Plants

45 pages, 100145 KiB

Open AccessArticle

The Search for Species Flocks in Marine Benthic Homoeocladia spp. (Diatomeae: Bacillariales). I. Variations on Three Themes, Seventeen New Species

by Christopher S. Lobban, Britney Sison and Matt P. Ashworth

Plants 2023, 12(23), 4073; https://doi.org/10.3390/plants12234073 - 4 Dec 2023

Cited by 2 | Viewed by 1537

Abstract

Exploration of the diversity in the diatom genus Homoeocladia across Micronesia revealed several clusters of undescribed species based on variations around several characters. Using ultrastructural data from scanning electron microscopy, we describe seventeen new species in three of these morphological groups. (1) A [...] Read more.

Exploration of the diversity in the diatom genus Homoeocladia across Micronesia revealed several clusters of undescribed species based on variations around several characters. Using ultrastructural data from scanning electron microscopy, we describe seventeen new species in three of these morphological groups. (1) A group with external thickenings includes eight new species with costae and/or bordered areolae on valve face and/or conopea and/or peri-raphe zone, and one with similar areolae but no ornamentation; this group includes the previously described H. jordanii. (2) Large, linear species, resembling H. asteropeae and H. tarangensis; we describe three new species close to the latter. (3) A sinuous-areolae group includes five new species with areola openings shaped like “~”, “s”, or “z” on the valve and/or girdle bands, or both, and leads to reconsideration of the diagnosis of Homoeocladia schefterae and the recognition that the globally widespread species in this complex is H. coacervata sp. nov. The three groups are based solely on morphology and no genetic relationships are implied within or between the groups, other than having the characteristics of the recently redefined genus Homoeocladia. However, the high diversity of species in Homoeocladia suggests the genus is a good candidate to test for species flocks in this region and in at least one other comparable location, incorporating DNA sampling through either culturing or metabarcoding. Full article

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12 pages, 2746 KiB

Open AccessArticle

Cambial Age Influences PCD Gene Expression during Xylem Development and Heartwood Formation

by Yulia L. Moshchenskaya, Natalia A. Galibina, Tatiana V. Tarelkina, Ksenia M. Nikerova, Maksim A. Korzhenevsky and Ludmila I. Semenova

Plants 2023, 12(23), 4072; https://doi.org/10.3390/plants12234072 - 4 Dec 2023

Cited by 1 | Viewed by 1461

Abstract

Heartwood formation is an important ontogenetic stage in Scots pine (Pinus sylvestris L.). The amount of heartwood determines the proportion of functionally active sapwood in the total trunk biomass as well as the quality of wood. The key criterion for heartwood formation [...] Read more.

Heartwood formation is an important ontogenetic stage in Scots pine (Pinus sylvestris L.). The amount of heartwood determines the proportion of functionally active sapwood in the total trunk biomass as well as the quality of wood. The key criterion for heartwood formation is the death of xylem ray parenchyma cells. Previously, models that described the patterns of heartwood formation, depending on the cambial age, were derived from Scots pine trees of different ages. The cambial age is the number of annual xylem layers at the core sampling site at a certain trunk height. We studied the features of the occurrence of programmed cell death (PCD) processes during the xylem differentiation and heartwood formation of 80-year-old Scots pine trees, depending on the cambial age, under the lingonberry pine forest conditions in the transition area of the northern taiga subzone and tundra. We have shown that the distance from the cambial zone to the heartwood boundary does not change significantly with stem height. As the cambial age increases, the lifespan of the formed xylem ray parenchyma cells increases and the activity of PCD genes decreases during the formation of both (1) xylem (in the outer layers of sapwood) and (2) heartwood (in the inner layers of sapwood and transition zone). We hypothesized that the decisive factor in the PCD initiation during heartwood formation is the distance of the xylem ray parenchyma cells from the cambial zone. The younger cambium forms wider annual increments, and therefore the xylem ray parenchyma cells in these parts of the trunk reach the distance from the cambial zone earlier, which is necessary for PCD initiation. Full article

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

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Number of annual rings of heartwood, sapwood, and transition zone (TZ) at different heights (H) of stem and cambial ages (CAs) (A); area percentage sapwood, transition zone, and heartwood of total stem area (%) (B); width of sapwood, heartwood and transition zone (mm) in 80-year-old Scots pine trees (C); values are averages of five biological replicates. Full article ">Figure 2
Expression level of PCD genes in different layers of xylem (outer sapwood, inner sapwood, and transition zone) of 80-year-old Scots pine trees in cambial dormancy (7–10 October 2021) and cambial activity period (28 June–3 July 2022) in the transition area of the northern taiga subzone and tundra (Pasvik Nature Reserve, Murmansk region, Pechenga district). Asterisks show differences in gene expression between cambial dormancy and cambial activity period. **—significant differences at p < 0.01; *—at p < 0.05. Relative expression level was calculated based on five biological replicates. Full article ">Figure 3
Principal component analysis based on gene expression of bifunctional endonuclease (BFN) genes family in trunk tissues at different heights (0.3, 1, 2, 3, 4, 5, 6, 7 m) of five model trees. Factor 1 (92% of the variance) was correlated with BFN (r = 0.64), BFN1 (0.41), BFN2 (0.64). Factor 2 (5% of the variance) was correlated with BFN (0.56), BFN1 (0.32), and negatively correlated with BFN2 (−0.76). The green grouping represents the outer sapwood. The red grouping represents the inner sapwood. The violet grouping represents the transition zone. The values shown are means with 95% confidence intervals. Full article ">Figure 4
Relative expression of PCD genes in the outer sapwood of 80-year-old Pinus sylvestris L. trees into cambial age (CA) and height (H). Expression is calculated relative to the reference gene (GAPDH) and expressed in arbitrary units (a.u.). The graphs show the Pearson correlation coefficient (r). Dots indicate expression values in each model tree. Relative expression level was calculated based on five biological replicates. Full article ">Figure 5
Ranked distance analysis of similarities (ANOSIM with Bray−Curtis similarity) to compare the sections on different trunk heights (permutation N = 9999, mean rank within = 125.6, mean rank between = 420.8, R = 0.7568, and p (same) = 0.0001). Full article ">Figure 6
Relative expression level of PCD genes in the inner sapwood and the transition zone of 80-year-old Scots pine trees into cambial age (CA) and trunk height (H). The graph shows the Pearson correlation coefficient. Insignificant correlation is stated in red. Dots indicate expression values in each model tree Relative expression level was calculated based on five biological replicates. Full article ">

21 pages, 952 KiB

Open AccessArticle

Biotechnology and Solutions: Insect-Pest-Resistance Management for Improvement and Development of Bt Cotton (Gossypium hirsutum L.)

by Abdul Razzaq, Muhammad Mubashar Zafar, Arfan Ali, Pengtao Li, Fariha Qadir, Laviza Tuz Zahra, Fiza Shaukat, Abdul Hafeez Laghari, Youlu Yuan and Wankui Gong

Plants 2023, 12(23), 4071; https://doi.org/10.3390/plants12234071 - 4 Dec 2023

Cited by 5 | Viewed by 4378

Abstract

Cotton (Gossypium spp. L.) is a major origin of natural fiber, and is projected at 117 million bales worldwide for 2021/22. A variety of biotic and abiotic stresses have considerable negative impacts on cotton. The significantly decreased applications of chemical insecticidal sprays [...] Read more.

Cotton (Gossypium spp. L.) is a major origin of natural fiber, and is projected at 117 million bales worldwide for 2021/22. A variety of biotic and abiotic stresses have considerable negative impacts on cotton. The significantly decreased applications of chemical insecticidal sprays in the agro-ecosystem have greatly affected the biodiversity and dynamics of primary and secondary insects. Various control measures were taken around the globe to increase production costs. Temperature, drought, and salinity, and biotic stresses such as bacteria, viruses, fungi, nematodes, insects, and mites cause substantial losses to cotton crops. Here, we summarize a number of biotic and abiotic stresses upsetting Bt cotton crop with present and future biotechnology solution strategies that include a refuge strategy, multi-gene pyramiding, the release of sterile insects, seed mixing, RNAi, CRISPR/Cas9, biotic signaling, and the use of bioagents. Surveillance of insect resistance, monitoring of grower compliance, and implementation of remedial actions can lead to the sustainable use of cotton across the globe. Full article

(This article belongs to the Special Issue Adaptive Mechanisms of Plants to Biotic or Abiotic Stresses)

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15 pages, 8515 KiB

Open AccessArticle

OsLEA1b Modulates Starch Biosynthesis at High Temperatures in Rice

by Gang Li, Ruijie Cao, Liuyang Ma, Guiai Jiao, Pengfei Chen, Nannan Dong, Xinwei Li, Yingqing Duan, Xiaoxue Li, Mingdong Zhu, Gaoneng Shao, Zhonghua Sheng, Shikai Hu, Shaoqing Tang, Xiangjin Wei, Yinghong Yu and Peisong Hu

Plants 2023, 12(23), 4070; https://doi.org/10.3390/plants12234070 - 4 Dec 2023

Cited by 5 | Viewed by 1533

Abstract

High temperatures accelerate the accumulation of storage material in seeds, often leading to defects in grain filling. However, the mechanisms regulating grain filling at high temperatures remain unknown. Here, we want to explore the quality factors influenced by the environment and have identified [...] Read more.

High temperatures accelerate the accumulation of storage material in seeds, often leading to defects in grain filling. However, the mechanisms regulating grain filling at high temperatures remain unknown. Here, we want to explore the quality factors influenced by the environment and have identified a LATE EMBROYGENESIS ABUNDANT gene, OsLEA1b, a heat-stress-responsive gene in rice grain filling. OsLEA1b is highly expressed in the endosperm, and its coding protein localizes to the nucleus and cytoplasm. Knock-out mutants of OsLEA1b had abnormal compound starch granules in endosperm cells and chalky endosperm with significantly decreased grain weight and grain number per panicle. The oslea1b mutants exhibited a lower proportion of short starch chains with degrees of polymerization values from 6 to 13 and a higher proportion of chains with degrees from 14 to 48, as well as significantly lower contents of starch, protein, and lipid compared to the wild type. The difference was exacerbated under high temperature conditions. Moreover, OsLEA1b was induced by drought stress. The survival rate of oslea1b mutants decreased significantly under drought stress treatment, with significant increase in ROS levels. These results indicate that OsLEA1b regulates starch biosynthesis and influences rice grain quality, especially under high temperatures. This provides a valuable resource for genetic improvement in rice grain quality. Full article

(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)

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Expression pattern and subcellular localization of OsLEA1b. (A) Relative OsLEA1b expression levels in various tissues and in developing endosperms at 5, 10, 15, 20, 25, and 30 days after fertilization (DAF). Values are means ± SD from three biological replicates. (B) GUS staining in root, stem, leaf, spikelet, and developing grains expressing ProOsLEA1b:GUS. (C) Subcellular localization of OsLEA1b in rice protoplasts. Confocal microscopy images show OsLEA1b–GFP localized in the nucleus and cytoplasm. GFP signaling, chlorophyll autofluorescence, bright field, and merged images are shown for each construct. Scale bars, 2 mm in (B) and 10 μm in (C). Full article ">Figure 2
Analysis of agronomic traits of oslea1b mutants compared to the wild type. (A–C) Grain length, width, and thickness of wild-type (WT) and oslea1b grains. Scale bars, 6 mm. (D) Appearance of brown rice grains from WT and oslea1b mutant plants. Scale bar, 2 mm. (E–G) Transverse sections of WT (E) and oslea1b (F,G) endosperm. Scale bars, 2 mm. (H–O) Quantification of grain length (H), grain width (I), 1000-grain weight (J), grain thickness (K), seed number per panicle (L), grain yield per plant (M), seed setting rate (N), and chalky grain percentage (O) for WT plants and oslea1b mutants. Data are means ± SD from at least three biological replicates. Statistically significant differences were determined using Student’s t-test (*, p < 0.05, **, p < 0.01). Full article ">Figure 3
Starch granule formation and amyloplast development in endosperm cells of wild-type and oslea1b mutants. (A–C) Scanning electron microscopy of transverse sections of wild-type (A) and oslea1b (B,C) endosperm. (D–I) Semi-thin sections of WT and oslea1b endosperm at 10 days after fertilization (DAF). (D–F) Micrographs showing the peripheral region; (G–I) micrographs showing the central region. Black stars in (D–F) indicate aleurone cells. Arrows in (H,I) indicate broken amyloplasts. (J–L) Transmission electron microscopy shows well-developed amyloplasts in WT endosperm cells (J,M) and broken amyloplasts in oslea1b endosperm cells (K,L,N,O). Scale bars, 15 μm in (A–C), 40 μm in (D–I), 5 μm in (J–L), and 2 μm in (M–O). Full article ">Figure 4
Starch physicochemical properties in the endosperm of oslea1b mutants. (A–D) Total starch content (A), amylose content (B), protein content (C), and gel consistency (D) of wild-type and Osesp1 mutant endosperm. (E) Differences in amylopectin chain length distribution between WT and oslea1b. (F) Pasting properties of WT and oslea1b endosperm starch determined using a Rapid Visco Analyzer (RVA). The gray line indicates temperature changes during the measurements. (G) Gelatinization temperature of endosperm starch. To, Tp, and Tc represent the onset, peak, and concluding gelatinization temperatures, respectively. Data in (A–D,G) are presented as means ± SD from three replicates. Statistically significant differences were determined using Student’s t-test (*, p < 0.05, **, p < 0.01). Full article ">Figure 5
The oslea1b mutants were more sensitive to high temperatures during the grain-filling stage. (A–F) Appearance of wild-type (WT) and oslea1b mutant grains under high-temperature treatment (35 °C for 12 h in light and 28 °C for 12 h in darkness) and normal temperature treatment (28 °C for 12 h in light and 22 °C for 12 h in darkness). Scale bars, 1 cm. (G–K) Chalky grain percentage (G), 1000-grain weight (H), total starch content (I), amylose content (J), and total protein content (K) of WT and oslea1b mutant grains under normal and high temperatures. Different letters indicate significant differences at p < 0.05 by ANOVA and Duncan’s test. Full article ">Figure 6
Transcription levels of genes related to regulate amylopectin synthesis in endosperm at 10 DAF. (A–I) Relative expression of genes related to amylopectin biosynthesis. Gene expression levels were measured in WT and oslea1b-1 grains at 9 days after fertilization under high (HT) and normal (RT) temperature conditions. Different letters indicate significant differences at p < 0.05 by ANOVA and Duncan’s test. Full article ">Figure 7
OsLEA1b gene positively regulates drought stress tolerance. (A,B) Phenotypes of seedlings of wild-type and oslea1b before and after 20% PEG treatment. (C) Survival rate of seedlings of WT and oslea1b after 20% PEG treatment. (D,E) Phenotypes of WT and oslea1b before and after drought stress. Water was withheld for 5 d followed by a 14-day recovery period. (F) Relative expression of OsLEA1b was induced by drought stress. (G–J) Peroxidase (POD) enzyme activity (G), and contents of hydrogen peroxide (H2O2; H), proline (I), and malondialdehyde (MDA; (J)) in WT and oslea1b mutant leaves. (K,L) Relative expression of genes related to reactive oxygen species scavenging and ABA signaling in wild type and mutants before (K) and after (L) 20% PEG treatment. Data are means ± SD from at least three biological replicates. Different letters in (C, G–J) indicate significant differences at p < 0.05 by ANOVA and Duncan’s test. In (K, L), statistically significant differences were determined using Student’s t-test (*, p < 0.05, **, p < 0.01). Full article ">

