is an important forage and aesthetic plant species, but it is susceptible to drought and heat stress. The phytohormone auxin regulates several aspects of plant development and alleviates the effects of drought stress in plants, including white clover, by involving auxin/indole acetic acid (Aux/IAA) family genes. However, Aux/IAA genes and the underlying mechanism of auxin-mediated drought response remain elusive in white clover. To extend our understanding of the multiple functions of Aux/IAAs, the current study described the characterization of a member of the Aux/IAA family TrIAA27 of white clover. TrIAA27 protein had conserved the Aux/IAA family domain and shared high sequence similarity with the IAA27 gene of a closely related species and Arabidopsis. Expression of TrIAA27 was upregulated in response to heavy metal, drought, salt, NO, Ca²⁺, H₂O₂, Spm, ABA, and IAA treatments, while downregulated under cold stress in the roots and leaves of white clover. TrIAA27 protein was localized in the nucleus. Constitutive overexpression of TrIAA27 in Arabidopsis thaliana led to enhanced hypocotyl length, root length, plant height, leaf length and width, and fresh and dry weights under optimal and stress conditions. There was Improved photosynthesis activity, chlorophyll content, survival rate, relative water content, endogenous catalase (CAT), and peroxidase (POD) concentration with a significantly lower electrolyte leakage percentage, malondialdehyde (MDA) content, and hydrogen peroxide (H₂O₂) concentration in overexpression lines compared to wild-type Arabidopsis under drought and salt stress conditions. Exposure to stress conditions resulted in relatively weaker roots and above-ground plant growth inhibition, enhanced endogenous levels of major antioxidant enzymes, which correlated well with lower lipid peroxidation, lower levels of reactive oxygen species, and reduced cell death in overexpression lines. The data of the current study demonstrated that TrIAA27 is involved in positively regulating plant growth and development and could be considered a potential target gene for further use, including the breeding of white clover for higher biomass with improved root architecture and tolerance to abiotic stress. Full article

