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Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings

Research Abstract

Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.

Research Authors
Ahmed Sallam, Mona F. A. Dawood, Diego Jarquín, Elsayed A. Mohamed, Mohamed Y. Hussein, Andreas Börner, Asmaa A. M. Ahmed First published: 13 March 2024 https://d
Research Date
Research Department
Research Journal
The Plant Genome
Research Publisher
Wielly
Research Rank
Q1
Research Website
https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20444
Research Year
2024

Genome-wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit under the Egyptian Conditions

Research Abstract

Drought has a significant impact on rice yield by restricting the crop's ability to grow and develop. Producing rice cultivars adapted to water deficit conditions is still the main interest of rice breeders and geneticists. To address this challenge, a set of 413 highly diverse rice populations were evaluated under normal and water deficit conditions for two growing seasons of 2021 and 2022. High genetic variation was found among genotypes for all studied traits. The heritability estimates ranged from 0.82 (panicle length) to 0.95 (plant height). Sterility percentage (SET%) was the most trait affected by water deficit in two growing seasons. 22 Rice genotypes were classified as drought tolerant in both years. Genome-wide association mapping was performed for all traits in the two growing seasons under both conditions using a total of 700,000 SNPs. The GWAS results revealed important and major SNPs associated with all traits. 26 Significant SNPs with stable allele effects were found to be associated with yield traits under water deficit conditions in both years. The results of this study provided rice genotypes that can be adapted under water deficit conditions and important stable SNP markers that can be used for marker-assisted selection after validation in different genetic backgrounds.

Research Authors
Mohamed Ibrahim Ghazy, Sabry A. EL-Naem, Ahmed G. Hefeina, Ahmed Sallam, Shamseldeen Eltaher
Research Date
Research Department
Research Journal
Rice
Research Member
Research Publisher
Springer
Research Rank
Q1
Research Year
2024

Molecular Genetic Diversity and Linkage Disequilibrium Structure of the Egyptian Faba Bean using Single Primer Enrichment Technology (SPET)

Research Abstract

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype 

Research Authors
Ahmed Sallam, Ahmed Amro, Amira M.I. Mourad, Rafeek Abdallah, Andreas Boerner, Shamseldeen Eltaher
Research Date
Research Department
Research Journal
BMC Genomics
Research Publisher
Springer
Research Rank
Q1
Research Year
2024

The antioxidative properties of thyme, cinnamon, and pomegranate oils in heat-stressed broilers

Research Abstract

This study evaluated the effects of different feed additives on growth performance and heat stress mitigation in
broiler chickens. Three hundred 1-d-old Cobb broiler chicks were randomly allocated into five treatments, each
treatment contained six replicates (10 birds/replicate). Treatment 1 (-Control) was fed a basal diet (BD) under
thermo-neutral conditions between d 1 and 42 of age. Treatment 2 (+Control) also fed the BD under thermoneutral conditions from d 1 to 28 of age, followed by exposure to cyclic heat stress (HS; 36◦C between 0900
and 1700 h, then to 24◦C between 1700 and 0900 h daily) during the fifth week. During the fifth week,
Treatments 3, 4, and 5 underwent the same HS regime and fed the same BD containing 15g/kg of thyme oil (TO),
cinnamon oil (CO), and pomegranate oil (PO) from d 1 to 42, respectively. Compared to the thermoneutral
control, HS control exhibited lower ADFI, higher FCR, increased mortality rate, altered plasma biochemicals, and
reduced anti-oxidant capacity. Broilers supplemented with PO showed a 14.4 % increase in final BW and a 25.8
% in ADG during recovery period. FCR was improved by 16.9 %, and mortality dropped to 6 % compared to 10 %
in the HS control, suggesting reduced losses under heat stress. TO and CO treatments also showed beneficial
effects compared to the HS control group. The supplemented feed additives decreased plasma cholesterol, triglycerides, and malondialdehyde content, while increasing plasma glutathione peroxidase activity and total
antioxidant capacity relative to the HS control. TO, CO, and PO treatments exhibited higher plasma superoxide
dismutase activity compared to the HS control. All supplemented treatments showed lower H/L ratio compared
to HS control (P < 0.05). The PO and TO treatments exhibited an increased jejunal villus/crypt ratio relative to
the control groups. In conclusion, supplementing broiler diets with PO, TO, and CO can alleviate heat stress
effects, improve growth performance, and potentially boost profitability for poultry farmers, with PO providing
the most significant benefits in both thermoneutral and heat stress conditions.
 