15 pages, 1566 KiB

Open AccessArticle

Rapid and High Throughput Hydroponics Phenotyping Method for Evaluating Chickpea Resistance to Phytophthora Root Rot

by Muhammad A. Asif, Sean L. Bithell, Ramethaa Pirathiban, Brian R. Cullis, David Glyn Dionaldo Hughes, Aidan McGarty, Nicole Dron and Kristy Hobson

Plants 2023, 12(23), 4069; https://doi.org/10.3390/plants12234069 - 4 Dec 2023

Viewed by 1647

Abstract

Phytophthora root rot (PRR) is a major constraint to chickpea production in Australia. Management options for controlling the disease are limited to crop rotation and avoiding high risk paddocks for planting. Current Australian cultivars have partial PRR resistance, and new sources of resistance [...] Read more.

Phytophthora root rot (PRR) is a major constraint to chickpea production in Australia. Management options for controlling the disease are limited to crop rotation and avoiding high risk paddocks for planting. Current Australian cultivars have partial PRR resistance, and new sources of resistance are needed to breed cultivars with improved resistance. Field- and glasshouse-based PRR resistance phenotyping methods are labour intensive, time consuming, and provide seasonally variable results; hence, these methods limit breeding programs’ abilities to screen large numbers of genotypes. In this study, we developed a new space saving (400 plants/m²), rapid (<12 days), and simplified hydroponics-based PRR phenotyping method, which eliminated seedling transplant requirements following germination and preparation of zoospore inoculum. The method also provided post-phenotyping propagation all the way through to seed production for selected high-resistance lines. A test of 11 diverse chickpea genotypes provided both qualitative (PRR symptoms) and quantitative (amount of pathogen DNA in roots) results demonstrating that the method successfully differentiated between genotypes with differing PRR resistance. Furthermore, PRR resistance hydroponic assessment results for 180 recombinant inbred lines (RILs) were correlated strongly with the field-based phenotyping, indicating the field phenotype relevance of this method. Finally, post-phenotyping high-resistance genotypes were selected. These were successfully transplanted and propagated all the way through to seed production; this demonstrated the utility of the rapid hydroponics method (RHM) for selection of individuals from segregating populations. The RHM will facilitate the rapid identification and propagation of new PRR resistance sources, especially in large breeding populations at early evaluation stages. Full article

(This article belongs to the Special Issue Advances in Legume Crops Research)

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13 pages, 2016 KiB

Open AccessArticle

Susceptibility Evaluation to Fire Blight and Genome-Wide Associations within a Collection of Asturian Apple Accessions

by Belén García-Fernández, Ramon Dolcet-Sanjuan, Diego Micheletti, María José Antón-Díaz, Cristina Solsona, Mercedes Fernández, Xavier Abad and Enrique Dapena

Plants 2023, 12(23), 4068; https://doi.org/10.3390/plants12234068 - 4 Dec 2023

Cited by 2 | Viewed by 2133

Abstract

Fire blight, caused by Erwinia amylovora, is one of the most devastating apple diseases. The selection of cultivars of low susceptibility and the study of the genetic mechanisms of the disease play important roles in fire blight management. The susceptibility level to [...] Read more.

Fire blight, caused by Erwinia amylovora, is one of the most devastating apple diseases. The selection of cultivars of low susceptibility and the study of the genetic mechanisms of the disease play important roles in fire blight management. The susceptibility level to fire blight was evaluated in 102 accessions originating from Asturias, a cider-producing region located in the north of Spain with a wide apple germplasm. Evaluations took place under quarantine conditions using artificial inoculations of grafted plants. The results revealed wide variation in susceptibility responses and low-susceptible cultivars were identified. In addition, 91 cultivars were genotyped using the Affymetrix Axiom^® Apple 480 K SNP array to conduct genome-wide association studies (GWAS). A statistically significant signal was detected on chromosome 10 using the multi-locus mixed model (MLMM). Two genes were identified as major putative candidate genes: a TIR-NBS-LRR class disease protein and a protein containing a development and cell death (DCD) domain. The outcomes of this study provide a promising source of information, particularly in the context of cider apples, and set a starting point for future genetic and breeding approaches. Full article

(This article belongs to the Special Issue Advances in Rosaceae Fruit Genomics and Breeding)

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Distribution of best linear unbiased prediction (BLUP) values ± standard deviation. Accessions were ranked in increasing order, from the lowest to the highest susceptibility levels. The orange column represents ‘Florina’ (FLO) and the yellow columns correspond to ‘Lagar’ (LG) and ‘No Raxao’ (NRX) (identical genotypes). Full article ">Figure 2
Population genetic structure analyses. (a) Principal Component Analysis (PCA). Principal Component 1 (PC1) was plotted against Principal Component 2 (PC2). The percentage of variance explained by each one is shown in parentheses; (b) Distribution of the genotypes after dividing the collection into 2, 3 and 4 subpopulations (k). Full article ">Figure 3
Manhattan plots and corresponding Q-Q plots for the mixed linear model (MLM) and the multiple loci mixed model (MLMM) after conducting genome-wide association analysis (GWAS) for fire blight. Different chromosomes are represented by different colors. The horizontal green line in the Manhattan plots indicates the threshold at a significant level of 5% after Bonferroni multiple test correction. Q-Q plots compare the expected value for the −log10(p-value) vs. the observed one for each SNP (blue point). The red line indicates a hypothetical distribution without association. Full article ">Figure 4
Scatter plot of the best linear unbiased prediction (BLUP) results grouped by allele (C/A) of AX-115639581. The grey rhombuses represent each cultivar while the red ones represent the mean of each group. Full article ">Figure 5
Representative examples of the scale used to measure necrosis progression: 0—no visible symptoms; 0.5—necrosis only affected veins of the inoculated leaf; 1—necrosis reached the petiole of the inoculated leaf; 1 + necrosis length—necrosis reached the stem of the plant. Full article ">

13 pages, 1134 KiB

Open AccessArticle

Influence of Nitrogen Supply on Growth, Antioxidant Capacity and Cadmium Absorption of Kenaf (Hibiscus cannabinus L.) Seedlings

by Wenlue Li, Changli Chen, Yong Deng, Xiahong Luo, Tingting Liu, Xia An, Lina Zou, Mingbao Luan and Defang Li

Plants 2023, 12(23), 4067; https://doi.org/10.3390/plants12234067 - 4 Dec 2023

Cited by 1 | Viewed by 1309

Abstract

Kenaf (Hibiscus cannabinus L.) is considered suitable for the remediation of cadmium (Cd)-contaminated farmlands, because of its large biomass and resistance to Cd stress. The addition of nitrogen (N) fertilizer is an important measure used to increase crop yields, and it may [...] Read more.

Kenaf (Hibiscus cannabinus L.) is considered suitable for the remediation of cadmium (Cd)-contaminated farmlands, because of its large biomass and resistance to Cd stress. The addition of nitrogen (N) fertilizer is an important measure used to increase crop yields, and it may also affect Cd accumulation in plants. To clarify the effects of different forms and concentrations of N on plant growth and Cd absorption in kenaf, a hydroponic experiment was conducted using three N forms (NH₄⁺–N, NO₃⁻–N and urea–N) at four concentrations (0, 2, 4 and 8 mM, 0 mM as control) under Cd stress (30 μM). The plant growth, the antioxidant enzyme activity and the Cd contents of various parts of the kenaf seedlings were measured. The results showed that the N form had the greatest impact on the growth of the kenaf and the absorption and transport of the Cd, followed by the interaction effect between the N type and the concentration. Compared to the control, the addition of N fertilizer promoted the growth of kenaf to varying degrees. Among all the treatments, the use of 2 mM of NO₃⁻–N enhanced the biomass and Cd accumulation to the greatest extent compared to CK from 2.02 g to 4.35 g and 341.30 μg to 809.22 μg per plant, respectively. The NH₄⁺–N significantly reduced the Cd contents of different parts but enhanced the translocation factors of Cd stem to root (TF S/R) and leaf to stem (TF L/S) by 34.29~78.57% and 45.10~72.55%, respectively. The peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) enzyme activities of the kenaf increased with the N treatments, especially with NH₄⁺–N. Overall, applying low concentrations of NO₃⁻–N can better promote the extraction of Cd by kenaf. Full article

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Chlorophyll contents of kenaf leaves under different treatments. Data are means ± SD, the black dots above the bar chart are individual data points, different lowercase letters indicate significant differences between treatments (p < 0.05, Duncan) and different uppercase letters represent significant differences between nitrogen fertilizer forms and CK (p < 0.05, Duncan). Full article ">Figure 2
Cd contents of different kenaf parts. Data are means ± SD, the black dots above the bar chart are individual data points, different lowercase letters in each part indicate a significant difference between treatments (p < 0.05, Duncan), different uppercase letters in each part indicate a significant difference between nitrogen fertilizer forms and CK (p < 0.05, Duncan). Full article ">Figure 3
Cd translocation factor of kenaf under different treatments. Data are means ± SD, the black dots above the bar chart are individual data points, different lowercase letters in each part indicate a significant difference between treatments (p < 0.05, Duncan), different uppercase letters in each part indicate a significant difference between nitrogen fertilizer forms and CK (p < 0.05, Duncan). Full article ">Figure 4
Assessment of Cd uptake under different treatments. (a) Cd accumulation in roots, (b) Cd accumulation in stems, (c) Cd accumulation in leaves, (d) the total Cd in kenaf. Data are means ± SD, the black dots above the bar chart are individual data points, different lowercase letters in each part indicate a significant difference between treatments (p < 0.05, Duncan), different uppercase letters in each part indicate a significant difference between nitrogen fertilizer forms and CK (p < 0.05, Duncan). Full article ">

26 pages, 5354 KiB

Open AccessArticle

Distribution Patterns of Gymnosperm Species along Elevations on the Qinghai–Tibet Plateau: Effects of Climatic Seasonality, Energy–Water, and Physical Tolerance Variables

by Muhammad Umair, Xiaofei Hu, Qi Cheng, Shahzad Ali and Jian Ni

Plants 2023, 12(23), 4066; https://doi.org/10.3390/plants12234066 - 4 Dec 2023

Cited by 1 | Viewed by 2470

Abstract

Climate change is one of the most prominent factors influencing the spatial distribution of plants in China, including gymnosperms. Climatic factors influence gymnosperm distribution along elevational gradients on the Qinghai–Xizang (Tibet) Plateau (QTP), and understanding how species adapt to these factors is important [...] Read more.

Climate change is one of the most prominent factors influencing the spatial distribution of plants in China, including gymnosperms. Climatic factors influence gymnosperm distribution along elevational gradients on the Qinghai–Xizang (Tibet) Plateau (QTP), and understanding how species adapt to these factors is important for identifying the impacts of global climate change. For the first time, we examined the county-level distribution of gymnosperm species on QTP using data from field surveys, published works, monographs, and internet sources. We used simulated distribution data of gymnosperms (N = 79) along the elevational gradients to investigate the overall impact of environmental variables in explaining the richness pattern of gymnosperms. Eighteen environmental variables were classified into three key variable sets (climatic seasonality, energy–water, and physical tolerance). We employed principal component analysis and generalized linear models to assess the impact of climatic variables on the gymnosperm’s richness pattern. Gymnosperm species are unevenly distributed across the plateau and decline gradually from the southeast to the northwest. The altitudinal gradients have a unimodal relationship with the richness of gymnosperms, with the maximum species richness at an elevation of 3200 m. The joint effects of physical tolerance and energy–water predictors have explained the highest diversity of gymnosperms at mid-elevation. Because the richness peak correlates significantly with the wettest month’s precipitation and moisture index, this confirms the significance of moisture on gymnosperm distributions due to increased precipitation during the wet season. Furthermore, our results provide evidence that climatic seasonality factors are involved in the decline of gymnosperm richness at high elevations. A total of 37% of gymnosperm species on QTP are listed as vulnerable, nearly threatened, or endangered, with elevations ranging from 600 m to 5300 m. As a result, we conclude that gymnosperms are at high risk of extinction because of the current climate fluctuations caused by global climate change. Our research offers fundamental data for the study and protection of gymnosperm species along the steepest elevation gradients. Full article

(This article belongs to the Special Issue Responses of Vegetation to Global Climate Change)

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19 pages, 34764 KiB

Open AccessArticle

Relict Plants Are Better Able to Adapt to Climate Change: Evidence from Desert Shrub Communities

by Ying Lu, Boran Zhang, Min Zhang, Meiyu Jie, Siqi Guo and Yange Wang

Plants 2023, 12(23), 4065; https://doi.org/10.3390/plants12234065 - 4 Dec 2023

Cited by 3 | Viewed by 1931

Abstract

Shrubs are the main dominant plants in arid desert systems and play an important role in maintaining the biodiversity, ecosystem services and stability of desert ecosystems. Studies have shown that the survival of a large number of shrub species in desert areas under [...] Read more.