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

► Show Figures

Figure 1

Figure 1
The gene sequence characteristics and phylogenetic analysis of the Tr-IAA27 gene of white clover. (a) Amplified band of Tr-IAA27 from white clover cDNA; (b) homology of nucleotides bases of Tr-IAA27 with closely related species; (c) comparison of amino acid sequences of Tr-IAA27 with other related IAA27 proteins, highly homolog amino acid residues are shaded; (d) phylogenetic relationship of Tr-IAA27 proteins with same protein from closely related species and Arabidopsis thaliana; triangles in branches represent bootstrap values, and the phylogenetic tree analysis was based on minimum evolution using Mega (version 11). Full article ">Figure 2
Relative expression of Tr-IAA27 in white clover in response to different external stimuli. (a–k) Show relative expression of TrIAA27 gene in response to treatments of heavy metal (600 mM CdSO4), cold (4 °C), heat (35 °C), drought (15% PEG6000 w/v), salt (200 mM NaCl), NO (25 μM), Ca2+ (5 mM), H2O2 (10 mM), Spm (20 mM), ABA (100 μM), and IAA (1 mM), respectively. (l) Expression of TrIAA27 in wild-type Arabidopsis and 5 overexpression lines (OE1-5) of Arabidopsis. Different alphabet letters over bars show statistically significant differences (ANOVA, p < 0.05), and the error bar shows standard error (SE). Full article ">Figure 3
Subcellular localization of TrIAA27 in tobacco leaves. The TrIAA27::GFP vector and an empty vector were transferred into tobacco leaves for transient expression and observed under the fluorescent microscope. The green color shows signals of the TrIAA27 protein. Full article ">Figure 4
Phenotypic comparison of growth performance indicators between wild-type (WT) and TrIAA27 overexpression Arabidopsis lines (OE3 and OE5). (a–c) Display hook angles of WT, OE3, and OE5, respectively. (d,i) Show a comparison of hypocotyl length between WT, OE3, and OE5. (e,j,k) Roots growth comparison of WT, OE3, and OE5 grown on ½ MS medium supplemented with 3% sucrose and 0.7% agar. (f,m,n) Leaf length and width differences among WT, OE3, and OE5. (g,h,i,l,o,p) Growth performance, hypocotyl length, plant height, fresh weight, and dry weight of WT, OE3, and OE5, respectively. Different alphabet letters over bars show statistically significant differences (ANOVA, p < 0.05) among genotypes, and the error bar shows standard error (SE). WT, OE3, and OE5 represent wild types, overexpression lines 3 and 5, respectively. Full article ">Figure 5
Growth performance of wild-type (WT) and TrIAA27 overexpression lines (OE3 and OE5) under drought stress conditions. (a) Phenotypical comparison of WT, OE3, and OE5 grown on ½ MS media containing 3% sucrose and 0.7% agar supplemented with 0 mM mannitol, 100 mM mannitol, or 200 mM mannitol on 5th and 10th d. (b) Phenotypes of WT, OE3, and OE5 grown in soil after irrigation withholding at 15 d. (c–j) Display statistical comparisons of secondary roots no., roots length, fresh weights, dry weights, photochemical efficiency (Fm/Fv ratio), performance index on an absorption basis (PI), relative water content %, and electrolyte leakage %, respectively. Different alphabet letters over bars show statistically significant differences (ANOVA, p < 0.05) among genotypes; N.S represents statistically non-significant differences. The error bar shows standard error (SE). WT, OE3, and OE5 represent wild types, overexpression line 3 and overexpression line 5, respectively. Full article ">Figure 6
Growth performance comparison of wild-type (WT) and TrIAA27 overexpression (OE) Arabidopsis lines under salt stress conditions. (a) Performance of WT, OE3, and OE5 on ½ MS media supplemented with 150 mM NaCl at day 10. (b) Performance of WT, OE3, and OE5 in soil irrigated with saline water. (c–i) Statistical comparisons of photochemical efficiency Fm/Fv, performance index on an absorption basis, relative water content %, electrolyte leakage %, chlorophyll contents, survival rates, and root length, respectively. Different alphabet letters over bars show statistically significant differences (ANOVA, p < 0.05) among genotypes, and the error bar shows standard error (SE). WT, OE3, and OE5 represent wild types, overexpression line 3, and overexpression line 5, respectively. Full article ">Figure 7
The comparative analysis of endogenous oxidants and antioxidant levels in the wild-type and overexpression TrIAA27 Arabidopsis under drought and salt stress conditions. (a) Relative malondialdehyde (MDA) contents, (b) relative hydrogen peroxide (H2O2) concentration, (c) endogenous catalase (CAT), and (d) the peroxidase (POD) concentration in the leaves of wild-type and TrIAA27-overexpressing Arabidopsis. Different alphabet letters over bars show statistically significant differences (ANOVA, p < 0.05) among genotypes, and the error bar shows standard error (SE). WT, OE3, and OE5 represent wild types, overexpression line 3, and overexpression line 5, respectively. Full article ">

15 pages, 4124 KiB

Open AccessArticle

Effect of Environmental and Anthropic Conditions on the Development of Solanum peruvianum: A Case of the Coastal Lomas, Lima-Peru

by Vladimir Camel, July Quispe-Huañahue, Edwin Felix, Zulema Ninanya-Parra, Yngrid Mendoza, Sebastian Peralta-Yalta, Freddy Pillpa and Rita Cabello-Torres

Plants 2024, 13(19), 2683; https://doi.org/10.3390/plants13192683 - 25 Sep 2024

Abstract

Land degradation and the effects of climate change are increasing arid lands, accelerating desertification, and leading to the loss of ecosystem services worldwide. This research focused on evaluating how human impact and environmental factors affect the development of Solanum peruvianum in its natural [...] Read more.