Research Authors
Dingfa Wang a, Mohamed Abdelhameed Mohamed Sayed, Ali Elsayed Galal, Abdelraheim Hassan Attaai , Mohamed Nabil Makled, Abdalla Hassan Hussein Ali, Chen Wei, Mohamed Ahmed Habib, Mostafa Galal Abdelfattah , Khaled Abouelezz
Research Date
Research Department
Research Journal
Poultry Science
Research Pages
105228
Research Publisher
Elsevier
Research Vol
104
Research Website
https://www.sciencedirect.com/science/article/pii/S0032579125004705
Research Year
2025

Comprehensive evaluation of using mineral and bio phosphorus fertilization on orange tree (Citrus sinensis) productivity

Research Authors
Ahmed ME Elazazi, El-Sayed AM Awad, Salah M Dahdoh, Azza S Hussein, Essam MA Radwan, Esraa ME Hussein, Hussein HM Saeed, Hesham S Ghazzawy, Mohamed FM Abdelkader, Mohamed H Mahmoud, Mostafa M Gouda, Xiaoli Li, Mohamed A Abdein, EL-Sayed M Qaoud
Research Date
Research Department
Research Journal
Heliyon
Research Member
Research Vol
10
Research Year
2024

Ecotoxicity and Removal of Pesticides by Aquatic Plants

Research Abstract

The agricultural sector is one of the most important sectors concerned with self-sufficiency in agricultural crops and food security, but these crops are threatened by many pests that cause severe infestation and decrease productivity. Pesticides play a vital role in pest control in that they are a quick and effective tool for reducing the severity of pest infestations. However, because of irresponsible and unwise use of pesticides, this led to an increase in pesticide residues in environmental components to the point that they became toxic to the environment and living organisms. Residual pesticides have the potential to stay at the application site longer due to their persistence. The current trend is to eliminate these residues through cost-effective, sustainable, economic, and ecologically friendly means. Among these techniques, using aquatic plants to eliminate pesticides and their harmful effects is one of the most significant. Multiple matrices have been subjected to remediation procedures classified as biological, chemical, physical, and physicochemical, which aim to eliminate organic and inorganic contaminants. Biological remediation, which comprises phytoremediation and bioremediation, has been used to clean up contaminated areas because of its low-cost energy efficiency and environmental friendliness.

Research Authors
Mohamed Ahmed Ibrahim Ahmed
Research Date
Research Department
Research Journal
The Handbook of Environmental Chemistry
Research Member
Research Pages
1-27
Research Publisher
Springer
Research Rank
International
Research Website
https://link.springer.com/chapter/10.1007/698_2024_1191
Research Year
2025

Harnessing plant growth promoting bacteria to combat watermelon mosaic virus in squash

Research Abstract

Plant diseases significantly threaten global food security, with viral infections, particularly Watermelon Mosaic Virus (WMV), causing substantial losses in economically important crops such as squash. This study aims to investigate the efficacy of beneficial bacteria isolated from various plants in promoting growth and mitigating the effects of WMV in squash. Understanding the interactions between plants and beneficial microbes could provide sustainable solutions for managing viral infections in agriculture. Sixty-two bacterial isolates were obtained from the rhizosphere of basil, mint, thyme, and squash plants. Among these, six strains exhibited notable plant growth-promoting activities, including the synthesis of indole acetic acid, solubilization of phosphate and zinc, ammonia production, and activity of 1-aminocyclopropane-1-carboxylate deaminase (ACCD). Morphological observations and 16S rRNA gene sequencing identified these isolates as Pseudomonas indica, Bacillus paramycoides, Bacillus thuringiensis, Bacillus mycoides, Paenibacillus glucanolyticus, and Niallia circulans. In pot experiments, squash plants inoculated with these bacterial strains demonstrated significant reductions in disease severity after being infected with WMV. Specifically, foliar applications of the bacteria resulted in the following reductions in disease severity: B. mycoides (87%), B. thuringiensis (73%), Paenibacillus glucanolyticus (73%), Niallia circulans (70%), B. paramycoides (65%), and Pseudomonas indica (65%). Additionally, plants treated with B. mycoides showed increased plant height and shoot dry weight, indicating enhanced growth performance relative to infected controls. Statistical analysis revealed that these growth promotions and disease severity reduction were significant (p < 0.05). GC–MS analysis of the six bacterial strains revealed a diverse array of 73 chemical metabolites, including common compounds such as 9-Octadecenoic acid (Z), benzene derivatives, and cyclopentanones. These findings suggest shared metabolic pathways among the strains and indicate potential roles in ecological interactions, plant defense mechanisms, and antiviral properties. These metabolites likely contribute to the observed reductions in viral severity and enhance plant resilience. The study indicates that inoculating squash plants with specific beneficial bacteria, especially B. mycoides, through foliar or soil application can significantly decrease the severity of WMV and promote plant growth. This approach offers an environmentally friendly alternative to chemical antiviral treatments and may reduce reliance on pesticides. This research highlights the potential of using plant growth-promoting bacteria (PGPB)as a sustainable approach to control viral infections in crops. Further field trials are necessary to PGPB validate the scalability of these findings and assess their effectiveness under diverse agricultural conditions. Incorporating these beneficial microbes into agricultural practices could enhance the resilience of cropping systems, ultimately fostering sustainable agriculture and enhancing food security.