Shrubs are the main dominant plants in arid desert systems and play an important role in maintaining the biodiversity, ecosystem services and stability of desert ecosystems. Studies have shown that the survival of a large number of shrub species in desert areas under the influence of climate change is significantly threatened, with different species showing different response strategies. To test the tolerance of different shrub species to climate change, this study selected 10 dominant shrub species (ancient relict shrub species and regional endemic shrub species) in the Alashan desert area as the research object. Based on a field survey of species distribution, a species distribution model was developed to simulate the suitable distribution area of shrub species under current conditions and under future climate change scenarios. The distribution changes of ancient relict and regional endemic shrub species under the climate change scenarios were tested, and the tolerance of the two types of shrub to climate change was analyzed. The results showed that under different climate change scenarios, except for Ammopiptanthus mongolicus, the total suitable area of four out of the five relict plants was relatively stable, the potential distribution area of Tetraena mongolica increased, and the future distribution pattern was basically consistent with the current distribution. However, the suitable area of typical desert plants was unstable under different climate change scenarios. Except for Kalidium foliatum, the suitable distribution areas of four out of the five shrubs showed different degrees of reduction, and the distribution location showed significant migration. Based on the research results, climate change will lead to the reduction and displacement of the distribution area of typical desert shrubs, while relict shrubs will be less affected by climate change. This is because, compared to desert species, relict plants have a longer evolutionary history and have developed a wider range of adaptations after experiencing dramatic environmental changes. This study provides a scientific basis for actively responding to the impacts of climate change on desert ecosystems. Full article

(This article belongs to the Special Issue Ecological Processes and Sandy Plant Adaptations to Climate Change)

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13 pages, 1599 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of ZF-HD Gene Family in Moso Bamboo (Phyllostachys edulis)

by Feiyi Huang, Jiaxin Wang and Chao Tang

Plants 2023, 12(23), 4064; https://doi.org/10.3390/plants12234064 - 3 Dec 2023

Cited by 3 | Viewed by 1770

Abstract

Zinc finger-homeodomain (ZF-HD) proteins play essential roles in plant growth, development and stress responses. However, knowledge of the expression and evolutionary history of ZF-HD genes in moso bamboo remains limited. In this study, a total of 24 ZF-HD genes were found unevenly distributed [...] Read more.

Zinc finger-homeodomain (ZF-HD) proteins play essential roles in plant growth, development and stress responses. However, knowledge of the expression and evolutionary history of ZF-HD genes in moso bamboo remains limited. In this study, a total of 24 ZF-HD genes were found unevenly distributed on 12 chromosomes in moso bamboo (Phyllostachys edulis). Phylogenetic analysis indicated that PeZF-HDs were divided into two subfamilies: ZHD and MIF. The ZHD subfamily genes were further classified into seven groups according to their orthologous relationships among the rice and Arabidopsis ZF-HD gene family. The gene structures and conserved motifs of PeZF-HDs were analyzed. Whole-genome duplication (WGD) or segmental duplication promoted the evolution and expansion of the moso bamboo ZF-HD gene family. Ka/Ks ratios suggested that the twenty-four duplication pairs had undergone purifying selection. Promoter analysis showed that most PeZF-HDs contained cis-elements associated with stress responses and hormones. Expression analysis demonstrated that many PeZF-HDs were responsive to abiotic stress treatment. Overall, this work investigated PeZF-HD genes in moso bamboo using bioinformatic approaches. The evolutionary research on gene structure, motif distribution and cis-regulatory elements indicated that PeZF-HDs play distinct roles in biological processes, which provides a theoretical basis for exploring the physiological functions of ZF-HDs and selecting candidate stress-related genes in moso bamboo. Full article

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

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Figure 1
Phylogenetic analysis of ZF-HD proteins from rice, Arabidopsis and moso bamboo. The tree was built using the Maximum Likelihood (ML) method with 1000 bootstrap replicates. The branched lines of the subtrees are colored to indicate different subgroups. Full article ">Figure 2
Phylogenetic relationships, gene structures and conserved domains of PeZF-HDs. (A) ML phylogenetic tree of PeZF-HDs. (B) Motif distributions in PeZF-HDs. The colored boxes represent motifs 1–8. Scale bar: 100 amino acids. (C) Exon–intron distribution of PeZF-HDs. The black lines and yellow boxes represent introns and exons, respectively. Scale bar: 500 bp. Full article ">Figure 3
Chromosome distribution and syntenic relationships of PeZF-HDs. Chromosomes are shown in a circular form. The duplicate PeZF-HD gene pairs are connected by black lines. Full article ">Figure 4
The cis-acting elements of PeZF-HDs promoters. The closed boxes of different colors represent different kinds of cis-acting elements. Full article ">Figure 5
Heatmap and cluster of PeZF-HDs expressions under cold (A), Nacl (B), PEG (C) and ABA (D) treatment. The relative expression levels of PeZF-HDs under these treatments are shown by fold-change values and converted to log2 format compared to the control. The x-axis represents the days of treatment. The color scale at the right of each heatmap represents relative expression levels. The qPCR results were obtained based on three biological and three technical replicates. Full article ">

15 pages, 2631 KiB

Open AccessArticle

Delayed Leaf Senescence Improves Radiation Use Efficiency and Explains Yield Advantage of Large Panicle-Type Hybrid Rice

by Jun Deng, Tian Sheng, Xuefen Zhong, Jiayu Ye, Chunhu Wang, Liying Huang, Xiaohai Tian, Ke Liu and Yunbo Zhang

Plants 2023, 12(23), 4063; https://doi.org/10.3390/plants12234063 - 3 Dec 2023

Cited by 7 | Viewed by 1420

Abstract

Super hybrid rice with predominantly large panicle types has achieved remarkable success in enhancing crop yield. However, when compared with multi-panicle-type varieties, the yield stability of large panicle-type varieties remains a challenge, and limited information is available on the comparative advantages of multi-panicle [...] Read more.

Super hybrid rice with predominantly large panicle types has achieved remarkable success in enhancing crop yield. However, when compared with multi-panicle-type varieties, the yield stability of large panicle-type varieties remains a challenge, and limited information is available on the comparative advantages of multi-panicle types. Consequently, a two-year experiment was conducted to evaluate the grain yield, biomass production, leaf area index (LAI), and radiation use efficiency (RUE) of large panicle-type hybrid rice (Y-liangyou 900, YLY900) and multi-panicle-type hybrid rice (C-liangyouhuazhan, CLYHZ) under three nitrogen (N) treatments (0, 180, 270 kg N ha⁻¹). The effects of increased N fertilization were more pronounced in the large panicle-type varieties. YLY900 outperformed CLYHZ in terms of average yield (6% higher), and its yield advantage was attributed to higher spikelets per panicle (28%). Due to YLY900’s RUE being 9% higher than CLYHZ, it results in a 12% greater accumulation of dry matter than CLYHZ. Furthermore, YLY900 exhibited significant improvements of 16%, 4%, and 14% in specific leaf weight, effective leaf area ratio, and LAI at 20 days after the heading stage (20DAH), respectively, compared with CLYHZ. YLY900 also demonstrated a stronger correlation between rice yield and intercepted photosynthetically active radiation (IPAR) compared with CLYHZ, with R² values of 0.80 and 0.66, respectively. These findings highlight the superior performance of YLY900, resulting from higher light interception percentage (IP) and IPAR values, which consequently led to enhanced RUE and grain yield. Our research reveals that delayed leaf senescence by increasing LAI at the post-heading stage for large panicle-type hybrid rice, thereby contributing to greater RUE, led to higher biomass production and grain yield. Full article

(This article belongs to the Special Issue Enhancing Crop Yield and Adaptability through Sustainable Soil Management: Effective and Eco-Friendly Practices)

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Figure 1
Daily maximum temperature, daily minimum temperature, and daily solar radiation during the rice-growing season at Jingzhou in 2020 (A) and 2021 (B). Full article ">Figure 2
Grain yield of two panicle-type varieties under different N rates at Jingzhou in 2020 and 2021. Vertical bars indicate standard errors (n = 3). Means with identical letters within each column do not exhibit statistically significant differences according to LSD (0.05). Full article ">Figure 3
The leaf area index (LAI) of two panicle-type varieties under different N rates at Jingzhou in 2020 (A) and 2021 (B). Vertical bars indicate standard errors (n = 3). MT: middle tillering, PI: panicle initiation, HD: heading stage, and 20 DAH: 20 days after heading stage. Means with identical letters within each column do not exhibit statistically significant differences according to LSD (0.05). Full article ">Figure 4
The specific leaf weight (SLW) (A) and effective leaf area ratio (B) of two panicle-type varieties during the heading stage under different N rates at Jingzhou in 2020 and 2021. Vertical bars indicate standard errors (n = 3). Means with identical letters within each column do not exhibit statistically significant differences according to LSD (0.05). Full article ">Figure 5
Relationships between grain yield and panicle number (A), spikelets per panicle (B), grain filling (C), and grain weight (D) in 2020 and 2021. Full article ">Figure 6
Relationship between grain yield and IP (A), IPAR (B), TDW (C), and RUE (D) in 2020 and 2021. Full article ">

18 pages, 4524 KiB

Open AccessArticle

Optimum Nitrogen, Phosphorous, and Potassium Fertilizer Application Increased Chrysanthemum Growth and Quality by Reinforcing the Soil Microbial Community and Nutrient Cycling Function

by Xinyan Fang, Yanrong Yang, Zhiguo Zhao, Yang Zhou, Yuan Liao, Zhiyong Guan, Sumei Chen, Weimin Fang, Fadi Chen and Shuang Zhao

Plants 2023, 12(23), 4062; https://doi.org/10.3390/plants12234062 - 3 Dec 2023

Cited by 9 | Viewed by 4847

Abstract

Nitrogen (N), phosphorus (P), and potassium (K) are three macronutrients that are crucial in plant growth and development. Deficiency or excess of any or all directly decreases crop yield and quality. There is increasing awareness of the importance of rhizosphere microorganisms in plant [...] Read more.

Nitrogen (N), phosphorus (P), and potassium (K) are three macronutrients that are crucial in plant growth and development. Deficiency or excess of any or all directly decreases crop yield and quality. There is increasing awareness of the importance of rhizosphere microorganisms in plant growth, nutrient transportation, and nutrient uptake. Little is known about the influence of N, P, and K as nutrients for the optimal production of Chrysanthemum morifolium. In this study, a field experiment was performed to investigate the effects of N, P, and K on the growth, nutrient use efficiency, microbial diversity, and composition of C. morifolium. Significant relationships were evident between N application rates, C. morifolium nutrient use, and plant growth. The N distribution in plant locations decreased in the order of leaf > stem > root; the distributions were closely related to rates of N application. Total P fluctuated slightly during growth. No significant differences were found between total P in the roots, stems, and leaves of C. morifolium vegetative organs. Principle component analysis revealed that combinations of N, P, and K influenced soil nutrient properties through their indirect impact on operational taxonomic units, Shannon index, and abundance of predominant bacterial taxa. Treatment with N, P, and K (600, 120, and 80 mg·plant⁻¹, respectively) significantly improved plant growth and quality and contributed to the bacterial richness and diversity more than other concentrations of N, P, and K. At the flowering time, the plant height, leaf fresh weight, root dry weight, stem and leaf dry weight were increased 10.6%, 19.0%, 40.4%, 27% and 34.0%, respectively, when compared to the CK. The optimal concentrations of N, P, and K had a positive indirect influence on the available soil nutrient content and efficiency of nutrient use by plants by increasing the abundance of Proteobacteria, decreasing the abundance of Actinobacteria, and enhancing the potential functions of nitrogen metabolism pathways. N, P, and K fertilization concentrations of 600, 120, and 80 mg·plant⁻¹ were optimal for C. morifolium cultivation, which could change environmental niches and drive the evolution of the soil microbial community and diversity. Shifts in the composition of soil microbes and functional metabolism pathways, such as ABC transporters, nitrogen metabolism, porphyrin, and the metabolism of chlorophyll II, glyoxylate, and dicarboxylate, greatly affected soil nutrient cycling, with potential feedback on C. morifolium nutrient use efficiency and growth. These results provide new insights into the efficient cultivation and management of C. morifolium. Full article

(This article belongs to the Special Issue Interactions between Plants and Soil Microorganisms, 2nd Edition)

