Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population

Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.

Enhancing Stevia rebaudiana growth and yield through exploring beneficial plant-microbe interactions and their impact on the underlying mechanisms and crop sustainability

Stevia rebaudiana is an important medicinal plant which represents the most important sugar substitute in many countries. Poor seed germination of this plant is a critical problem that affects the final yield and the availability of the products in the market. Continuous cropping without supplying soil nutrients is also a serious issue as it results in declining soil fertility. This review highlights the important use of beneficial bacteria for the enhancement of Stevia rebaudiana growth and its dynamic interactions in the phyllosphere, rhizosphere, and endosphere. Fertilizers can increase crop yield and preserve and improve soil fertility. There is a rising concern that prolonged usage of chemical fertilizers may have negative impacts on the ecosystem of the soil. On the other hand, soil health and fertility are improved by plant growth-promoting bacteria which could eventually increase plant growth and productivity. Accordingly, a biocompatible strategy involving beneficial microorganisms inoculation is applied to boost plant growth and reduce the negative effects of chemical fertilizers. Plants benefit extensively from endophytic bacteria, which promote growth and induce resistance to pathogens and stresses. Additionally, several plant growth-promoting bacteria are able to produce amino acids, polyamines, and hormones that can be used as alternatives to chemicals. Therefore, understanding the dynamic interactions between bacteria and Stevia can help make the favorable bacterial bio-formulations, use them more effectively, and apply them to Stevia to improve yield and quality.

Conferring of Drought and Heat Stress Tolerance in Wheat (Triticum aestivum L.) Genotypes and Their Response to Selenium Nanoparticles Application

In this study, the role of selenium nanoparticles (SeNPs, 10 mg·L^-1) has been investigated in modulating the negative effects of drought and heat stresses on eight bread wheat (Triticum aestivum L.) genotype seedlings. Those genotypes included Giza-168, Giza-171, Misr-1, Misr-3, Shandweel-1, Sids-1, Sids-12, and Sids-14. The study included six treatments as follows: regular irrigation with 100% Field Capacity (FC) at a temperature of 23 ± 3 °C (T1), drought stress with 60% FC (T2), heat stress of 38 °C for 5 h·day^-1 (T3), foliar spray of 10 mg·L^-1 of SeNPs only (T4), a combination of drought stress with foliar spray of 10 mg·L^-1 of SeNPs (T5), and heat stress with foliar spray of 10 mg·L^-1 of SeNPs (T6). The experiment continued for 31 days. Foliar application of SeNPs improved the plant growth, morpho-physiological and biochemical responses, and expression of stress-responsive genes in wheat (T. aestivum L.) seedlings. Overall, morpho-physiological traits such as plant height (PH), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), and root dry weight (RDW) of wheat genotypes grown under different conditions ranged from 25.37-51.51 cm, 3.29-5.15 g, 0.50-1.97 g, 0.72-4.21 g, and 0.11-1.23 g, respectively. From the morpho-physiological perspective, drought stress had a greater detrimental impact on wheat plants than heat stress, whereas heat stress significantly impacted the expression of stress-responsive genes. Stress responses to drought and heat varied between wheat genotypes, suggesting that different genotypes are more resilient to stress. Exogenous spraying of 10 mg·L^-1 of SeNPs improved the photosynthetic pigments, photosynthetic rate, gas exchange, and transpiration rate of wheat plants and enhanced drought and heat tolerance by increasing the activity of antioxidant enzymes including catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) and the expression level of stress-responsive genes. Our results showed that spraying wheat seedlings with 10 mg·L^-1 of SeNPs enhanced SOD activity for all genotypes as compared to the control, with the Sids-12 genotype having the highest value (196.43 U·mg^-1 FW·min^-1) and the Giza-168 genotype having the lowest (152.30 U·mg^-1 FW·min^-1). The expression of PIP1, LEA-1, HSP70, and HSP90 stress-responsive genes was more significant in tolerant genotypes (Giza-171 and Giza-168) than in sensitive ones (Misr-1 and Misr-3) in response to drought and heat stresses. Under stress conditions, the shoot and root fresh weights, photosynthetic pigment content, stomatal conductance (SC), and transpiration rate (TR) were positively correlated with plant height (PH), while root and shoot dry weights, malondialdehyde (MDA), proline, hydrogen peroxide (H₂O₂), and APX were negatively correlated. Multivariate analysis and biplot results revealed that genotypes Giza-168, Giza-171, Sids-12, and Sids-14 performed well in both stress situations and were classified as stress-tolerant genotypes. These best genotypes may be employed in future breeding projects as tools to face climate change. This study concluded that various physio-biochemicals and gene expression attributes under drought and heat stress could be modulated by foliar application of SeNPs in wheat genotypes, potentially alleviating the adverse effects of drought and heat stress.

Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers

Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into "rounded" and "nearly elongated". Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.

Genetic variation and molecular characterization of Zygophyllum coccineum L. ecotypes of the iron mining area of El-Wahat El-Bahariya in Egypt

Remediation and mitigation processes can recover the ecosystems affected by mining operations. Zygophyllum coccineum L. is a native indigenous xerophyte that grows in Egypt's Western Desert, particularly around the iron mining ore deposits, and accumulates high rates of potentially toxic elements (PTEs) in its succulent leaves. The present study evaluated the genetic variation and molecular responses of Z. coccineum to heavy metal stressful conditions in three sites. Results revealed that Z. coccineum bioaccumulation capacity was greater than unity and varied amongst the three locations. In response to heavy metal toxicity, Z. coccineum plants boosted their antioxidative enzymes activity and glutathione levels as a tolerance strategy. Anatomically, a compact epidermis, a thick spongy mesophyll with water storage cells, and a thicker vascular system were observed. Protein electrophoretic analysis yielded 20 fragments with a polymorphism rate of 85%. The antioxidant genes (CAT: catalase, POD: peroxidase and GST: polyphenol oxidase) showed greater levels of expression. In addition, DNA-based molecular genetic diversity analyses using Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers yielded 54 amplified fragments (i.e. 24 monomorphic and 30 polymorphic), with 12 unique fragments and a polymorphism rate of 55.5%. The greatest PIC values were recorded for SCoT-6 (0.36) and for both of the 14 A and 44 B ISSR primers (0.25). Diversity index (DI) of all SCoT and ISSR amplified primers was 0.23. The present findings reveal the distinct heavy metal's adaption attributes of Z. coccineum, indicating its improved survival in severely arid mining environments.

Synergistic effects of Azospirillum brasilense and Bacillus cereus on plant growth, biochemical attributes and molecular genetic regulation of steviol glycosides biosynthetic genes in Stevia rebaudiana

The current study aimed to scale up the favorable bio-stimulants for enhancing the growth and breeding strategies of Stevia rebaudiana to increase sugar productivity. Inoculation of 45-day-old S. rebaudiana plantlets with Bacillus cereus and Azospirillum brasilense alone or in combination for 30 days allowed comparisons among their effects on enhancement and improvement of plant growth, production of bioactive compounds and expression of steviol glycoside genes. B. cereus SrAM1 isolated from surface-sterilized Stevia rebaudiana leaves was molecularly identified using 16s rRNA and tested for its ability to promote plant growth. Beneficial endophytic B. cereus SrAM1 induced all plant growth-promoting traits, except solubilization of phosphate, therefore it showed high effectiveness in the promotion of growth and production of bioactive compounds. Treatment of plants with B. cereus SrAM1 alone revealed carbohydrates content of 278.99 mg/g, total soluble sugar of 114.17 mg/g, total phenolics content of 34.05 mg gallic acid equivalent (GAE)/g dry weight) and total antioxidants activity of 32.33 mg (A.A)/g dry weight). Thus, plantlets inoculated with B. cereus SrAM1 alone exhibited the greatest responses in physiological and morphological parameters, but plantlets inoculated with B. cereus SrAM1 + A. brasilense showed a maximal upregulation of genes responsible for the biosynthesis of steviol glycosides (Kaurene oxidase, ent-KO; UDP-dependent glycosyl transferases of UGT85C2, UGT74G1, UGT76G1). Taken together, the used bacterial strains, particularly B. cereus SrAM1 could significantly improve the growth of S. rebaudiana via dynamic interactions in plants.

Eco-biochemical responses, phytoremediation potential and molecular genetic analysis of Alhagi maurorum grown in metal-contaminated soils

BACKGROUND

Alhagi maurorum Medik. (camelthorn) is a dominant desert plant indigenous in various habitats, including the Western Desert of Egypt. The plant is especially prevalent in and around economic iron ore deposits. Nutrient and heavy metal levels in A. maurorum tissues and soil samples were assessed to identify associations between heavy metal levels in plants and soil. The objective was to evaluate this species as an indicator of heavy metal pollution. Photosynthetic pigments, protein, proline, alkaloids, flavonoids, 2,2-diphenyl-1-picrylhydrazylscavenging, reduced glutathione, malondialdehyde, antioxidant enzymes, and stress-related gene expression were assessed to determine their functional roles in metal stress adaptation in ultra- and molecular structure. Additionally, the molecular genetic variation in A. maurorum samples was assessed using co-dominant sequence-related amplified polymorphism (SRAP) and inter simple sequence repeats (ISSR).