Land degradation and the effects of climate change are increasing arid lands, accelerating desertification, and leading to the loss of ecosystem services worldwide. This research focused on evaluating how human impact and environmental factors affect the development of Solanum peruvianum in its natural habitat of coastal lomas. The study was carried out in the coastal lomas of Mangomarca-Peru, where phenotypic and ecological data on the plants were collected. Information was also gathered on human impacts on the nutritional characteristics of the soils. Then, five types of organic amendments were used to improve the physical and chemical characteristics of the degraded soil, and the development and photosynthetic activity of S. peruvianum were evaluated. As a result, under the study conditions, it was found that S. peruvianum was established approximately 33.74 cm from the rocks, in a range of 300 to 650 m asl. The maximum height of the plants was 90 cm, with a stem diameter at ground level of 2 cm. S. peruvianum produced fruits between January and July, with a seed germination rate of 36% in 25 days. On the other hand, the anthropogenic impact on the soil reduced 58% of organic material (OM), 71% of nitrogen, 40% of P₂O₅, and 13% of K₂O and increased the concentration of magnesium oxide, calcium oxide, pH, and electric conductivity (EC). The organic amendments bokashi, compost, and biochar, when mixed with the degraded soil, increased the pH, OM, N, P, and EC; however, the plants died after 25 days. On the other hand, the application of the Premix5 substrate for 100 days favored the growth of 52.84 cm and 38.29 cm in the preserved soil and 23.21 cm in the black soil mixed with blond peat, and it should be noted that the substrates presented an acid pH and EC > 0.1. Regarding photosynthetic phenotyping, S. peruvianum plants grown in their natural habitat and in Premix5 showed a higher proton flux (vH+), linear electron flow (LEF), and maximum quantum yield (Fv’/Fm’). On the contrary, they showed a lower NPQt value than plants grown in preserved and black soil mixed with blond peat. Full article

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

► Show Figures

Figure 1

Figure 1
Average coefficients of the model that influence the parameters of the structure of Solanum peruvianum: (a) total height, (b) diameter ground level, (c) number of stems, and (d) natural regeneration. Error bars represent 95% confidence intervals. Black boxes with asterisks indicate significant effects on structure parameters (p < 0.05). Full article ">Figure 2
Comparisons of soil characteristics in preserved and degraded coastal Lomas: (a) organic material (%), (b) nitrogen (%), (c) diphosphorus oxide (P2O5), (d) potassium oxide (K2O %), (e) magnesium oxide (MgO %), (f) calcium oxide, known as quicklime (CaO %), (g) pH, and (h) electric conductivity (C.E. dS m−1). Different letters are significantly different at p ≤ 0.05, as per Tukey’s test after GLMM. Error bars represent the 95% confidence intervals. Full article ">Figure 3
Morphological evaluation of Solanum peruvianum. (a) Correlation between diameter at ground level and total height; (b) Relationship between fruit diameter and number of seeds. (c) Correlation between fruit weight and number of seeds. The grey band indicates the 95% confidence limit. Full article ">Figure 4
Statistical differences in the growth of S. peruvianum under different organic substrates. Full article ">Figure 5
Photosynthetic performance of S. peruvianum: (a) PSII; (b) relative chlorophyll; (c) total non-photochemical quenching corrected for Fm (NPQt); (d) proton conductivity of the chloroplast ATP synthase (vH+); (e) leaf thickness; (f) maximum quantum efficiency (Fv’/Fm’); (g) fraction of photosystem II open center (qL); (h) linear electron flow (LEF). Different letters significantly differ at p ≤ 0.05 with Tukey’s test after GLMM. The grey band indicates photosynthetic measurements in the natural habitat of S. peruvianum, in the Mangomarca Lomas. Full article ">Figure 6
S. peruvianum plants and location of coastal lomas ecosystems in Peru. (a) Location of Peru in South America. (b) On the map of Peru, green dots indicate the position of other coastal lomas, and red dot indicates the position of the Mangomarca Lomas. (c) Map of the coastal lomas of Mangomarca. The polygon indicates the region where the S. peruvianum plants are distributed. Full article ">

