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Mokhtar, M. M., A. S. Fouad, H. M. Abd-Elhalim, and A. El Allali, "CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database", Plant Genomic and Cytogenetic Databases, New York, NY, Springer US, pp. 71 - 82, 2023. Abstract

To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.

Adly, W. M. R. M., G. Niedbała, M. E. EL-Denary, M. A. Mohamed, M. Piekutowska, T. Wojciechowski, E. - S. T. Abd El-Salam, and A. S. Fouad, "Somaclonal Variation for Genetic Improvement of Starch Accumulation in Potato (Solanum tuberosum) Tubers", Plants, vol. 12, issue 2, 2023. Abstract

Starch content is one of the major quality criteria targeted by potato breeding programs. Traditional potato breeding is a laborious duty due to the tetraploid nature and immense heterozygosity of potato genomes. In addition, screening for functional genetic variations in wild relatives is slow and strenuous. Moreover, genetic diversity, which is the raw material for breeding programs, is limited due to vegetative propagation used in the potato industry. Somaclonal variation provides a time-efficient tool to breeders for obtaining genetic variability, which is essential for breeding programs, at a reasonable cost and independent of sophisticated technology. The present investigation aimed to create potato somaclones with an improved potential for starch accumulation. Based on the weight and starch content of tubers, the somaclonal variant Ros 119, among 105 callus-sourced clones, recorded a higher tuberization potential than the parent cv Lady Rosetta in a field experiment. Although this somaclone was similar to the parent in the number of tubers produced, it exhibited tubers with 42 and 61% higher fresh and dry weights, respectively. Additionally, this clone recorded 10 and 75% increases in starch content based on the dry weight and average content per plant, respectively. The enhanced starch accumulation was associated with the upregulation of six starch-synthesis-related genes, namely, the AGPase, GBSS I, SBE I, SBE II, SS II and SS III genes. AGPase affords the glycosyl moieties required for the synthesis of amylose and amylopectin. GBSS is required for amylose elongation, while SBE I, SBE II, SS II and SS III are responsible for amylopectin.

Adly, W. M. R. M., H. S. Abdelkader, M. A. Mohamed, M. E. EL-Denary, E. S. T. Sayed, and A. S. Fouad, "Development of SSR Markers to Characterize Potato (Solanum tuberosum L.) Somaclones with Improved Starch Accumulation", Egyptian Journal of Botany, vol. 63, issue 3: National Information and Documentation Center (NIDOC), Academy of Scientific Research and Technology (ASRT), pp. 1173-1185, 2023. AbstractWebsite

This study investigated potato tubers' starch and sugar content from different callus-sourced clones compared to the original cultivar Lady Rosetta. The clones were categorized based on their starch content, with some clones having similar starch content to Lady Rosetta, some with lower starch content, and others with higher starch content. The tubers were grown in a specific mixture of sand, peat moss, perlite, vermiculite, and foam for four months, after which their dry matter, starch, and sugar content were analyzed. The sugar content was determined using ethanol extraction, while the starch content was measured using the anthrone method. The results unveiled significant differences in starch and sugar contents among the tested potato clones. While soluble sugar content showed no significant correlation with starch content, a significant positive correlation was found between dry matter content and starch content. The dry matter content varied among the clones, with some showing significantly higher values than Lady Rosetta. SSR-PCR analysis was performed using six SSR primers to assess genetic diversity among potato clones. The analysis generated distinct and reproducible banding patterns, with 68 bands, of which 62 were polymorphic. The primers amplified unique bands specific to certain clones, and the polymorphic information content (PIC) was calculated for each marker. The genetic relationships among the clones were illustrated using a clustering dendrogram based on Jaccard's coefficient. In conclusion, the utilized SSR markers effectively identified the starch content in potato tubers clones originating from callus, thereby contributing to advancements in potato breeding and crop improvement endeavors.

