Huang, P., M. El-Soda, K. W. Wolinska, K. Zhao, N. H. Davila Olivas, J. J. A. van Loon, M. Dicke, and M. G. M. Aarts, "Genome-wide association analysis reveals genes controlling an antagonistic effect of biotic and osmotic stress on Arabidopsis thaliana growth", Molecular Plant PathologyMolecular Plant Pathology, vol. 25, issue 3: John Wiley & Sons, Ltd, pp. e13436, 2024. AbstractWebsite

Abstract While the response of Arabidopsis thaliana to drought, herbivory or fungal infection has been well-examined, the consequences of exposure to a series of such (a)biotic stresses are not well studied. This work reports on the genetic mechanisms underlying the Arabidopsis response to single osmotic stress, and to combinatorial stress, either fungal infection using Botrytis cinerea or herbivory using Pieris rapae caterpillars followed by an osmotic stress treatment. Several small-effect genetic loci associated with rosette dry weight (DW), rosette water content (WC), and the projected rosette leaf area in response to combinatorial stress were mapped using univariate and multi-environment genome-wide association approaches. A single-nucleotide polymorphism (SNP) associated with DROUGHT-INDUCED 19 (DI19) was identified by both approaches, supporting its potential involvement in the response to combinatorial stress. Several SNPs were found to be in linkage disequilibrium with known stress-responsive genes such as PEROXIDASE 34 (PRX34), BASIC LEUCINE ZIPPER 25 (bZIP25), RESISTANCE METHYLATED GENE 1 (RMG1) and WHITE RUST RESISTANCE 4 (WRR4). An antagonistic effect between biotic and osmotic stress was found for prx34 and arf4 mutants, which suggests PRX34 and ARF4 play an important role in the response to the combinatorial stress.

Galal, A. A., F. A. SAFHI, M. A. El-Hity, M. M. Kamara, E. M. Gamal El-Din, M. Rehan, M. Farid, S. I. Behiry, M. El-Soda, and E. Mansour, "Molecular Genetic Diversity of Local and Exotic Durum Wheat Genotypes and Their Combining Ability for Agronomic Traits under Water Deficit and Well-Watered Conditions", Life, vol. 13, issue 12, 2023. Abstract

Water deficit poses significant environmental stress that adversely affects the growth and productivity of durum wheat. Moreover, projections of climate change suggest an increase in the frequency and severity of droughts, particularly in arid regions. Consequently, there is an urgent need to develop drought-tolerant and high-yielding genotypes to ensure sustained production and global food security in response to population growth. This study aimed to explore the genetic diversity among local and exotic durum wheat genotypes using simple sequence repeat (SSR) markers and, additionally, to explore the combining ability and agronomic performance of assessed durum wheat genotypes and their 28 F1 crosses under normal and drought stress conditions. The investigated SSRs highlighted and confirmed the high genetic variation among the evaluated parental durum wheat genotypes. These diverse eight parental genotypes were consequently used to develop 28 F1s through a diallel mating design. The parental durum genotypes and their developed 28 F1s were assessed under normal and drought stress conditions. The evaluated genotypes were analyzed for their general and specific combining abilities as well as heterosis for agronomic traits under both conditions. The local cultivar Bani-Suef-7 (P8) is maintained as an effective combiner for developing shortened genotypes and improving earliness. Moreover, the local cultivars Bani-Suef-5 (P7) and Bani-Suef-7 (P8) along with the exotic line W1520 (P6) demonstrated excellent general combining ability for improving grain yield and its components under drought stress conditions. Furthermore, valuable specific hybrid combinations, W988 × W994 (P1 × P2), W996 × W1518 (P3 × P5), W1011 × W1520 (P4 × P6), and Bani-Suef-5 × Bani-Suef-7 (P7 × P8), were identified for grain yield and its components under drought stress conditions. The assessed 36 genotypes were grouped according to tolerance indices into five clusters varying from highly drought-sensitive genotypes (group E) to highly drought-tolerant (group A). The genotypes in cluster A (two crosses) followed by thirteen crosses in cluster B displayed higher drought tolerance compared to the other crosses and their parental genotypes. Subsequently, these hybrids could be considered valuable candidates in future durum wheat breeding programs to develop desired segregants under water-deficit conditions. Strong positive relationships were observed between grain yield and number of grains per spike, plant height, and 1000-grain weight under water-deficit conditions. These results highlight the significance of these traits for indirect selection under drought stress conditions, particularly in the early stages of breeding, owing to their convenient measurability.