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Figure 1
Effect of different NPK ratios on the available nutrient content of chrysanthemum cultivation soil. Note: (a) is the content of ammonium nitrogen (N), (b) is the content of available phosphorus (P); (c) is the content of available potassium (K). Different lowercase letters on bar chart indicate significant differences among the treatments (p < 0.05). Full article ">Figure 2
Effects of different NPK ratios on the uptake and tissue distribution of N, P, and K in chrysanthemum plants: (A,a) total nitrogen (N) content and N distribution in different organs and growth stages; (B,b) total phosphorus (P) content and P distribution in different organs and growth stages; (C,c) total potassium (K) content and K distribution in different organs and growth stages; (D) total contents of N, P, and K in flowers. (A–D) correspond to differences of total nitrogen in root + stem + leaf, total phosphorus, and total potassium in root + stem + leaf between treatments at the flowering stage; (a–c) correspond to differences of total nitrogen, total phosphorus, and total potassium content between seedling (30 d), reproductive (60 d) and flowering stages (90 d) in the root, stem, and leaf, respectively. Full article ">Figure 3
Venn diagrams showed shared unique OTUs of (a) bacteria and (b) fungi in the soils after treatments with different NPK ratios in the flowering stage (90 d). NX-1, NX-2, and NX-3 represent sampling at the seedling stage (30 d), reproductive stage (60 d), and flowering stage (90 d), respectively. Full article ">Figure 4
Principal coordinates analysis (PCoA) plot of (a) bacterial and (a) fungal community structures based on Bray–Curtis differences. Full article ">Figure 5
Relative abundance of (a) bacterial and (b) fungal phyla in the chrysanthemum rhizosphere using different NPK fertilization ratios. Full article ">Figure 6
Heatmap of bacterial (a) and fungal (b) distribution of the top-20 most abundant gene-predicted functional profiles in the KEGG pathway present in the chrysanthemum rhizosphere soil using various NPK ratios. Red and green represent high and low enrichment of function abundance, respectively. Full article ">Figure 7
Redundancy analysis (RDA) demonstrating the relationships between soil environmental factors, growth indexes, and (a) soil bacterial and (b) fungal community structures among soil samples. Note: PH, RFW, and RDW indicate plant height, root fresh weight, and root dry weight, respectively. AN, AP, and AK indicate soil ammonium nitrogen, available phosphorus, and potassium, respectively. RTN, STN, and LTN indicate the total nitrogen content of roots, stems, and leaves, respectively. Full article ">Figure 8
Correlation coefficients between soil environmental factors, growth indices, and relative abundances of bacterial (a) and fungal (b) communities in chrysanthemum rhizosphere. Notes: Significant correlation coefficients are indicated * p < 0.05 and ** p < 0.01 based on Pearson’s correlation test. PH, RFW, and RDW indicate plant height, root fresh weight, and root dry weight, respectively. AN, AP, and AK indicate soil ammonium nitrogen, available phosphorus, and potassium, respectively. RTN, STN, and LTN indicate the total nitrogen content of the roots, stems, and leaves, respectively. Full article ">

16 pages, 2318 KiB

Open AccessArticle

Post-Emergence Water-Dispersal Application Provides Equal Herbicidal Activity against Echinochloa crus-galli and Rice Safety as Foliar Spraying of Penoxsulam

by Jinqiu Sun, Xiaoyue Yu, Hongxing Xu, Yongjie Yang, Mengjie Liu, Yanchao Zhang, Yongliang Lu and Wei Tang

Plants 2023, 12(23), 4061; https://doi.org/10.3390/plants12234061 - 3 Dec 2023

Cited by 2 | Viewed by 1580

Abstract

Penoxsulam is an acetolactate synthase (ALS)-inhibiting herbicide usually applied by post-emergence foliar spraying (PFS) for the control of Echinochloa crus-galli and numerous annual weeds in paddy fields. Herbicides applied by foliar spraying can have negative impacts on the environment, ecosystems, and human health. [...] Read more.

Penoxsulam is an acetolactate synthase (ALS)-inhibiting herbicide usually applied by post-emergence foliar spraying (PFS) for the control of Echinochloa crus-galli and numerous annual weeds in paddy fields. Herbicides applied by foliar spraying can have negative impacts on the environment, ecosystems, and human health. In this study, the response of E. crus-galli and rice to the PFS and post-emergence water-dispersal (PWD) applications of penoxsulam, and the differences in the detoxification displayed by them between the two treatment methods were compared. The results showed that the PWD application of penoxsulam provides a similar control efficacy against E. crus-galli as PFS at the 1-, 3-, and 5-leaf stages. Meanwhile, the PWD application had a higher safety for the rice. After being treated with 30 g a.i. ha⁻¹ penoxsulam, residues were not detected in the rice treated by the PWD application method, whereas, with the PFS treatment, there was 59.0 µg/kg penoxsulam remaining. With the PFS application, there were many more residues of penoxsulam in the E. crus-galli than with the PWD method; the amount of residues was 32-fold higher 12 h after treatment. The in vitro enzyme activity assays revealed that the activities of ALS, glutathione-S-transferase (GST), and cytochrome P450 monooxygenases (P450) were increased in the PWD treatments, and were 1.5-, 1.3-, and 2.3-fold higher than with PFS 72 h after treatment. The real-time quantitative PCR (qRT-PCR) revealed that the GST1 and P450 genes, CYP81A14, CYP81A12, CYP81A18, and CYP81A21 were upregulated with the PWD application versus PFS in the E. crus-galli. In summary, these results demonstrate that the herbicidal activity was not affected by the upregulation of target and metabolic enzyme activities with the PWD application of penoxsulam. This research could contribute to application strategies reducing the risk of rice injury and environmental impacts by using water-dispersal formulations of penoxsulam. Full article

(This article belongs to the Special Issue Sustainable Weed Management II)

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Figure 1
Photographs of barnyard grass after 21 days of treatment with different doses of penoxsulam by post-emergence foliar spraying (PFS) and water-dispersal application (PWD). The first, second, and third rows represent E. crus-galli at 1- (first row), 3- (second row), and 5-leaf stages (third row), respectively. Full article ">Figure 2
Dose–response curve of E. crus-galli at 1-leaf stage (a), 3-leaf stage (b) and 5-leaf stage (c) at different doses of penoxsulam by post-emergence foliar spraying (PFS) and water-dispersal application (PWD). Each point represents the mean ± SE of twice-repeated experiments, each including three replicates. Full article ">Figure 3
Activity of ALS (a), P450 (b), and GST (c) at 0, 12, 24, 72, and 120 h after treatment with penoxsulam by post-emergence foliar spraying (PFS) and water-dispersal application (PWD). Each point refers to mean ± SE of twice-repeated experiments, each including three replicates. The significance between the two methods was detected by t-tests (** p < 0.01). Full article ">Figure 4
The gene expression levels of ALS (a), GST1 (b), and CYP81A14 (c) at different time intervals, and the relative gene expression levels of CYP81A12, CYP81A18, and CYP81A21 after 24 h treatment by post-emergence foliar spraying (PFS) and water-dispersal application (PWD) of penoxsulam treatment (d). Data are presented as mean ± SE; significant differences between the two methods were detected by t-tests (* p < 0.05, ** p < 0.01). Full article ">

14 pages, 6682 KiB

Open AccessArticle

Physiological and Physical Strategies to Minimize Damage at the Branch–Stem Junction of Trees: Using the Finite Element Method to Analyze Stress in Four Branch–Stem Features

by Tung-Chi Liu, Yi-Sen Peng and Bai-You Cheng

Plants 2023, 12(23), 4060; https://doi.org/10.3390/plants12234060 - 3 Dec 2023

Viewed by 1455

Abstract

This study analyzed the mechanical and physiological strategies associated with four features in the branch–stem junction of a tree, namely the U-shaped branch attachment, the branch collar, the branch bark ridge, and the roughened lower stem. Models were established for each stage of [...] Read more.

This study analyzed the mechanical and physiological strategies associated with four features in the branch–stem junction of a tree, namely the U-shaped branch attachment, the branch collar, the branch bark ridge, and the roughened lower stem. Models were established for each stage of tree growth by adding these four features sequentially to a base model, and the finite element method (FEM) was employed to create three-dimensional models of an Acer tree’s branch–stem structure for static force analysis. According to the results, the development of the branch collar shifted the point of breakage to the outer part of the collar and, thus, constituted a physiological strategy that prevented decay in the stem. Additionally, the concentration of stress in the branch bark ridge limited the area of tear in the bark following breakage. Finally, the U-shaped branch attachment reduced stress and shifted the point of peak stress toward the branch, while the thickening of the lower stem reduced the overall stress. The development of these features, including the spatial positioning of the branch bark ridge and branch collar, resulted in two breakage points constituting a physical and a physiological strategy that limited damage to the tree and protected the xylem structure. This is the part that has been challenging to decipher in previous discussions of tree-related self-protection mechanisms. Full article

(This article belongs to the Special Issue In Vitro Morphogenesis of Plants)

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16 pages, 1649 KiB

Open AccessArticle

Exploring the Differential Impact of Salt Stress on Root Colonization Adaptation Mechanisms in Plant Growth-Promoting Rhizobacteria

by Lorena del Rosario Cappellari, Pablo Cesar Bogino, Fiorela Nievas, Walter Giordano and Erika Banchio

Plants 2023, 12(23), 4059; https://doi.org/10.3390/plants12234059 - 3 Dec 2023

Cited by 2 | Viewed by 2228

Abstract

Salinity inhibits plant growth by affecting physiological processes, but soil microorganisms like plant growth-promoting rhizobacteria (PGPR) can alleviate abiotic stress and enhance crop productivity. However, it should be noted that rhizobacteria employ different approaches to deal with salt stress conditions and successfully colonize [...] Read more.

Salinity inhibits plant growth by affecting physiological processes, but soil microorganisms like plant growth-promoting rhizobacteria (PGPR) can alleviate abiotic stress and enhance crop productivity. However, it should be noted that rhizobacteria employ different approaches to deal with salt stress conditions and successfully colonize roots. The objective of this study was to investigate the effect of salt stress on bacterial survival mechanisms such as mobility, biofilm formation, and the autoaggregation capacity of three plant growth-promoting strains: Pseudomonas putida SJ04, Pseudomonas simiae WCS417r, and Bacillus amyloliquefaciens GB03. These strains were grown in diluted LB medium supplemented with 0, 100, 200, or 300 mM NaCl. Swimming and swarming mobility were evaluated in media supplemented with 0.3 and 0.5% agar, respectively. Biofilm formation capacity was quantified using the crystal violet method, and the autoaggregation capacity was measured spectrophotometrically. In addition, we evaluated in vitro the capacity of the strains to ameliorate the effects of saline stress in Mentha piperita. The study found that the GB03 strain exhibited enhanced swarming mobility when the salt concentration in the medium increased, resulting in a two-fold increase in the halo diameter at 300 mM. However, high concentrations of NaCl did not affect the swimming mobility. In contrast, swimming motility was reduced in WCS417r and SJ04 under salt stress. On the other hand, exposure to 300 mM NaCl resulted in a 180% increase in biofilm formation and a 30% rise in the percentage of autoaggregation in WCS417r. Conversely, the autoaggregation percentage of the strains SJ04 and GB03 remained unaffected by saline stress. However, for GB03, biofilm formation decreased by 80% at 300 mM. Simultaneously, inoculation with the three evaluated strains alleviated the detrimental effects of salinity on plant growth. Under 150 mM salt stress, all strains showed increased fresh weight, with GB03 and WCS417r improving by 40% and SJ04 exhibiting the most remarkable effect with a 70% rise compared to non-inoculated plants. Despite their different strategies for mitigating salt stress, the application of these strains presents a promising strategy for effectively mitigating the negative consequences of salt stress on plant cultivation. Full article

(This article belongs to the Special Issue Mitigation Strategies and Tolerance of Plants to Abiotic Stresses)

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Figure 1
Effect of exposure to different concentrations of NaCl on the swimming (A) and swarming (B) motility of the strains P. simiae WCS417r, P. putida SJ04, and B. amyloliquefaciens GB03. Full article ">Figure 2
Percentage of autoaggregation of the strains P. simiae WCS417r, P. putida SJ04, and B. amyloliquefaciens GB03 under salt stress conditions (0 mM, 100 mM, 200 mM, and 300 mM). Values are means ± standard errors (SEs) of three independent replicates (n = 3). Means followed by the same letter in a given column are not significantly different according to Fisher’s LSD test (p ≤ 0.05). Full article ">Figure 3
Biofilm formation of the strains P. simiae WCS417r, P. putida SJ04, and B. amyloliquefaciens GB03 under saline conditions (0, 100, 200, and 300 mM). (A) Growth of strains under different salt concentrations (OD). (B) Biofilm development on polystyrene surfaces shown as an average of OD measurements at 570 nm. (C) The relation between biofilm and growth is shown as the ratio between ODs at 570 and 620 nm. Values are means ± standard errors (SEs) of three independent replicates (n = 3). Means followed by the same letter in a given column are not significantly different according to Fisher’s LSD test (p ≤ 0.05). Full article ">Figure 4
Effects of inoculation with different PGPR strains (P. simiae WCS417r, P. putida SJ04, and B. amyloiquefaciens GB03) on fresh weight of Mentha piperita plants grown in Murashige–Skoog medium with 0, 100, and 1500 mM NaCl. Values are means ± standard errors (SEs) of three independent replicates (n = 3). Values with different letters (capital letters for the same strains at different NaCl concentrations and lowercase letters for different strains at the same NaCl concentration) denote significant differences among treatment groups according to Fisher’s LSD test (p ≤ 0.05). Full article ">

17 pages, 8605 KiB

Open AccessArticle

Deficiency of Auxin Efflux Carrier OsPIN1b Impairs Chilling and Drought Tolerance in Rice

by Chong Yang, Huihui Wang, Qiqi Ouyang, Guo Chen, Xiaoyu Fu, Dianyun Hou and Huawei Xu

Plants 2023, 12(23), 4058; https://doi.org/10.3390/plants12234058 - 2 Dec 2023

Cited by 4 | Viewed by 1931

Abstract

Significant progress has been made in the functions of auxin efflux transporter PIN-FORMED (PIN) genes for the regulation of growth and development in rice. However, knowledge on the roles of OsPIN genes in abiotic stresses is limited. We previously reported that [...] Read more.