17 pages, 2373 KiB

Open AccessArticle

Comparative Analysis of Volatile Compounds and Biochemical Activity of Curcuma xanthorrhiza Roxb. Essential Oil Extracted from Distinct Shaded Plants

by Waras Nurcholis, Rahmadansah Rahmadansah, Puji Astuti, Bambang Pontjo Priosoeryanto, Rini Arianti and Endre Kristóf

Plants 2024, 13(19), 2682; https://doi.org/10.3390/plants13192682 - 25 Sep 2024

Abstract

The application of shade during plants’ growth significantly alters the biochemical compounds of the essential oil (EO). We aimed to analyze the effect of shade on the volatile compounds and biochemical activities of EO extracted from Curcuma xanthorrhiza Roxb. (C. xanthorrhiza) [...] Read more.

The application of shade during plants’ growth significantly alters the biochemical compounds of the essential oil (EO). We aimed to analyze the effect of shade on the volatile compounds and biochemical activities of EO extracted from Curcuma xanthorrhiza Roxb. (C. xanthorrhiza) plants. Four shading conditions were applied: no shading (S0), 25% (S25), 50% (S50), and 75% shade (S75). The volatile compounds of EO extracted from each shaded plant were analyzed by gas chromatography–mass spectrometry. The antioxidant, antibacterial, and antiproliferative activities of EO were also investigated. We found that shade application significantly reduced the C. xanthorrhiza EO yield but increased its aroma and bioactive compound concentration. α-curcumene, xanthorrhizol, α-cedrene, epicurzerenone, and germacrone were found in EO extracted from all conditions. However, β-bisabolol, curzerene, curcuphenol, and γ-himachalene were only detected in the EO of S75 plants. The EO of the shaded plants also showed higher antioxidant activity as compared to unshaded ones. In addition, the EO extracted from S75 exerted higher antiproliferative activity on HeLa cells as compared to S0. The EO extracted from S0 and S25 showed higher antibacterial activity against Gram-positive bacteria than kanamycin. Our results suggest that shade applications alter the composition of the extractable volatile compounds in C. xanthorrhiza, which may result in beneficial changes in the biochemical activity of the EO. Full article

(This article belongs to the Special Issue Secondary Metabolites in Plants)

► Show Figures

Figure 1

Figure 1
(a) The workflow of essential oil extraction from C. xanthorrhiza Roxb. rhizomes. (b) Yield (% v/w) of C. xanthorrhiza essential oil. Extraction was performed in 3 independent plants, with statistical analysis by one-way ANOVA followed by Tukey’s post hoc test, *** p < 0.001. S0, no shade; S25, 25% shade; S50, 50% shade; S75, 75% shade. Full article ">Figure 2
Chemical compositions of C. xanthorrhiza Roxb. essential oil. (a) Pie chart displaying the groups of secondary metabolites in C. xanthorrhiza essential oil from 4 shading conditions detected by GC-MS. (b) Heatmap displaying the abundance of 64 compounds detected by GC-MS in C. xanthorrhiza essential oil from each shade condition. Three replicates of EO extraction were pooled and subjected to chemical compound analysis. Full article ">Figure 3
Antioxidant activity of C. xanthorrhiza Roxb. essential oil measured by DPPH and FRAP assays. n = 3, statistical analysis by one-way ANOVA followed by Tukey’s post hoc test, * p < 0.05, ** p < 0.01, *** p < 0.001. S0, no shade; S25, 25% shade; S50, 50% shade; S75, 75% shade. DPPH, 2,2′-diphenyl-1-picrylhydrazyl; DW, dry weight; FRAP, ferric reducing antioxidant power; TE, Trolox equivalent; DW: dry weight. Full article ">Figure 4
Antiproliferative activity of C. xanthorrhiza Roxb. essential oil (4 µg/mL) measured in vero (left), MCF-7 (middle), or HeLa (right) cells. n = 3, statistical analysis by one-way ANOVA followed by Tukey’s post hoc test, ** p < 0.01, *** p < 0.001. S0, no shade; S25, 25% shade; S50, 50% shade; S75, 75% shade. Doxo: doxorubicin (0.2 µg/mL). Full article ">Figure 5
Antibacterial activity of C. xanthorrhiza Roxb. essential oil (4 µg/mL) tested against S. aureus (left) or E. coli (right). n = 3, statistical analysis by one-way ANOVA followed by Tukey’s post hoc test, */# p < 0.05, ### p < 0.001. * Analysis was performed by using S0 as reference. # Analysis was performed by using KS as reference. S0, no shade; S25, 25% shade; S50, 50% shade; S75, 75% shade. KS: kanamycin sulfate (1 mg/mL). Full article ">