RESULTS

A substantial difference in enzymatic and non-enzymatic antioxidants of A. maurorum was observed in samples collected from three sites. A. maurorum is suited to the climate in mineralized regions. Morphologically, the stem shows spines, narrow leaves, and a reduced shoot system. Anatomically, modifications included a cuticle coating on leaves and stems, sunken stomata, a compact epidermis, and a thick cortex. Significant anatomical-physiological differences were observed with varying heavy metal soil content, antioxidative enzyme activities increased as a tolerance strategy, and glutathione levels decreased in response to heavy metal toxicity. Heavy metal accumulation also affected the expression of stress-related genes. The highest levels of expression of GST, G6PDH, 6PGD, nitrate reductase 1, and sulfate transporter genes were found in plants collected from site A1. However, auxin-induced protein exhibited its highest expression in plants collected from A2. Six SRAP combinations yielded 25 scoreable markers with a polymorphism rate of 64%, and 5 ISSR markers produced 11 bands with a polymorphism rate of 36.36% for three A. maurorum genotypes. The ME1xEM7 primer combinations provided the most polymorphic information content and resolving power, making it the most useful primer for differentiating A. maurorum genotypes. SRAP markers exhibited a higher diversity index (0.24) than ISSR markers (0.16).

CONCLUSIONS

A. maurorum displayed adaptive characteristics for heavy metal sequestration from mining site soils and is proposed as a strong candidate for phytoremediation.

Green synthesized silver nanoparticles induced cytogenotoxic and genotoxic changes in Allium cepa L. varies with nanoparticles doses and duration of exposure

This study aimed to test the ability of aqueous leaf extract of Eichhornia crassipes (Mart.) Solms-Laubach to synthesize silver nanoparticles (AgNPs) and to estimate the cytotoxicity and genotoxicity of AgNPs using Allium cepa assay. Fresh Eichhornia crassipes plants were collected from the Nile River of Egypt. The mixed-shaped structures of the biogenic AgNPs were qualitatively characterized by UV-vis spectroscopy, scanning electron microscopy and transmission electron microscopy. Selected area electron diffraction confirmed the crystalline structure of AgNPs and energy dispersive X-ray analysis clarified the presence of the elemental silver in a percentage of 83.29%. The biogenic AgNPs were quite stable (0.316) and negatively charged (-18.5 mV) based on the polydispersity index values. Allium cepa L. roots were exposed to several AgNPs concentrations (0, 5, 10, 20, 40 and 80 mg L^-1) for different time intervals 2, 4 and 6 h. Cytotoxicity measured by both the spectrophotometric and macroscopic techniques recorded the maximum cell death of root tips of A. cepa after 20 mg L^-1 treatment. The analysis of comet assay output images showed an alteration of DNA repair kinetics. The use of aqueous leaf extract of E. crassipes (Mart.) Solms-Laubach in the large-scale production of AgNPs by the method proposed in this study may be a step in improving the water loss in the Nile River. At the same time, a sensitive approach to the cytogenotoxicity of AgNPs must be considered.

Phytoremediation efficiency of Portulaca oleracea L. naturally growing in some industrial sites, Dakahlia District, Egypt

Phytoremediation is an economic process through exploitation of plants capacity to accumulate heavy metals in polluted habitats by their harvestable parts. In the present investigation, Portulaca oleracea was examined to estimate its role in the accumulation of Mn(II), Cu(II), Zn(II), Fe(III) and Pb(II) ions and recognize its persistence against the industrial effluent toxicity from different farmlands located beside these regions (S1:S9) in Dakahlia district, Egypt. The most recorded associate plants were; Amaranthus viridus, Malva parviflora, Chenopodium murale and Echinochloa colonum, which have high potentiality of heavy metals (HM) accumulation. The phytoremediation efficiency (bioconcentration factor (BCF), bioaccumulation factor (BF), translocation factor (TF), enrichment coefficient of shoot (ECS) and element accumulation index (EAI)) of P. oleracea were calculated. Considering the results, S7 showed the highest BCF value for Cu(II), 7.40; Fe(III), 2.06; and Zn(II), 4.33, while Mn(II), 2.06 at S1 and Pb(II), 3.89 at S3. BF and TF values were less than unity 1.0 for most of the sites. However, ECS values showed small variations among the investigated HM at the nine sites. EAI values were higher in shoots out of all the sites except S2 > EAI of roots of the same sites. Also, there was positive correlation between the soil HM concentrations in most sites. Moreover, total protein was estimated quantitatively and qualitatively. The protein profile showed 16 bands of molecular weight ranged from 30.9 to 240.6 KDa. Finally, P. oleracea can be used for decontamination of soils with heavy metals due to the high ecological amplitude and phytoremediation characteristics.