Significant progress has been made in the functions of auxin efflux transporter PIN-FORMED (PIN) genes for the regulation of growth and development in rice. However, knowledge on the roles of OsPIN genes in abiotic stresses is limited. We previously reported that the mutation of OsPIN1b alters rice architecture and root gravitropism, while the role of OsPIN1b in the regulation of rice abiotic stress adaptations is still largely elusive. In the present study, two homozygous ospin1b mutants (C1b-1 and C1b-2) were employed to investigate the roles of OsPIN1b in regulating abiotic stress adaptations. Low temperature gradually suppressed OsPIN1b expression, while osmotic stress treatment firstly induced and then inhibited OsPIN1b expression. Most OsPIN genes and auxin biosynthesis key genes OsYUC were up-regulated in ospin1b leaves, implying that auxin homeostasis is probably disturbed in ospin1b mutants. The loss of function of OsPIN1b significantly decreased rice chilling tolerance, which was evidenced by decreased survival rate, increased death cells and ion leakage under chilling conditions. Compared with the wild-type (WT), ospin1b mutants accumulated more hydrogen peroxide (H₂O₂) and less superoxide anion radicals

(O_{2}^{-})

after chilling treatment, indicating that reactive oxygen species (ROS) homeostasis is disrupted in ospin1b mutants. Consistently, C-repeat binding factor (CBF)/dehydration-responsive element binding factor (DREB) genes were downregulated in ospin1b mutants, implying that OsDREB genes are implicated in OsPIN1b-mediated chilling impairment. Additionally, the mutation of OsPIN1b led to decreased sensitivity to abscisic acid (ABA) treatment in seed germination, impaired drought tolerance in the seedlings and changed expression of ABA-associated genes in rice roots. Taken together, our investigations revealed that OsPIN1b is implicated in chilling and drought tolerance in rice and provide new insight for improving abiotic stress tolerance in rice. Full article

(This article belongs to the Special Issue Role of Auxin in Plant Growth and Development)

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Figure 1
Expression profile analysis of OsPIN1b under chilling (A) or 20% PEG6000 (B) conditions. Values are means ± standard deviation (SD) (n = 3). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. ***: p < 0.001. Full article ">Figure 2
Expression analysis of auxin efflux genes OsPIN (A) and auxin biosynthesis genes OsYUC (B) in wild-type (WT) and ospin1b leaves. Values are means ± standard deviation (SD) (n = 3). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. *: p < 0.05; **: p < 0.01; ***: p < 0.001. Full article ">Figure 3
Mutation of OsPIN1b impairs rice chilling tolerance. (A) The 14-day-old seedlings were treated in 4 °C for 3 days followed by 4-day recovery. Bar = 4 cm. (B) Trypan blue staining. Bar = 1 mm. (C) Electrolyte leakage. Values are means ± standard deviation (SD) (n = 6). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. **: p < 0.01; ***: p < 0.001. Full article ">Figure 4
DAB and NBT staining in wild-type (WT) and ospin1b mutants before (A) and after (B) cold stress. Bar = 0.5 cm. At least three independent experiments with 6 seedling leaves per experiment were performed. Full article ">Figure 5
Expression analysis of OsDREB1A, OsDREB1BI and OsPP2C27 before (A) and after (B) chilling treatments. Values are means ± standard deviation (SD) (n = 3). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. **: p < 0.01; ***: p < 0.001. Full article ">Figure 6
Mutation of OsPIN1b influences ABA response. The wild-type (WT) and ospin1b seeds were cultured in 1/2 MS medium (A), 1/2 MS medium added 1 μM ABA (B) and 1/2 MS medium added 2 μM ABA (C). The photos were shot after germination for 5 d. Values are means ± standard deviation (SD) (n = 3). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. ***: p < 0.001. Full article ">Figure 7
Mutation of OsPIN1b impairs rice drought tolerance. The 14-day-old seedlings were exposed to air for 12 h followed by another 4-day recovery. Bar = 4 cm (A), and then the survival rate was assessed statistically (n = 24). Data were analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. ***, p < 0.001 (B). Water loss of detached leaves was analyzed every 30 min (C). Values are means ± standard deviation (SD) (n = 3). Full article ">Figure 8
Relative expression of ABA biosynthesis genes (A) and ABA acceptor genes (B) in wild-type (WT) and ospin1b roots. Data are means ± SD and analyzed via ANOVA and Tukey’s tests at p < 0.05 significance level. *: p < 0.05; **, p < 0.01, ***, p < 0.001. Full article ">

13 pages, 2741 KiB

Open AccessArticle

Expression of Cry1Ab/2Aj Protein in Genetically Engineered Maize Plants and Its Transfer in the Arthropod Food Web

by Yi Chen, Michael Meissle, Jiabao Xue, Nan Zhang, Shulin Ma, Anping Guo, Biao Liu, Yufa Peng, Xinyuan Song, Yan Yang and Yunhe Li

Plants 2023, 12(23), 4057; https://doi.org/10.3390/plants12234057 - 2 Dec 2023

Viewed by 1685

Abstract

While transgenic Bacillus thuringiensis (Bt) maize provides pest resistance and a reduced application of chemical pesticides, a comprehensive environmental risk assessment is mandatory before its field release. This research determined the concentrations of Bt protein in plant tissue and in arthropods [...] Read more.

While transgenic Bacillus thuringiensis (Bt) maize provides pest resistance and a reduced application of chemical pesticides, a comprehensive environmental risk assessment is mandatory before its field release. This research determined the concentrations of Bt protein in plant tissue and in arthropods under field conditions in Gongzhuling City, northeastern China, to provide guidance for the selection of indicator species for non-target risk assessment studies. Bt maize expressing Cry1Ab/2Aj and non-transformed near-isoline were grown under identical environmental and agricultural conditions. Cry1Ab/2Aj was detected in plant tissues and arthropods collected from Bt maize plots during pre-flowering, flowering, and post-flowering. The expression of Cry1Ab/2Aj varied across growth stages and maize tissues, as well as in the collected arthropods at the three growth stages. Therefore, representative species should be chosen to cover the whole growing season and to represent different habitats and ecological functions. Dalbulus maidis (Hemiptera: Cicadellidae), Rhopalosiphum padi (Hemiptera: Aphididae), Heteronychus arator (Coleoptera: Scarabaeidae), and Somaticus angulatus (Coleoptera: Tenebrionidae) are suitable non-target herbivores. Propylea japonica (Coleoptera: Coccinellidae), Paederus fuscipes (Coleoptera: Staphylinidae), Chrysoperla nipponensis (Neuroptera: Chrysopidae), and spiders are suggested predators. Apis cerana and Apis mellifera ligustica (both Hymenoptera: Apidae) represent pollinators and Folsomia candida (Collembola: Isotomidae) decomposers. Full article

(This article belongs to the Special Issue Insect-Plant Interaction)

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Cry1Ab/2Aj protein concentrations (μg/g dry weight) in the same stage of different maize tissues: leaves, stems, and roots before flowering (BF); pollen, tassels, leaves, stems, and roots during flowering (DF); tassels, leaves, stems, and roots after flowering (AF). Bars represent medians, and red lines with error bars represent means and 95CIs for each stage (n = 6 for pollen; n = 28, 8, 28 for leaves BF, DF, and AF, respectively; n = 4 for tassels, stems, and roots in each stage). Different small letters indicate significant differences between maize stages, and capital letters indicate significant differences between tissue types based on non-overlapping CIs. Black dots represent the individual values. Full article ">Figure 2
Concentrations of Cry1Ab/2Aj protein (μg/g dry weight) in fresh maize leaves (July sample) and in maize leaves buried in soil for 4 months (August–November samples). Bars represent medians, and red lines with error bars represent means and 95CIs for each month (n = 6 for each month). Different letters indicate significant differences. Black dots represent individual values. Full article ">Figure 3
Cry1Ab/2Aj protein concentrations (μg/g dry weight) in each collected arthropod species for 3 maize stages (BF: before flowering; DF: during flowering; AF: after flowering). Species are grouped into orders. The colored circles following arthropod species or families indicate the detected median concentrations. Full article ">

16 pages, 2640 KiB

Open AccessArticle

Genome Studies in Four Species of Calendula L. (Asteraceae) Using Satellite DNAs as Chromosome Markers

by Tatiana E. Samatadze, Olga Yu. Yurkevich, Firdaus M. Khazieva, Irina V. Basalaeva, Olga M. Savchenko, Svyatoslav A. Zoshchuk, Alexander I. Morozov, Alexandra V. Amosova and Olga V. Muravenko

Plants 2023, 12(23), 4056; https://doi.org/10.3390/plants12234056 - 2 Dec 2023

Cited by 1 | Viewed by 1903

Abstract

The taxonomically challenging genus Calendula L. (Asteraceae) includes lots of medicinal species characterized by their high morphological and karyological variability. For the first time, a repeatome analysis of a valuable medicinal plant Calendula officinalis L. was carried out using high-throughput genome DNA sequencing [...] Read more.

The taxonomically challenging genus Calendula L. (Asteraceae) includes lots of medicinal species characterized by their high morphological and karyological variability. For the first time, a repeatome analysis of a valuable medicinal plant Calendula officinalis L. was carried out using high-throughput genome DNA sequencing and RepeatExplorer/TAREAN pipelines. The FISH-based visualization of the 45S rDNA, 5S rDNA, and satellite DNAs of C. officinalis was performed on the chromosomes of C. officinalis, C. stellata Cav., C. tripterocarpa Rupr., and C. arvensis L. Three satellite DNAs were demonstrated to be new molecular chromosome markers to study the karyotype structure. Karyograms of the studied species were constructed, their ploidy status was specified, and their relationships were clarified. Our results showed that the C. officinalis karyotype differed from the karyotypes of the other three species, indicating its separate position in the Calendula phylogeny. However, the presence of common repeats revealed in the genomes of all the studied species could be related to their common origin. Our findings demonstrated that C. stellata contributed its genome to allotetraploid C. tripterocarpa, and C. arvensis is an allohexaploid hybrid between C. stellata and C. tripterocarpa. At the same time, further karyotype studies of various Calendula species are required to clarify the pathways of chromosomal reorganization that occurred during speciation. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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Types of highly and moderately repeated DNA sequences in the Calendula officinalis genome. A TE proportion of each repeat type or family is shown inside parenthesis. Full article ">Figure 2
Localization of the studied molecular cytogenetic markers on chromosomes of Calendula officinalis. Merged images after multicolor FISH with 45S rDNA, 5S rDNA, Cal 2, Cal 39, Cal 43, and Cal 163. The names of the probes and their pseudocolors are indicated on the lower right of each metaphase plate. Scale bar—5 µm. Full article ">Figure 3
Karyograms of C. officinalis after multicolor FISH with 45S rDNA, 5S rDNA, Cal 2, Cal 43, Cal 163, and Cal 39. The same metaphase plates are shown as in <a href="#plants-12-04056-f002" class="html-fig">Figure 2</a>. I–II—subgenomes. The names of the probes and their pseudocolors are indicated on the left. Full article ">Figure 4
Metaphase plates of C. stellata, C. tripterocarpa and C. arvensis after multicolour FISH with 45S rDNA (green), 5S rDNA (red), and Cal 39 (yellow). Scale bar—5 µm. Full article ">Figure 5
Localization of 45S rDNA(green), 5S rDNA (red), Cal 2 (pink), Cal 43 (yellow), and Cal 163 (blue) on chromosomes of C. stellata. Scale bar—5 µm. Full article ">Figure 6
Localization of (A) 45S rDNA (green), 5S rDNA (red), Cal 2 (pink), Cal 43 (yellow), Cal 163 (blue), and DAPI-staining (grey) and also (B) 45S rDNA (green), 5S rDNA (red), and DAPI-staining (blue) on chromosomes of C. tripterocarpa and C. arvensis. I–III—subgenomes. Scale bar—5 µm. Full article ">

17 pages, 4386 KiB

Open AccessArticle

New Insights on the Role of ß-Cyanoalanine Synthase CAS-C1 in Root Hair Elongation through Single-Cell Proteomics

by Lucía Arenas-Alfonseca, Masashi Yamada, Luis C. Romero and Irene García

Plants 2023, 12(23), 4055; https://doi.org/10.3390/plants12234055 - 2 Dec 2023

Cited by 2 | Viewed by 1893

Abstract

(1) Background: Root hairs are specialized structures involved in water and plant nutrient uptake. They elongate from epidermal cells following a complex developmental program. ß-cyanoalanine synthase (CAS), which is mainly involved in hydrogen cyanide (HCN) detoxification in Arabidopsis thaliana, plays a role [...] Read more.