16 pages, 1477 KiB

Open AccessArticle

Stimulation of Arabidopsis thaliana Seed Germination at Suboptimal Temperatures through Biopriming with Biofilm-Forming PGPR Pseudomonas putida KT2440

by Chandana Pandey, Anna Christensen, Martin N. P. B. Jensen, Emilie Rose Rechnagel, Katja Gram and Thomas Roitsch

Plants 2024, 13(19), 2681; https://doi.org/10.3390/plants13192681 - 24 Sep 2024

Abstract

This study investigated the germination response to temperature of seeds of nine Arabidopsis thaliana ecotypes. They are characterized by a similar temperature dependency of seed germination, and 10 °C and 29 °C were found to be suboptimal low and high temperatures for all [...] Read more.

This study investigated the germination response to temperature of seeds of nine Arabidopsis thaliana ecotypes. They are characterized by a similar temperature dependency of seed germination, and 10 °C and 29 °C were found to be suboptimal low and high temperatures for all nine ecotypes, even though they originated from regions with diverse climates. We tested the potential of four PGPR strains from the genera Pseudomonas and Bacillus to stimulate seed germination in the two ecotypes under these suboptimal conditions. Biopriming of seeds with only the biofilm-forming strain Pseudomonas putida KT2440 significantly increased the germination of Cape Verde Islands (Cvi-0) seeds at 10 °C. However, biopriming did not significantly improve the germination of seeds of the widely utilized ecotype Columbia 0 (Col-0) at any of the two tested temperatures. To functionally investigate the role of KT2440’s biofilm formation in the stimulation of seed germination, we used mutants with compromised biofilm-forming abilities. These bacterial mutants had a reduced ability to stimulate the germination of Cvi-0 seeds compared to wild-type KT2440, highlighting the importance of biofilm formation in promoting germination. These findings highlight the potential of PGPR-based biopriming for enhancing seed germination at low temperatures. Full article

(This article belongs to the Special Issue New Horizons in Plant–Microbe Interactions)