Fouad, A. S., A. B. Hamed, W. M. Amer, and R. M. Hafez, "Barcoding of Some Plant Species Using the rbcL Gene in the Mediterranean Oolitic Sand Dunes West of Alexandria, Egypt", Egyptian Journal of Botany, vol. 62, issue 1: National Information and Documentation Center (NIDOC), Academy of Scientific Research and Technology (ASRT), pp. 159-168, 2022. AbstractWebsite

IN the Mediterranean Basin, oolitic sand dunes extend along the northeastern coast of Africa between the Gulf of Gabes (Tunisia) and the Nile Delta (Egypt), attenuating coastal vulnerability to storms and saltwater intrusion and protecting inland infrastructure. Psammophytes are typical and distinctive plants for dune habitats; they are the primary drivers for dune growth and stabilization by trapping sand particles in their shoot and root systems. The Anthropocene fingerprint may create an environment favorable for nonpsammophyte invasion and subsequent alteration in sand dune habitat structure and functions. The authentication of sand dune-inhabiting species should be a priority for conservation or restoration measures concerning sand dune habitats. This study is the first rbcL-based DNA barcoding documentation of 20 plant species inhabiting the vulnerable Egyptian oolitic sand dune habitats in Burg El Arab area, west of Alexandria. Results highlighted the applicability of the rbcL locus sequence for species authentication and recognition of the examined plant taxa sharing the same habitat. The phylogenetic analysis of rbcL barcode polymorphism revealed current taxonomic relationships among the assigned species. Results added valuable information to the authentication of sand dune plants, providing the first rbcL barcodes for species growing in oolitic sand dune habitats in Egypt, six of which were submitted for the first time to GenBank.

Adly, W. M. R. M., Y. S. A. Mazrou, M. E. EL-Denary, M. A. Mohamed, E. - S. T. Abd El-Salam, and A. S. Fouad, "Boosting Polyamines to Enhance Shoot Regeneration in Potato (Solanum tuberosum L.) Using AgNO3", Horticulturae, vol. 8, no. 2, 2022. AbstractWebsite

Advancements in shoot regeneration systems support biotechnology-based tools used in the genetic improvement of plant crops. This study aims to enhance shoot regeneration in potatoes by boosting polyamine content by adding AgNO3 to the shoot regeneration medium (MS medium supplemented with 30 g L−1 sucrose, 100 mg L−1 myoinositol, and 2.25 BA mg L−1). Five concentrations of AgNO3 (2, 4, 6, 8, and 10 mg L−1) were used in addition to a control. The effect of AgNO3 on regeneration assumed a more or less concentration-dependent bell-shaped curve peaking at 4 mg L−1. Enhancements in shoot regeneration were attributed to the known role of AgNO3 as an ethylene action blocker in addition to improvements in polyamine accumulation without an increase in H2O2 content, lipid peroxidation, or DNA damage. The uncoupling of shoot regeneration and polyamine content recorded at high AgNO3 concentrations can be attributed to the consumption of polyamines to counteract the synchronized oxidative stress manifested by increases in H2O2 content, lipid peroxidation, and DNA damage.

Emam, M. A., A. M. Abd EL-Mageed, G. Niedbała, S. A. Sabrey, A. S. Fouad, T. Kapiel, M. Piekutowska, and S. A. Mahmoud, "Genetic Characterization and Agronomic Evaluation of Drought Tolerance in Ten Egyptian Wheat (Triticum aestivum L.) Cultivars", Agronomy, vol. 12, no. 5, 2022. AbstractWebsite

This investigation was carried out for genetic characterization and determination of drought tolerance of ten Egyptian cultivars of wheat (Triticum aestivum L.), namely Misr 1, Misr 2, Gemmiza 9, Gemmiza 10, Gemmiza 11, Gemmiza 12, Shandawel 1, Giza 168, Giza 171, and Sids 14. These cultivars were grown in two winter seasons: 2018/2019 and 2019/2020 at the experimental farm Fac. of Agric., Suez Canal Univ., Ismailia, Egypt, under two watering regimes: normal (100%) and stress (50% FC) conditions. Six agronomic traits and five tolerance indices, namely stress tolerance (TOL), mean productivity (MP), geometric mean productivity (GMP), yield stability index (YSI), and drought susceptibility index (DSI), were used to evaluate the impact of drought stress. The results reflected Giza 171, Misr 2, and Giza 168 as precious germplasm for breeding of high-yielding drought-tolerant wheat. A highly significant positive correlation was recorded between yield under normal and stress conditions on the one hand and each of MP and GMP on the other hand. In addition, YSI appeared engaged in a highly significant positive correlation with yield under drought conditions only. TOL and DSI appeared insignificantly correlated with yield. Therefore, MP and GMP were reflected as the first runners among indices suitable to distinguish the high-yielding cultivars under drought conditions. At the molecular level, five primers of Start Codon Targeted (SCoT) markers were able to resolve and characterize the studied cultivars, which reflected SCoT as a potent gene-targeting molecular marker, able to characterize and resolve genetic diversity in wheat at the cultivar level using few primers. Therefore, SCoT is a time-efficient molecular marker, and it can efficiently replace indices in characterization of drought-tolerant genotypes with a high confidence level and reasonable cost.