(1) Background: Root hairs are specialized structures involved in water and plant nutrient uptake. They elongate from epidermal cells following a complex developmental program. ß-cyanoalanine synthase (CAS), which is mainly involved in hydrogen cyanide (HCN) detoxification in Arabidopsis thaliana, plays a role in root hair elongation, as evidenced by the fact that cas-c1 mutants show a severe defect in root hair shape. In addition to root hairs, CAS C1 is expressed in the quiescent center and meristem. (2) Methods: To identify its role in root hair formation, we conducted single-cell proteomics analysis by isolating root hair cells using Fluorescence-activated Cell Sorting (FACS) from wild-type and cas-c1 mutants. We also analyzed the presence of S-cyanylation, a protein post-translational modification (PTM) mediated by HCN and affecting cysteine residues and protein activity in proteins of wild type and cas-c1 mutants. (3) Results and Conclusions: We have found that the cas-c1 mutation has no visible effect on quiescent center or meristem root tissue, in both control and nutrient-deprivation conditions. We have identified more than 3900 proteins in root hairs and we have found that several proteins involved in root hair development, related to the receptor kinase FERONIA signaling and DNA methylation, are modified by S-cyanylation. Full article

(This article belongs to the Special Issue Cyanide-Mediated Signaling in Plants)

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Root meristem phenotype in wild type (a) and cas-c1 mutant (b). Seedlings were grown for 7 d on MS medium supplemented with sucrose in vertical plates. Representative images are shown. *** indicate QC cells. Propidium iodide was used to visualize cell walls. Scale bars are 200 µm. Full article ">Figure 2
Root meristem size in MS medium. (a) A representative root of 7-day-old wild-type (wt) and cas-c1 mutant was stained with propidium iodide. White arrows indicate the transition between the elongation and transition zones in wild-type and cas-c1 mutant seedlings. Representative images are shown. (b) Root meristem length of wild type and cas-c1 mutants in MS medium. Media ± SD are shown in the graph. N > 20. Scale bars are 50 µm. Full article ">Figure 3
Root length measurement in nutrient deficient media. Wild-type and cas-c1 mutant seedlings were grown for 9 d in vertical plates of MS medium or MS medium in the absence of different nutrient compounds. Root length was measured with ImageJ 1.51j8 software. Values are means ± SD of three independent experiments; ANOVA. Full article ">Figure 4
GFP localization in roots from the wt-pCOBL9:GFP and cas-c1-pCOBL9:GFP transgenic lines. Plants were grown for 6 days in MS medium. Representative images are shown. Scale bars are 50 μm. Full article ">Figure 5
(a) Venn diagram showing the unique and intersection of the identified protein in the proteomic analysis of Petrika et al., 2012 and this work. (b) Venn diagram showing the unique and intersection of the identified proteins in wild-type and cas-c1 root hair samples. Full article ">Figure 6
Bubble plot of the functional classification of the identified proteins according to the plant-specific database MapMan. Bubble columns represent the proteins classified within each bin of the total proteins identified in wild-type (wt), cas-c1 root hair samples, and those only present in wt or cas-c1 root hair samples. Numbers beside the bubbles represent the amount of proteins classified within the bin. Full article ">Figure 7
LC-MS/MS mass spectra of the tryptic peptide containing the cyanylated Cys346 residue of the S-Adenosyl homocysteine hydrolase SAHH1/HOG1 protein. The table contains the predicted ion type for the modified peptide, and the ions detected in the spectrum are highlighted in green color. Full article ">Figure 8
LC-MS/MS mass spectra of the tryptic peptide containing the cyanylated Cys10 residue of the Glycine Rich Protein 7, (GRP7). The table contains the predicted ion type for the modified peptide, and the ions detected in the spectrum are highlighted in green color. Full article ">

19 pages, 1730 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Siderophores Generated by Pseudomonas Bacteria and Their Possible Application as Fe Biofertilizers

by José María Lozano-González, Silvia Valverde, Mónica Montoya, Marta Martín, Rafael Rivilla, Juan J. Lucena and Sandra López-Rayo

Plants 2023, 12(23), 4054; https://doi.org/10.3390/plants12234054 - 2 Dec 2023

Cited by 4 | Viewed by 2611

Abstract

The application of synthetic iron chelates to overcome iron deficiency in crops is leading to a high impact on the environment, making it necessary to find more friendly fertilizers. A promising alternative is the application of biodegradable iron chelates, such as those based [...] Read more.

The application of synthetic iron chelates to overcome iron deficiency in crops is leading to a high impact on the environment, making it necessary to find more friendly fertilizers. A promising alternative is the application of biodegradable iron chelates, such as those based on siderophores. In the present work, seven bacterial strains of the genus Pseudomonas were selected for their ability to secrete pyoverdine, a siderophore with a high affinity for iron, which could be used as a biofertilizer. The concentration of siderophores secreted by each bacterium expressed as desferrioxamine B equivalents, and the pyoverdine concentration was determined. Their potential as Fe biofertilizers was determined based on their capacity to complex Fe, determining the maximum iron complexation capacity at alkaline pH and selecting the RMC4 strain. The biostimulant capacity of the RMC4 strain was evaluated through the secretion of organic acids such as the hormone Indol-3-acetic acid or glutamic acid, among others, in a kinetic assay. Finally, the genome of RMC4 was determined, and the strain was identified as Pseudomonas monsensis. The annotated genome was screened for genes and gene clusters implicated in biofertilization and plant growth promotion. Besides iron mobilization, genes related to phosphorus solubilization, production of phytohormones and biological control, among others, were observed, indicating the suitability of RMC4 as an inoculant. In conclusion, RMC4 and its siderophores are promising sources for Fe biofertilization in agriculture. Full article

(This article belongs to the Special Issue Biochemical Interactions of Iron Nutrition in Plants)

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Concentration of siderophore expressed as DFOB equivalents (µM). The data are the mean ± SE (n = 9). Different letters indicate significant differences according to Duncan’s test (p < 0.05). Full article ">Figure 2
Concentration of pyoverdine (µM) produced by the selected bacterial strains. The data are the mean ± SE (n = 9). Different letters indicate significant differences according to Duncan’s test (p < 0.05). Full article ">Figure 3
Molar ratio values of Fe: siderophore determined by the representation of the concentration of soluble Fe (µM)/siderophore concentration (µM) vs. concentration of added Fe (µM)/siderophore concentration (µM) for each bacterial strain. Full article ">Figure 4
The grey circular dots represent the corrected absorbance for mL of Fe added. The rhomboid dots represent the second derivative of the absorbance versus mL of Fe added. Full article ">Figure 5
Concentration (mmol/L) of (A) acetic acid; (B) aminobutyric acid; (C) glutamic acid; (D) IAA; (E) succinic acid, and (F) pyoverdine (µmol/L) over time (n = 3) in the bacterial extract of the Pseudomonas RMC4. Full article ">Figure 5 Cont.
Concentration (mmol/L) of (A) acetic acid; (B) aminobutyric acid; (C) glutamic acid; (D) IAA; (E) succinic acid, and (F) pyoverdine (µmol/L) over time (n = 3) in the bacterial extract of the Pseudomonas RMC4. Full article ">

25 pages, 6694 KiB

Open AccessArticle

Genetic Diversity and Genome-Wide Association Study for the Phenology Response of Winter Wheats of North America, Western Asia, and Europe

by Adil El Baouchi, Mohammed Ibriz, Susanne Dreisigacker, Marta S. Lopes and Miguel Sanchez Garcia

Plants 2023, 12(23), 4053; https://doi.org/10.3390/plants12234053 - 1 Dec 2023

Cited by 1 | Viewed by 2085

Abstract

Wheat is a staple food in many areas around the World. In the 20th century, breeders and scientists were able to boost wheat yield considerably. However, a yield plateau has become a concern and is threatening food security. Investments in cutting-edge technologies, including [...] Read more.

Wheat is a staple food in many areas around the World. In the 20th century, breeders and scientists were able to boost wheat yield considerably. However, a yield plateau has become a concern and is threatening food security. Investments in cutting-edge technologies, including genomics and precision phenology measurements, can provide valuable tools to drive crop improvement. The objectives of this study were to (i) investigate the genetic diversity in a set of winter wheat lines, (ii) characterize their phenological response under different vernalization and photoperiod conditions, and (iii) identify effective markers associated with the phenological traits. A total of 249 adapted genotypes of different geographical origin were genotyped using the 35K Axiom^® Wheat Breeder’s Array. A total of 11,476 SNPs were used for genetic analysis. The set showed an average polymorphism information content of 0.37 and a genetic diversity of 0.43. A population structure analysis revealed three distinct subpopulations mainly related to their geographical origin (Europe, North America, and Western Asia). The lines of CGIAR origin showed the largest diversity and the lowest genetic distance to all other subpopulations. The phenology of the set was studied under controlled conditions using four combinations of long (19 h light) and short photoperiod (13 h light) and long vernalization (49 days at 5 °C) and no vernalization. With this, phenological traits such as earliness per se (Eps), relative response to vernalization (RRV), and relative response to photoperiod (RRP) were calculated. The phenotypic variation of growing degree days was significant in all phenology combinations. RRV ranged from 0 to 0.56, while RRP was higher with an overall average of 0.25. The GWAS analysis detected 30 marker-trait associations linked to five phenological traits. The highest significant marker was detected on chromosome 2D with a value of −log10(p) = 11.69. Only four loci known to regulate flowering exceeded the Bonferroni correction threshold of −log10(p) > 5.1. These results outline a solid foundation to address global food security and offer tremendous opportunities for advancing crop improvement strategies. Full article

(This article belongs to the Special Issue Cereal Genetics and Molecular Genetics)

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20 pages, 4210 KiB

Open AccessArticle

Phenotypic Diversity and Genetic Parameters of Coffea canephora Clones

by Caroline de Souza Bezerra, Jennifer Souza Tomaz, Mágno Sávio Ferreira Valente, Marcelo Curitiba Espindula, Ricardo Lívio Santos Marques, Hugo Cesar Tadeu, Fábio Medeiros Ferreira, Gabriel de Sousa Silva, Carlos Henrique Salvino Gadelha Meneses and Maria Teresa Gomes Lopes

Plants 2023, 12(23), 4052; https://doi.org/10.3390/plants12234052 - 1 Dec 2023

Cited by 2 | Viewed by 1589

Abstract

The simultaneous analysis of the maximum number of chemical elements present in plant tissues provides more comprehensive information about their chemical constitution and increases the number of characteristics for the selection process in various plant breeding programs. The objective of this study was [...] Read more.

The simultaneous analysis of the maximum number of chemical elements present in plant tissues provides more comprehensive information about their chemical constitution and increases the number of characteristics for the selection process in various plant breeding programs. The objective of this study was to analyze productivity, grain yield, and concentration of chemical elements in tissues of Coffea canephora clones to study phenotypic diversity and estimate genetic parameters for use in breeding. This experiment was carried out in Manaus, Amazonas, Brazil, in randomized blocks with four replications. The concentrations of elements in various organs were quantified using total reflection X-ray fluorescence (TXRF). Genetic parameters and genetic divergence were estimated, and genotypes were clustered using the UPGMA hierarchical method and non-metric multidimensional scaling analysis. The study allowed us to differentiate the performance of the clones in terms of the absorption of essential and non-essential chemical elements for plant development and to analyze the correlation of the characteristics in the selection process. TXRF efficiently characterizes the presence and concentration of multiple elements, aiding genotype discrimination for C. canephora improvement. Full article

(This article belongs to the Special Issue Coffee Breeding and Stress Biology)

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17 pages, 4633 KiB

Open AccessArticle

Nitric Oxide (NO) Improves Wheat Growth under Dehydration Conditions by Regulating Phytohormone Levels and Induction of the Expression of the TADHN Dehydrin Gene

by Chulpan Allagulova, Azamat Avalbaev, Alsu Lubyanova, Anton Plotnikov, Ruslan Yuldashev and Oksana Lastochkina

Plants 2023, 12(23), 4051; https://doi.org/10.3390/plants12234051 - 1 Dec 2023

Cited by 1 | Viewed by 1474

Abstract

Nitric oxide (NO) is a universal signaling molecule with important regulatory functions in the plant’s life cycle and adaptation to a wide spectrum of environmental stresses including drought. The effect of pre-sowing seed treatment with the donor of NO sodium nitroprusside (SNP, 200 [...] Read more.

Nitric oxide (NO) is a universal signaling molecule with important regulatory functions in the plant’s life cycle and adaptation to a wide spectrum of environmental stresses including drought. The effect of pre-sowing seed treatment with the donor of NO sodium nitroprusside (SNP, 200 μM) on wheat Triticum aestivum L. plants subjected to dehydration (PEG-8000, 12%) was investigated. SNP pretreatment stimulated germination and seedling growth in normal conditions and protected them under dehydration. These effects were confirmed by percentage of seed germination, changes in fresh and dry weight of 5–6-day-old seedlings, as well as by seedlings’ linear dimensions, visual appearance, and mitotic index of the root apical meristem. Assessment of the transpiration intensity (TI) and relative water content (RWC) showed that SNP pretreatment helped to maintain the water status of seedlings subjected to dehydration stress. The data obtained by enzyme-linked immunosorbent assay (ELISA) suggested that the positive effects of SNP may be due to its influence on the phytohormonal system. SNP pretreatment induced an increase in the level of indolylacetic acid (IAA) and especially cytokinins (CK), while essential changes in ABA content were not detected. Water deficiency caused a substantial increase in ABA content and a decrease in the levels of CK and IAA. Pre-sowing SNP treatment decreased stress-induced fluctuations in the content of all studied phytohormones. Using reverse-transcription PCR (RT-PCR), we obtained data on the increase in expression of the TADHN dehydrin gene in SNP-pretreated seedlings under normal and, especially, under dehydration conditions. These findings may indicate the participation of dehydrins in NO-induced defense reactions in wheat plants under water stress. Furthermore, exogenous NO had a stabilizing effect on membrane cellular structures, as evidenced by the reduction of electrolyte leakage (EL) levels and malondialdehyde (MDA) content in dehydrated wheat seedlings under the influence of pre-sowing SNP treatment. Full article

(This article belongs to the Special Issue The Role of Signaling Molecules in Plant Stress Tolerance)

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18 pages, 2454 KiB

Open AccessArticle

Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions

by Chenchen Hu, Jinghui Li, Jiajia Liu, Dazhong Zhang, Liqiao Jin, Nian Yang, Bipo Bai, Zenghao Wang, Suwei Feng, Zhengang Ru and Tiezhu Hu

Plants 2023, 12(23), 4050; https://doi.org/10.3390/plants12234050 - 1 Dec 2023

Viewed by 1654

Abstract

Nitrogen fertilizer input is the main determinant of wheat yield, and heavy nitrogen fertilizer application causes serious environmental pollution. It is important to understand the genetic response mechanism of wheat to nitrogen and select wheat germplasm with high nitrogen efficiency. In this study, [...] Read more.