Research Authors
Shymaa R. Bashandy, Omima Abdelsater Mohamed, Osama A. Abdalla, A. Elfarash & Mohamed Hemida Abd-Alla
Research Date
Research Department
Research Journal
Scientific Reports
Research Pages
1-19
Research Publisher
Springer
Research Rank
Plant Pathology
Research Vol
15
Research Website
https://www.nature.com/articles/s41598-025-92268-2
Research Year
2025

New Insights into Red and White Quinoa Protein Isolates: Nutritional, Functional, Thermal Properties

Research Abstract

Quinoa (Chenopodium quinoa Willd.) seeds, renowned for their nutritional richness and balanced amino acid profile, offer promising potential as food ingredients. This study focused on extracting and characterizing the protein isolates from red and white quinoa varieties to evaluate their physicochemical and functional properties. Protein isolation involved alkaline solubilization and isoelectric precipitation, followed by characterization through amino acid analysis, phenolic profiling, scanning electron microscopy (SEM), zeta potential measurement, particle size distribution analysis, Differential Scanning Calorimetry (DSC), and rheological studies. The results showed that both the red and white quinoa protein isolates exhibited high protein content and essential amino acids, with notable differences in their amino acid compositions. The phenolic and flavonoid content varied between the red and white quinoa seeds, highlighting their potential antioxidant properties. SEM revealed distinct microstructural differences between the red and white quinoa protein isolates. Zeta potential measurements indicated the negative surface charges, influencing the stability in the solution. A particle size distribution analysis showed the monomodal distributions with minor variations in the mean particle size. The DSC profiles demonstrated multiple denaturation peaks, reflecting the complex protein compositions. Rheological studies indicated diverse gelation behaviors and mechanical properties. Overall, this comprehensive characterization underscores the potential of quinoa protein isolates as functional food ingredients with diverse applications in the food industry.

Research Authors
Alsaleem, K. A., Moftah, R. F., & El-Geddawy, M. A.
Research Date
Research Journal
Processes
Research Year
2024

Harnessing plant growth-promoting bacteria to combat watermelon mosaic virus in squash

Research Abstract

Plant diseases significantly threaten global food security, with viral infections, particularly Watermelon Mosaic Virus (WMV), causing substantial losses in economically important crops such as squash. This study aims to investigate the efficacy of beneficial bacteria isolated from various plants in promoting growth and mitigating the effects of WMV in squash. Understanding the interactions between plants and beneficial microbes could provide sustainable solutions for managing viral infections in agriculture. Sixty-two bacterial isolates were obtained from the rhizosphere of basil, mint, thyme, and squash plants. Among these, six strains exhibited notable plant growth-promoting activities, including the synthesis of indole acetic acid, solubilization of phosphate and zinc, ammonia production, and activity of 1-aminocyclopropane-1-carboxylate deaminase (ACCD). Morphological observations and 16S rRNA …

Research Authors
Shymaa R Bashandy, Omima Abdelsater Mohamed, Osama A Abdalla, A Elfarash, Mohamed Hemida Abd-Alla
Research Date
Research Department
Research Journal
Scientific Reports
Research Pages
9440
Research Publisher
Nature Publishing Group UK
Research Vol
Volume 15, Issue 1
Research Website
https://scholar.google.com/scholar?oi=bibs&cluster=1090432303784260082&btnI=1&hl=en
Research Year
2025

Micropropagation of Robinia pseudoacacia L. Genotypes, Selected for Late Flowering Characteristics

Research Abstract

Robinia pseudoacacia L., commonly known as black locust, is a nitrogen-fixing species characterized by multiple uses. Among these uses, black locust is of special interest to beekeepers due to its abundant flowering and delicious honey. Given the great importance of honey production in Italy, beekeepers are looking for genotypes that have a delayed flowering time. As a consequence, the aim of the present study was to develop a complete protocol of micropropagation for genotypes, which have been selected in the Veneto region due to their delayed flowering, ie, about 3 months, in comparison with the normal flowering time (from late April to early June). The subsequent steps of the micropropagation protocol (explant decontamination, shoot induction, proliferation, and rooting) were investigated and optimized. The most effective decontamination treatment of explants (axillary buds from shoots developed in a greenhouse) was obtained using 50 mg/L AgNO3 for 20 min. This method resulted in the highest survival and regeneration rates for the explants (90%), although contamination was slightly higher than when using HgCl2 and NaOCl. The best medium for shoot establishment was MS with 1 mg/L of mT, which achieved 100% regeneration of the explants. In comparison with BA, mT at 1 mg/L was shown to be the best stimulator of shoot proliferation, especially in combination with 0.7 mg/L GA3 (Proliferation Rate, 4.7). An intermediate 2 h treatment with AgNO3, in combination with mT, was shown to be beneficial in improving the shoot proliferation and quality in the subsequent subculture in a gelled medium. As for shoot rooting, the shoots …

Research Authors
Doaa Elazab, Giancarlo Fascella, Claudia Ruta, Andrea Vitale, Maurizio Lambardi
Research Date
Research Department
Research Journal
Horticulturae
Research Pages
1317
Research Publisher
Multidisciplinary Digital Publishing Institute
Research Vol
10
Research Year
2024
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