Nasrallah, A. K., A. A. Kheder, M. A. Kord, A. S. Fouad, M. M. El-Mogy, and M. A. M. Atia, "Mitigation of Salinity Stress Effects on Broad Bean Productivity Using Calcium Phosphate Nanoparticles Application", Horticulturae, vol. 8, no. 1, 2022. AbstractWebsite

Water salinity is one of the major abiotic stresses, and the use of saline water for the agricultural sector will incur greater demand in the coming decades. Recently, nanoparticles (NPs) have been used for developing numerous plant fertilizers as a smart and powerful form of material with dual action that can alleviate the adverse effects of salinity and provide the plant with more efficient nutrient forms. This study evaluated the influence of calcium phosphate NPs (CaP-NPs) as a soil fertilizer application on the production and bioactive compounds of broad bean plants under salinity stress. Results showed that salinity had deleterious effects on plant yield with 55.9% reduction compared to control. On the other hand, CaP-NPs dramatically improved plant yield by 30% compared to conventional fertilizer under salinity stress. This improvement could be attributed to significantly higher enhancement in total soluble sugars, antioxidant enzymes, proline content, and total phenolics recorded use of nano-fertilizer compared to conventional use under salt stress. Additionally, nano-fertilizer reflected better mitigatory effects on plant growth parameters, photosynthetic pigments, and oxidative stress indicators (MDA and H2O2). Therefore, our results support the replacement of traditional fertilizers comprising Ca2+ or P with CaP-nano-fertilizers for higher plant productivity and sustainability under salt stress.

Nasrallah, A. K., M. A. M. Atia, R. M. Abd El-Maksoud, M. A. Kord, and A. S. Fouad, "Salt Priming as a Smart Approach to Mitigate Salt Stress in Faba Bean (Vicia faba L.)", Plants, vol. 11, no. 12, 2022. AbstractWebsite

The present investigation aims to highlight the role of salt priming in mitigating salt stress on faba bean. In the absence of priming, the results reflected an increase in H2O2 generation and lipid peroxidation in plants subjected to 200 mM salt shock for one week, accompanied by a decline in growth, photosynthetic pigments, and yield. As a defense, the shocked plants showed enhancements in ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), peroxidase (POX), and superoxide dismutase (SOD) activities. Additionally, the salt shock plants revealed a significant increase in phenolics and proline content, as well as an increase in the expression levels of glutathione (GSH) metabolism-related genes (the L-ascorbate peroxidase (L-APX) gene, the spermidine synthase (SPS) gene, the leucyl aminopeptidase (LAP) gene, the aminopeptidase N (AP-N) gene, and the ribonucleo-side-diphosphate reductase subunit M1 (RDS-M) gene). On the other hand, priming with increasing concentrations of NaCl (50–150 mM) exhibited little significant reduction in some growth- and yield-related traits. However, it maintained a permanent alert of plant defense that enhanced the expression of GSH-related genes, proline accumulation, and antioxidant enzymes, establishing a solid defensive front line ameliorating osmotic and oxidative consequences of salt shock and its injurious effect on growth and yield.

El-Mogy, M. M., M. A. M. Atia, F. Dhawi, A. S. Fouad, E. S. A. Bendary, E. Khojah, B. N. Samra, K. F. Abdelgawad, M. F. M. Ibrahim, and E. A. Abdeldaym, "Towards Better Grafting: SCoT and CDDP Analyses for Prediction of the Tomato Rootstocks Performance under Drought Stress", Agronomy, vol. 12, no. 1, 2022. AbstractWebsite

This study aims to predict the behavior of different tomato rootstocks under drought stress conditions. SCoT and CDDP analyses were employed to characterize the genetic relatedness among a commercial drought-sensitive tomato hybrid (cv. Bark) and four wild tomato accessions (LA2711, LA1995, LA3845, and LA4285) known for their tolerance to adverse conditions. The Bark plants were grafted onto the aforementioned wild accessions and self-grafted as control, and then the behavior of all graft unions was followed under normal and drought stress conditions. Our results showed a general genotype-dependent better growth and yield of heterografts than autografts under all growth conditions. Furthermore, clustering analysis based on growth, yield quantity and quality traits, and the leaf content of minerals, ABA, GA3, and proline, in addition to the activity of APX, POD, and DHAR reflected the same grouping pattern of the studied rootstocks exhibited by SCoT and CDDP. The identical grouping pattern supports the utilization of SCoT and CDDP as a robust screening tool helpful to predict the physiological and agronomical behavior of grafting on different tomato rootstocks. Furthermore, grafting could be a cost-efficient alternative method to improve drought tolerance in sensitive tomato genotypes.