Nitrogen fertilizer input is the main determinant of wheat yield, and heavy nitrogen fertilizer application causes serious environmental pollution. It is important to understand the genetic response mechanism of wheat to nitrogen and select wheat germplasm with high nitrogen efficiency. In this study, 204 wheat species were used to conduct genome-wide association analysis. Nine phenotypic characteristics were obtained at the seedling stage in hydroponic cultures under low-, normal, and high-nitrogen conditions. A total of 765 significant loci were detected, including 438, 261, and 408 single nucleotide polymorphisms (SNPs) associated with high-, normal, and low-nitrogen conditions, respectively. Among these, 14 SNPs were identified under three conditions, for example, AX-10887638 and AX-94875830, which control shoot length and root–shoot ratio on chromosomes 6A and 6D, respectively. Additionally, 39 SNPs were pleiotropic for multiple traits. Further functional analysis of the genes near the 39 SNPs shows that some candidate genes play key roles in encoding proteins/enzymes, such as transporters, hydrolases, peroxidases, glycosyltransferases, oxidoreductases, acyltransferases, disease-resistant proteins, ubiquitin ligases, and sucrose synthetases. Our results can potentially be used to develop low-nitrogen-tolerant species using marker-assisted selection and provide a theoretical basis for breeding efficient nitrogen-using wheat species. Full article

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21 pages, 9124 KiB

Open AccessArticle

Biochemical and Structural Diversification of C₄ Photosynthesis in Tribe Zoysieae (Poaceae)

by Nuria K. Koteyeva, Elena V. Voznesenskaya, Varsha S. Pathare, Tatyana A. Borisenko, Peter M. Zhurbenko, Grigory A. Morozov and Gerald E. Edwards

Plants 2023, 12(23), 4049; https://doi.org/10.3390/plants12234049 - 30 Nov 2023

Cited by 4 | Viewed by 1167

Abstract

C₄ photosynthesis has evolved independently multiple times in grass lineages with nine anatomical and three biochemical subtypes. Chloridoideae represents one of the separate events and contains species of two biochemical subtypes, NAD-ME and PEP-CK. Assessment of C₄ photosynthesis diversification is limited [...] Read more.

C₄ photosynthesis has evolved independently multiple times in grass lineages with nine anatomical and three biochemical subtypes. Chloridoideae represents one of the separate events and contains species of two biochemical subtypes, NAD-ME and PEP-CK. Assessment of C₄ photosynthesis diversification is limited by species sampling. In this study, the biochemical subtypes together with anatomical leaf traits were analyzed in 19 species to reveal the evolutionary scenario for diversification of C₄ photosynthesis in tribe Zoysieae (Chloridoideae). The effect of habitat on anatomical and biochemical diversification was also evaluated. The results for the 19 species studied indicate that 11 species have only NAD-ME as a decarboxylating enzyme, while eight species belong to the PEP-CK subtype. Leaf anatomy corresponds to the biochemical subtype. Analysis of Zoysieae phylogeny indicates multiple switches between PEP-CK and NAD-ME photosynthetic subtypes, with PEP-CK most likely as the ancestral subtype, and with multiple independent PEP-CK decarboxylase losses and its secondary acquisition. A strong correlation was detected between C₄ biochemical subtypes studied and habitat annual precipitation wherein NAD-ME species are confined to drier habitats, while PEP-CK species prefer humid areas. Structural adaptations to arid climate include increases in leaf thickness and interveinal distance. Our analysis suggests that multiple loss of PEP-CK decarboxylase could have been driven by climate aridization followed by continued adaptive changes in leaf anatomy. Full article

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

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Figure 1
Western blots for three decarboxylases from total proteins extracted from leaves of 19 Zoysieae species. Blots were probed with antibodies raised against PEP-CK, NAD-ME, and NADP-ME: representative Western blots are presented, showing detection of each protein. The originals were modified for alignment according to species or to avoid replicate species (vertical lines); there were no selective changes in the mass or densities of bands on the membrane. The molecular mass is indicated to the right of the blots. Full article ">Figure 2
Light microscopy of leaf cross sections for 11 species of the tribe Zoysieae (Poaceae) that are classified as NAD-ME C4 biochemical subtype. Arrows indicate the centripetal (towards the vascular bundle) position of BS organelles. BS, bundle sheath; M, mesophyll. Scale: (A–J), 100 µm; (K), 200 µm. Full article ">Figure 3
Light microscopy of leaf cross sections for eight species of the tribe Zoysieae (Poaceae) that are classified as PEP-CK C4 biochemical subtype. Arrows indicate centrifugal (towards the mesophyll) position of BS organelles. BS, bundle sheath; M, mesophyll. Scale: (A), 200 µm; (B–H), 100 µm. Full article ">Figure 4
Ultrastructure of representative species of the tribe Zoysieae (Poaceae) that are classified as NAD-ME (A–D,I–L) and PEP-CK (E–H,M–P) C4 biochemical subtypes. (A,E,I,M) bundle sheath cell chloroplasts. (B,F,J,N) mesophyll chloroplasts. (C,G,K,O) bundle sheath cell mitochondria. (D,H,L,P) plasmodesmata pit field in the cell wall between BS and M, showing absence (D,L) and deposition (H,P) of suberin lamellae. G, grana; M, mitochondria; SL, suberin lamellae; ST, stromal thylakoid. Scale: (A–C,J–K) 1 µm; (D–I,L–P) 0.5 µm. Full article ">Figure 5
Habitat mean annual precipitation (A) and habitat mean annual temperature (B) for eight NAD-ME and seven PEP-CK C4 species used in current study. Gray bars indicate mean values ± SE (n = 7 and 8 species), and small black circles indicate the replicates. t-test results are indicated above the barplots, where ‘*’ indicates significant differences at p ≤ 0.05 and ‘ns’ indicates non-significant differences at p > 0.1. Full article ">Figure 6
Relationship between mean annual precipitation (MAP) and leaf anatomical traits for 15 Zoysieae C4 grasses: (A) maximal (Thickness VB) and (B) minimal (Thickness_min) leaf thicknesses; (C) interveinal distance (IVD); (D) adaxial stomatal density (SD_ada); (E) abaxial stomatal density (SD_aba); (F) abaxial stomata size (Size_aba); (G) adaxial stomata size (Size_ada), µm; (H) BS (CW_BS) and (I) mesophyll (CW_mes) cell wall thicknesses. NAD-ME species are labeled with brown dots, PEP-CK species are labeled with blue dots. Regression coefficient (R2) is shown when p ≤ 0.03. For A and B, the regression coefficient was analyzed after exclusion of the influential point (S. anglicus). Full article ">Figure 7
Relationship between mean annual temperature (MAT) and leaf anatomical traits for 15 Zoysieae C4 grasses: (A) maximal (Thickness VB) and (B) minimal (Thickness_min) leaf thicknesses; (C) interveinal distance (IVD); (D) adaxial stomatal density (SD_ada); (E) abaxial stomatal density (SD_aba); (F) abaxial stomata size (Size_aba); (G) adaxial stomata size (Size_ada); (H) BS (CW_BS) and (I) mesophyll (CW_mes) cell wall thicknesses. NAD-ME species are labeled with brown dots, PEP-CK species are labeled with blue dots. Regression coefficient (R2) is shown when p ≤ 0.06. Full article ">Figure 8
Molecular phylogenetic tree of tribe Zoysyeae based on combined plastome (rpl32-trnL, ndhA, rps16, and rps16-trnK) data for 35 species (67 accessions). Species with the NAD-ME C4 biochemical subtype are marked in red, and species with the PEP-CK C4 biochemical subtype are marked in blue. Full article ">

40 pages, 8393 KiB

Open AccessArticle

The Effect of Leaf Plasticity on the Isolation of Apoplastic Fluid from Leaves of Tartary Buckwheat Plants Grown In Vivo and In Vitro

by Natalya I. Rumyantseva, Alfia I. Valieva, Yulia A. Kostyukova and Marina V. Ageeva

Plants 2023, 12(23), 4048; https://doi.org/10.3390/plants12234048 - 30 Nov 2023

Cited by 3 | Viewed by 2016

Abstract

Vacuum infiltration–centrifugation (VIC) is the most reproducible technique for the isolation of apoplast washing fluid (AWF) from leaves, but its effectiveness depends on the infiltration–centrifugation conditions and the anatomical and physiological peculiarities of leaves. This study aimed to elaborate an optimal procedure for [...] Read more.

Vacuum infiltration–centrifugation (VIC) is the most reproducible technique for the isolation of apoplast washing fluid (AWF) from leaves, but its effectiveness depends on the infiltration–centrifugation conditions and the anatomical and physiological peculiarities of leaves. This study aimed to elaborate an optimal procedure for AWF isolation from the leaves of Tartary buckwheat grown in in vivo and in vitro conditions and reveal the leaf anatomical and physiological traits that could contribute to the effectiveness of AWF isolation. Here, it was demonstrated that leaves of buckwheat plants grown in vitro could be easier infiltrated, were less sensitive to higher forces of centrifugation (900× g and 1500× g), and produced more AWF yield and apoplastic protein content than in vivo leaves at the same forces of centrifugation (600× g and 900× g). The extensive study of the morphological, anatomical, and ultrastructural characteristics of buckwheat leaves grown in different conditions revealed that in vitro leaves exhibited significant plasticity in a number of interconnected morphological, anatomical, and physiological features, generally driven by high RH and low lighting; some of them, such as the reduced thickness and increased permeability of the cuticle of the epidermal cells, large intercellular spaces, increase in the size of stomata and in the area of stomatal pores, higher stomata index, drop in density, and area of calcium oxalate druses, are beneficial to the effectiveness of VIC. The size of stomata pores, which were almost twice as large in in vitro leaves as those in in vivo ones, was the main factor contributing to the isolation of AWF free of chlorophyll contamination. The opening of stomata pores by artificially created humid conditions reduced damage to the in vivo leaves and improved the VIC of them. For Fagopyrum species, this is the first study to develop a VIC technique for AWF isolation from leaves. Full article

(This article belongs to the Special Issue Plant Plasticity)

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15 pages, 3442 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Roots of Rice Seedlings under Nitrogen Deficiency

by Dongfeng Qiu, Yan Wu, Kuaifei Xia, Mingyong Zhang, Zaijun Zhang and Zhihong Tian

Plants 2023, 12(23), 4047; https://doi.org/10.3390/plants12234047 - 30 Nov 2023

Cited by 2 | Viewed by 1221

Abstract

Long non-coding RNAs (lncRNAs) regulate gene expression in eukaryotic organisms. Research suggests that lncRNAs may be involved in the regulation of nitrogen use efficiency in plants. In this study, we identified 1628 lncRNAs based on the transcriptomic sequencing of rice roots under low-nitrogen [...] Read more.

Long non-coding RNAs (lncRNAs) regulate gene expression in eukaryotic organisms. Research suggests that lncRNAs may be involved in the regulation of nitrogen use efficiency in plants. In this study, we identified 1628 lncRNAs based on the transcriptomic sequencing of rice roots under low-nitrogen (LN) treatment through the implementation of an integrated bioinformatics pipeline. After 4 h of LN treatment, 50 lncRNAs and 373 mRNAs were significantly upregulated, and 17 lncRNAs and 578 mRNAs were significantly downregulated. After 48 h LN treatment, 43 lncRNAs and 536 mRNAs were significantly upregulated, and 42 lncRNAs and 947 mRNAs were significantly downregulated. Moreover, the interaction network among the identified lncRNAs and mRNAs was investigated and one of the LN-induced lncRNAs (lncRNA24320.6) was further characterized. lncRNA24320.6 was demonstrated to positively regulate the expression of a flavonoid 3′-hydroxylase 5 gene (OsF3′H5). The overexpression of lncRNA24320.6 was shown to improve nitrogen absorption and promote growth in rice seedlings under LN conditions. Our results provide valuable insights into the roles of lncRNAs in the rice response to nitrogen starvation. Full article