El-Soda, M., and M. Aljabri, "Genome-Wide Association Mapping of Grain Metal Accumulation in Wheat", Genes, vol. 13, issue 6, 2022. Abstract

Increasing wheat grain yield while ignoring grain quality and metal accumulation can result in metal deficiencies, particularly in countries where bread wheat accounts for the majority of daily dietary regimes. When the accumulation level exceeds a certain threshold, it becomes toxic and causes various diseases. Biofortification is an effective method of ensuring nutritional security. We screened 200 spring wheat advanced lines from the wheat association mapping initiative for Mn, Fe, Cu, Zn, Ni, and Cd concentrations. Interestingly, high-yielding genotypes had high essential metals, such as Mn, Fe, Cu, and Zn, but low levels of toxic metals, such as Ni and Cd. Positive correlations were found between all metals except Ni and Cd, where no correlation was found. We identified 142 significant SNPs, 26 of which had possible pleiotropic effects on two or more metals. Several QTLs co-located with previously mapped QTL for the same or other metals, whereas others were new. Our findings contribute to wheat genetic biofortification through marker-assisted selection, ensuring nutritional security in the long run.

Bassetti, N., L. Caarls, G. Bukovinszkine’Kiss, M. El-Soda, J. van Veen, K. Bouwmeester, B. J. Zwaan, E. M. Schranz, G. Bonnema, and N. E. Fatouros, "Genetic analysis reveals three novel QTLs underpinning a butterfly egg-induced hypersensitive response-like cell death in Brassica rapa", BMC Plant Biology, vol. 22, issue 1: BioMed Central, pp. 1-17, 2022. Abstract
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Said, A. A., A. H. MacQueen, H. Shawky, M. Reynolds, T. E. Juenger, and M. El-Soda, "Genome-wide association mapping of genotype-environment interactions affecting yield-related traits of spring wheat grown in three watering regimes", Environmental and Experimental Botany, vol. 194: Elsevier, pp. 104740, 2022. Abstract
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El‐Soda, M., and M. S. Sarhan, "From Gene Mapping to Gene Editing, A Guide from the Arabidopsis Research", Annual Plant Reviews online: John Wiley & Sons, Ltd, pp. 733-766, 2021. Abstract
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Anwar, A. M., M. Aljabri, and M. El-Soda, "Patterns of genome-wide codon usage bias in tobacco, tomato and potato", Biotechnology & Biotechnological EquipmentBiotechnology & Biotechnological Equipment, vol. 35, issue 1: Taylor & Francis, pp. 657 - 664, 2021. AbstractWebsite
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Alarfaj, R., M. El-Soda, L. Antanaviciute, R. Vickerstaff, P. Hand, R. J. Harrison, and C. Wagstaff, "Mapping QTL underlying fruit quality traits in an F1 strawberry population", The Journal of Horticultural Science and BiotechnologyThe Journal of Horticultural Science and Biotechnology, vol. 96, issue 5: Taylor & Francis, pp. 634 - 645, 2021. AbstractWebsite
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Abdel-Wahab, M., M. Aljabri, M. Sarhan, G. Osman, S. Wang, M. Mabrouk, H. El-Shabrawi, A. M. M. Gabr, A. Abd El-Haliem, D. O'Sullivan, et al., "High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover", Genes, vol. 11, issue 8, pp. 893, 2020.
Johansson, K. S. L., M. El-Soda, E. Pagel, R. C. Meyer, K. Tõldsepp, A. K. Nilsson, M. Brosché, H. Kollist, J. Uddling, and M. X. Andersson, Genetic controls of short- and long-term stomatal CO2 responses in Arabidopsis thaliana, , vol. 126, issue 1, pp. 179 - 190, 2020/04/16/. AbstractWebsite

The stomatal conductance (gs) of most plant species decreases in response to elevated atmospheric CO2 concentration. This response could have a significant impact on plant water use in a future climate. However, the regulation of the CO2-induced stomatal closure response is not fully understood. Moreover, the potential genetic links between short-term (within minutes to hours) and long-term (within weeks to months) responses of gs to increased atmospheric CO2 have not been explored.We used Arabidopsis thaliana recombinant inbred lines originating from accessions Col-0 (strong CO2 response) and C24 (weak CO2 response) to study short- and long-term controls of gs. Quantitative trait locus (QTL) mapping was used to identify loci controlling short- and long-term gs responses to elevated CO2, as well as other stomata-related traits.Short- and long-term stomatal responses to elevated CO2 were significantly correlated. Both short- and long-term responses were associated with a QTL at the end of chromosome 2. The location of this QTL was confirmed using near-isogenic lines and it was fine-mapped to a 410-kb region. The QTL did not correspond to any known gene involved in stomatal closure and had no effect on the responsiveness to abscisic acid. Additionally, we identified numerous other loci associated with stomatal regulation.We identified and confirmed the effect of a strong QTL corresponding to a yet unknown regulator of stomatal closure in response to elevated CO2 concentration. The correlation between short- and long-term stomatal CO2 responses and the genetic link between these traits highlight the importance of understanding guard cell CO2 signalling to predict and manipulate plant water use in a world with increasing atmospheric CO2 concentration. This study demonstrates the power of using natural variation to unravel the genetic regulation of complex traits.