Fouad, A., A. E. HEGAZY, E. Azab, E. Khojah, and T. Kapiel, "Boosting of Antioxidants and Alkaloids in Catharanthus roseus Suspension Cultures Using Silver Nanoparticles with Expression of CrMPK3 and STR Genes", Plants, vol. 10, no. 10, 2021. AbstractWebsite

Global agricultural systems are under unprecedented pressures due to climate change. Advanced nano-engineering can help increase crop yields while ensuring sustainability. Nanotechnology improves agricultural productivity by boosting input efficiency and reducing waste. Alkaloids as one of the numerous secondary metabolites that serve variety of cellular functions essential for physiological processes. This study tests the competence of silver nanoparticles (AgNPs) in boosting alkaloids accumulation in Catharanthus roseus suspension cultures in relation to the expression of C. roseus Mitogen Activated Protein Kinase 3 (CrMPK3) and Strictosidine Synthase (STR) genes. Five concentrations (5, 10, 15, 20 and 25 mg·L−1) of AgNPs were utilized in addition to deionized water as control. Results reflected binary positive correlations among AgNPs concentration, oxidative stress indicated with increase in hydrogen peroxide and malondialdehyde contents, activities of ascorbate peroxidase and superoxide dismutase, expression of the regulatory gene CrMPK3 and the alkaloid biosynthetic gene STR as well as alkaloids accumulation. These correlations add to the growing evidence that AgNPs can trigger the accumulation of alkaloids in plant cells through a signaling pathway that involves hydrogen peroxide and MAPKs, leading to up-regulation of the biosynthetic genes, including STR gene.

Ahmed, H. S. I., A. Badr, H. H. El-Shazly, L. Watson, A. S. Fouad, and F. Y. Ellmouni, "Molecular Phylogeny of Trifolium L. Section Trifolium with Reference to Chromosome Number and Subsections Delimitation", Plants, vol. 10, no. 10, 2021. AbstractWebsite

The genus Trifolium is one of the largest genera of the legume family Fabaceae with ca. 255 species. The genus is divided into eight sections; the section Trifolium is a major section of the genus, comprising 73 species mainly distributed in the Mediterranean region. We used nuclear ribosomal DNA internal transcribed spacer (ITS) and morphological variation to reconsider the delimitation and phylogenetic relationships of species in the section Trifolium with reference to chromosomal variations. Bayesian analysis of ITS data delimited the species as three clades based on the analysis of ITS sequence and informative indels in combination with morphological variation. The phylogeny of the species by different analyses methods does not support their current delimitation in 17 subsections. The basic chromosome number x = 8 is the number for the genus Trifolium, from which x = 7, 6 and 5 were derived through successive aneuploidy events. With reference to the distribution of these numbers in the species of the section Trifolium, species in clade III and clade II are more evolved than species in clade I.

Fouad, A. S., and R. M. Hafez, "Effects of cobalt ions and cobalt nanoparticles on transient expression of gus gene in catharanthus roseus suspension cultures", Journal of Radiation Research and Applied Sciences , vol. 13, issue 1, pp. 765-775, 2020.
Hafez, R., and A. S. Fouad, "Mitigation of Genotoxic and Cytotoxic Effects of Silver Nanoparticles on Onion Root Tips using some Antioxidant Scavengers", Egyptian Journal of Botany, vol. 60, issue 1, pp. 133-145, 2020.
Fouad, A. S., R. Hafez, and R. Hamdy, "Authentication of Cordia dentata Poir. Growing in Egypt using ISSR and DNA barcoding", Bioscience Research, vol. 16, issue 2, 2019.
Fouad, A. S., R. Hafez, and H. Hosni, "Authentication of Three Endemic Species of the Family Caryophyllaceae from Sinai Peninsula Using DNA Barcoding", Egyptian Journal of Botany, vol. 59, 2019.
Fouad, A. S., and R. M. Hafez, "In silico characterization of CDKB1 and its coding gene in some Oryza species", Bioscience Research, vol. 16, issue 2, pp. 1679-1690, 2019.
Shanab, S. M. M., R. M. Hafez, and A. S. Fouad, "A review on algae and plants as potential source of arachidonic acid", Journal of Advanced Research, vol. 11, pp. 3-11, 2018. 2_arachidonic_acid_review.pdf