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

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Figure 1
Identification of differentially expressed (DE) lncRNAs in rice roots under low nitrogen treatment. (A) Preparation of nitrogen-starved ‘Zhonghua 11’ (ZH11) rice seedlings for RNA sequencing. The 14-day-old rice roots were subjected to nitrogen deficiency for 4 h and 48 h prior to sampling. (B) Screening of total and DE lncRNAs. Full article ">Figure 2
Identification and characterization of lncRNAs in rice seedlings. (A) Venn diagram of putative lncRNAs screened via coding potential analysis methods, including CNCI, CPC, Pfam, and CPAT. Numbers within circles represent the number of lncRNA transcripts predicted to be positive. The intersection of the four circles is taken as the prediction result. (B) lncRNA composition. lincRNA: long chain non-coding RNA in intergenic region; antisense lncRNA: antisense long chain non-coding RNA; intronic lncRNA: intronic long chain non-coding RNA; sense lncRNA: long strand non-coding RNA. (C) Comparison of lncRNA and mRNA transcript lengths. The x-axis is the length, and the y-axis is the number of lncRNAs/mRNAs whose length is distributed within the range. (D) Comparison of the number of exons between lncRNAs and mRNAs. (E) Comparison of open reading frame (ORF) lengths between lncRNAs and mRNAs. (F) Comparison of lncRNA and mRNA expression levels. The bottom of the box chart is the maximum, the upper quartile, the median, the lower quartile, and the minimum. (G) Comparison of isoform numbers per gene between lncRNAs and mRNAs. The x-axis represents the distribution of the number of variable shear isomers per gene, and the y-axis represents log2 (number of genes+1). Full article ">Figure 3
Differentially expressed (DE) genes and functional annotation involved in nitrogen deficiency. (A) Volcano plot of DE mRNAs and lncRNAs 4 h after nitrogen starvation. (B) Volcano plot of DE mRNAs and lncRNAs 48 h after nitrogen starvation. (C) Venn diagram of DE lncRNAs 4 h and 48 h after nitrogen starvation. (D) GO enrichment analysis of cis-regulated target genes. (E) GO enrichment analysis of trans-regulated target genes. Red represents high enrichment functional classification, and blue represents terms with relatively low enrichment. The numbers in each term label indicate the number of DE genes. (F) KEGG annotation of DE lncRNA-targeted genes 4 h after nitrogen starvation. (G) KEGG annotation of DE lncRNA-targeted genes 48 h after nitrogen starvation. The vertical axis represents the name of the KEGG metabolic pathway, and the horizontal axis represents the number of lncRNA-targeted genes annotated to this pathway and their proportion to the total number of lncRNA-targeted genes annotated. Full article ">Figure 4
Location and targeted gene prediction of lncRNA24320.6. (A) Location of lncRNA24320.6. (B) Predicted genes cis-targeted by lncRNA24320.6. (C) Relative expression of lncRNA24320.6 and its predicted cis-targeted genes in lncRNA-24320.6-ox plants. The housekeeping gene eEF-1α (Os03g0178000) was used as a reference gene to normalize the relative expression. Three biological and three technical replicates were used for each experiment. *** represents p-value < 0.001. Full article ">Figure 5
Expression patterns of lncRNA24320.6 and OsF3′H5. (A) Relative expression of lncRNA24320.6 in different tissues of heading rice plants. (B) Relative expression of OsF3′H5 in different tissues of heading rice plants. (C) Relative expression of lncRNA24320.6 in nitrogen-starved rice seedlings. (D) Relative expression of OsF3′H5 in nitrogen-starved rice seedlings. *** represents p-value < 0.001. Full article ">Figure 6
Total carbon and nitrogen contents in lncRNA24320.6-ox and ‘ZH11′ rice under various nitrogen conditions. (A) Total carbon content in roots. (B) Total carbon content in shoots. (C) Total nitrogen content in roots. (D) Total nitrogen content in shoots. * represents p-value < 0.05. Full article ">Figure 7
Agronomic traits of lncRNA24320.6-ox and ‘ZH11′ rice under normal (CK) and low nitrogen (LN) field conditions. (A) Plant height. (B) Tiller number. (C) Weight of one thousand seeds. (D) Seed setting rate. Data are the means of three biological replicates with a standard deviation (n = 30). * represents p-value < 0.05. Full article ">

15 pages, 4168 KiB

Open AccessEditor’s ChoiceArticle

Assessment of Mediterranean Citrus Peel Flavonoids and Their Antioxidant Capacity Using an Innovative UV-Vis Spectrophotometric Approach

by Rosario Mare, Roberta Pujia, Samantha Maurotti, Simona Greco, Antonio Cardamone, Anna Rita Coppoletta, Sonia Bonacci, Antonio Procopio and Arturo Pujia

Plants 2023, 12(23), 4046; https://doi.org/10.3390/plants12234046 - 30 Nov 2023

Cited by 9 | Viewed by 2806

Abstract

Citrus fruits exert various beneficial health effects due to the large amount of polyphenols they contain. Citrus peels, often considered food waste, contain several health-promoting polyphenols. Among these, flavonoids have long been quantified through colorimetric assays which, if not adequately applied, can lead [...] Read more.

Citrus fruits exert various beneficial health effects due to the large amount of polyphenols they contain. Citrus peels, often considered food waste, contain several health-promoting polyphenols. Among these, flavonoids have long been quantified through colorimetric assays which, if not adequately applied, can lead to conflicting results. Flavonoids possess strong antioxidant properties and can decrease circulating free radicals, thereby reducing oxidative stress phenomena. Quantifying flavonoids and properly estimating their antioxidant capacity allows us to predict plausible beneficial effects of citrus fruits on human health. The aim of this research was to analyze the advantageous phenolic compounds found in the peels of citrus fruits commonly found in the Mediterranean region. The objective was to measure their antioxidant capacity and ability to neutralize free radicals. To achieve this purpose, UV-visible spectrophotometric analyses, liquid chromatography (LC) and Electron Paramagnetic Spectroscopy (EPR) were utilized and compared, finally suggesting an innovative approach for assessing the overall flavonoid content by the nitrite-aluminum assay. HPLC data demonstrated that hesperidin was the most abundant flavonoid in all peel extracts except for orange peels, in which naringin was the predominant flavonoid. The total flavonoid content was greater than 1.3 mg/mL in all extracts, with tangerine and orange yielding the best results. Citrus peel polyphenols exerted strong antioxidant and free radical scavenging effects, inhibiting up to 75% of the free radicals used as reference in the EPR analyses. Full article

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UV-Visible spectrophotometric analyses of pure flavonoid standard solutions (rutin, naringin, apigenin and hesperidin, respectively, for panels (A–D)) with wavelengths between 200 nm and 600 nm. Panel (E) is the analysis of a mixture obtained with all standard molecules previously listed in weight ratio 1:1:1:1. Full article ">Figure 2
UV-Visible spectrophotometric analyses of nitrite-aluminum assay executed with pure flavonoid standard solutions (rutin, naringin, apigenin and hesperidin, respectively, for panels (A–D)). Panel (E) is the analysis of a mixture obtained with all standard molecules previously listed in weight ratio 1:1:1:1. Full article ">Figure 3
HPLC analyses of standard pure flavonoid mixture before (panel (A)) and after (panel (B–D)) executing the nitrite-aluminum assay with detector set at different wavelengths. Full article ">Figure 4
UV-Visible spectrophotometric analyses of citrus extracts in wavelengths between 200 nm and 600 nm and their comparison with the spectrophotometric data obtained with standard flavonoid mixture. All extracts were diluted (molar ratio 1:80) with extraction medium before analyses in order to respect Lambert–Beer law. Full article ">Figure 5
UV-Visible spectrophotometric analyses of citrus peel extracts analyzed with nitrite aluminum assay for flavonoids quantification. Last panel shows the data obtained with standard flavonoid mixture used for comparison. All extracts were diluted (molar ratio 1:50) with extraction medium before analyses in order to respect Lambert–Beer law. Full article ">Figure 6
EPR spectra of DPPH in the absence (blue) and presence of the tested extracts. Ascorbic acid has been used as positive control. mT: millitesla. Full article ">

12 pages, 558 KiB

Open AccessArticle

Impact of Harvest Time on the Dry Matter Content, and Nutritional Parameters Related to Forage Quality of Maralfalfa (Cenchrus purpureus (Schumach.) Morrone, Poaceae) under Mediterranean Climate

by Joaquín Fayos-Febrer, Jorge Juan-Vicedo, Alba Rodríguez-Mengod, Javier Mazón and Juan Carlos Gardón

Plants 2023, 12(23), 4045; https://doi.org/10.3390/plants12234045 - 30 Nov 2023

Cited by 1 | Viewed by 1513

Abstract

Maralfalfa (Cenchrus purpureus (Schumach.) Morrone) is a productive fodder crop in tropical regions that has been evaluated for forage nutritional value in a Mediterranean climate. To assess the nutritional value, parameters including dry matter content (DM), ash, ether extract (EE), protein (CP), [...] Read more.

Maralfalfa (Cenchrus purpureus (Schumach.) Morrone) is a productive fodder crop in tropical regions that has been evaluated for forage nutritional value in a Mediterranean climate. To assess the nutritional value, parameters including dry matter content (DM), ash, ether extract (EE), protein (CP), fiber contents (NDF and ADF), and the amino acids profile were determined at eight harvest times (HTs) in a non-fertilized and non-irrigated crop based in Silla (Valencia, Spain). The results showed significant differences in most of the parameters studied. While CP and ash significantly decreased over the eight HTs, NDF and ADF increased. In contrast, EE and the ratio of essential amino acids/total amino acids remained constant. Values of CP remained higher than 15% during the first two HTs (16 and 28 days). According to the analyses performed, the optimum HT can be stated at 28 days as it combines high levels of CP (including an optimal combination of essential amino acids) with low levels of fibers (NDF = 57.13%; ADF = 34.76%) and a considerable amount of dry matter (15.40%). Among the essential amino acids (EA) determined, lysine and histidine showed similar values (Lys ≈ 6%, His ≈ 1.70%) when comparing the composition of these EA to other forage species and cultivars studied, whereas methionine showed lower values. This work establishes the basis for the appropriate HT of maralfalfa according to the nutritional parameters measured. Further studies could be aimed to optimize the nutritional and phytogenic properties of maralfalfa to improve its value as a fodder crop, and to finally introduce it for sustainable livestock production in Mediterranean countries. Full article

(This article belongs to the Section Phytochemistry)

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24 pages, 3856 KiB

Open AccessArticle

Rice (Oryza sativa L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers

by Nkulu Rolly Kabange, Gamenyah Daniel Dzorkpe, Dong-Soo Park, Youngho Kwon, Sais-Beul Lee, So-Myeong Lee, Ju-Won Kang, Seong-Gyu Jang, Ki-Won Oh and Jong-Hee Lee

Plants 2023, 12(23), 4044; https://doi.org/10.3390/plants12234044 - 30 Nov 2023

Cited by 3 | Viewed by 2227

Abstract

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway [...] Read more.

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and QTLs for grain length, co-detected by all GAPIT models on chromosomes (Chr) 1–3, 5, 7, and 11, were qGL1-1^BFSG (AX-95918134, Chr1: 3,820,526 bp) explains 65.2–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1^BFSG (AX-273945773, Chr1: 5,623,288 bp) for grain width explains 15.5–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1^Blink, AX-279261704, Chr1: 18,023,142 bp) and 54.9% (qGT2-1^Farm, AX-154787777, Chr2: 2,118,477 bp) of the observed PVE. For the grain length-to-width ratio (LWR), the qLWR2^BFSG (AX-274833045, Chr2: 10,000,097 bp) explains nearly 15.2–32% of the observed PVE. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6^BFSG, AX-115737727, 28,484,619 bp) and explains 32.8–54% of PVE. The qTGW6^BFSG QTL coincides with qGW6-1^Blink for grain width and explained 32.8–54% of PVE. Putative candidate genes pooled from major QTLs for each grain trait have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Figure 1
Differential phenotypic difference between parental lines. (A) Comparison of rice grain trait values (grain length, width, and grain thickness) of Ilpum (japonica) and Tung Tin Wan 1 (indica), (B) grain length-to-width ratio, (C) thousand-grain weight of parent lines, and (D) visualization of grain phenotypes of parental lines (Ilpum, upper side and TTWH1 downside). Bars (with hatches and those filled in black) are mean values (n = 10) ± SE. *** p < 0.001, ns non-significant. Full article ">Figure 2
Frequency distribution of traits, box plots, and Quantile–Quantile (Q–Q) plot. (A) Frequency distribution for grain length, (D) grain width, (G) length-to-width ratio, (J) grain thickness, (M) thousand-grain weight. (B) box plots showing the shift in grain length of the recombinant inbred lines relative to their parental lines, (E) grain width, (H) grain length-to-width ratio, (K) grain thickness, (N) thousand-grain weight, (C) Quantile–Quantile (Q–Q) plot for grain length, (F) grain weight, (I) grain length-to-width ratio, (L) grain thickness, and (O) thousand-grain weight, with the y-axis representing the quantile in the sample (RIL population) and the x-axis denoting data falling in the probability distribution. The blue thick lines in the Q–Q plots represent the observed quantile (set of values of a variate that divides a frequency distribution into equal groups, each containing the same fraction of the total population) plotted against the expected quantile (red line). Full article ">Figure 3
Kinship matrix, marker density, PCA, heritability, and genome selection results. (A) heat map showing the relatedness or the level of co-ancestry of the population, (B) density map of SNP Chip DNA markers, (C) principal component analysis (PCA), (D) narrow sense heritability of grain length, (E) grain width, (F) grain thickness, (G) grain length-to-width ratio, (H) thousand-grain weight, and (I,J) results of the genome selection analysis that predict the genomic estimated breeding value (GEBV) of individuals in the RIL population in the reference group (Ref) and the inference group (Inf). Full article ">Figure 4
Pearson correlation analysis results between traits. (A) Correlation results between grain length and thousand-grain weight, (B) grain width and thousand-grain weight, (C) length-to-width and thousand-grain weight, and (D) grain thickness and thousand-grain weight. The closer the data points come to forming a straight line (around the red line), the higher the correlation between the two variables, or the stronger the relationship. Full article ">Figure 5
Detected significant SNP Chip markers by GWAS. Genome-wise Manhattan plots of showing significant SNP Chip DNA markers detected by BLINK, FarmCPU, SUPER, and/or GLM GAPIT models, with their associated with (A) grain length, (B), grain width, (C) grain thickness, (D) grain length-to-width ratio, and (E) thousand-grain weight. Full article ">Figure 6
QTL logarithm of the odds, estimated effects and phenotypic variance explained. Logarithm of the odds (LOD) scores for significant SNP Chip DNA markers linked to (A) grain length, (D) width, and (G) thousand-grain weight. (B,E,H) Estimated effects of QTLs, and (C,F,I) phenotypic variance explained (PVE) values of QTLs for grain length, width, and thousand-grain weight, respectively. −log10(p) is the negative logarithm base 10 of the p-value denoting the logarithm of the odds (LOD) of SNP Chip markers linked to detected genetic loci for each trait. MAF plotted in the x-axis of all panels indicates the minor allelic frequency referring to the lower allelic frequency at a given genetic locus in the RIL population. Full article ">

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Plants, Volume 12, Issue 23 (December-1 2023) – 156 articles

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