► Show Figures

Figure 1

Figure 1
Illustration of the experimental design. (1) Plant Growth-Promoting Rhizobacteria (PGPR) were grown on solid LB plates. (2) Approximately 10 mg of Arabidopsis thaliana seeds were sterilized and stratified at 4 °C for two days. (3) Fresh bacterial colonies were inoculated in liquid LB medium and grown overnight. (4) The bacterial culture was centrifuged and the pellet was resuspended in 10 mM MgCl2. The optical density at 600 nm was adjusted to 0.4. (5) A. thaliana seeds were inoculated with the bacterial suspension; for the control treatment, the seeds were inoculated with 10 mM MgCl2. (6) The bacterial suspension and A. thaliana seeds were then transferred to a germination box. The box contained an insert surrounded by two filter paper strips to absorb the suspension from the reservoir, with a square filter paper on top where the seeds were placed. (7) The effect of PGPR on A. thaliana seed germination was investigated at suboptimal low and high temperatures. (8) Germination was assessed using a magnifying lens. Full article ">Figure 2
Seed germination percentages at different temperatures for the nine ecotypes. Germination of seeds from nine A. thaliana ecotypes observed at different temperatures (10 °C, 17 °C, 24 °C, and 29 °C) after a 7 dai (days after inoculation). Germination was assessed under in-vitro conditions using germination boxes. The highest point on the curve indicates the most favorable temperature for germination specific to each ecotypes, Col0 (Col-0; 19.6 °C), Cvi (Cvi-0; 19.6 °C), Bur (20.6 °C), C24 (17.7 °C), Bla1 (Bla-1; 17.6 °C), Neo6 (Neo-6; 18.2 °C), N13 (20.2 °C), Dja1 (Dja-1; 18.7 °C), and MS0 (17.8 °C). The dotted line represents the polynomial regression, and the fitted polynomial regression equation is shown in <a href="#app1-plants-13-02681" class="html-app">Supplementary Table S1</a>. Full article ">Figure 3
Effect of PGPR on seed germination at suboptimal temperatures (10 °C and 29 °C) in Col-0 and Cvi-0 ecotypes. Seed germination was assessed at suboptimal temperatures (10 °C and 29 °C) for two A. thaliana ecotypes in the presence of Pseudomonas and Bacillus PGPR. Strain KT2440 (KT) showed increased germination in the Cvi (Cvi-0) ecotype under suboptimal low temperatures (10 °C). Significant differences between each bacterial treatment are depicted using different lowercase letters. Error bars in each figure represent the standard deviation of independent experiments. Full article ">Figure 4
Impact of KT2440 (KT) and its biofilm mutants on seed germination under suboptimal low temperatures (10 °C) in the Cvi-0 ecotype. Seed germination was investigated at a suboptimal low temperature (10 °C) in the presence of biofilm-forming KT2440 and its mutant q/alg−, with compromised biofilm-forming ability. Significant differences between each bacterial treatment are depicted using lowercase letters. Error bars in each figure represent the standard deviation among the independent experiments. Full article ">

25 pages, 12604 KiB

Open AccessArticle

Decoding the Transcriptomics of Oil Palm Seed Germination

by Padungsak Suksa-Ard, Sunya Nuanlaong, Chettupon Pooljun, Azzreena Mohamad Azzeme and Potjamarn Suraninpong

Plants 2024, 13(19), 2680; https://doi.org/10.3390/plants13192680 - 24 Sep 2024

Abstract

Seed dormancy and germination are critical factors affecting oil palm production efficiency. The typical dormancy-breaking process involves dry heat treatment (38–40 °C for 40–60 days) followed by germination at 30–32 °C. To understand the molecular mechanisms behind this process and improve germination rates [...] Read more.

Seed dormancy and germination are critical factors affecting oil palm production efficiency. The typical dormancy-breaking process involves dry heat treatment (38–40 °C for 40–60 days) followed by germination at 30–32 °C. To understand the molecular mechanisms behind this process and improve germination rates and speed, we conducted transcriptome analysis at three stages: pre-incubation, 45-day incubation at 40 °C, and 14-day germination at 32 °C. Our findings, supported by qRT–PCR and DEGs analysis, identified four key stages: ABA degradation, energy mobilization, starch mobilization, and cell elongation and division. ABA pathway genes (SnRK2, PYR/PYL) were active during dormancy release, while GAE and GPI were upregulated after heat treatment, indicating increased energy metabolism and structural changes. During germination, genes involved in starch/sucrose metabolism (SPS, TPP, SS, MGAM) and cell wall biosynthesis (GAUT1, PE, GAE) supported embryo expansion, with BAM, PGM, GlgB fueling early growth. Auxin (TIR1, AUX/IAA, ARF), brassinosteroid (BRI1, BSK, BIN2, CYCD3), ethylene (ETR, CTR1), and jasmonic acid (JAR1, COI1) pathway genes regulated cell growth and stress response, promoting seedling development. Though gibberellins were not crucial for this oil palm variety, gene expression varied between varieties. This study provides information on oil palm seed germination that could be applied to other oil palm species, particularly in terms of incubation times and chemical treatments. Full article

(This article belongs to the Special Issue Advancements in Plant Genetics and Genome Characterization)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Plants, Volume 13, Issue 19 (October-1 2024) – 40 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI