Identification of Genes for Wheat Fungal Resistance Using Bioinformatics Techniques

Ahmed E. Nassar, Khaled H. Mousa, Ahmed A. Madbouly, Shafik D. Ibrahim, Alsamman M. Alsamman


For the majority of world populations, wheat (Triticum aestivum L.) would be the first essential and economic cereal grain crop. Pests and pathogens in both rich and developing countries are constantly threatening wheat production and sustainable development. Multiple gene pathways were recorded to share an association with fungal pathogens with wheat biological resistance. Our aim to use such tools in order to detect and classify fungal resistance genes in wheat through sequence alignment, protein domain identification and phylogenetic analysis. In addition the introduction for restriction fragment length polymorphism (RFLP) for such genes in the new primer database. Approximately 138 sequences of DNA were recovered from the wheat genome by aligning 3845 anti-fungal amino acids through tblastn tool. The NCBI blastn online tool used to detect sequences with functional genes, where 92 genes have been detected. The total number of nucleotides was 48385, where the smallest DNA sequence have 302 bp and the longest contains 977 bp with an average length of 525.9 bp per sequence. The wheat chromosomes 3D, and 4B have the highest number of sequences (9) followed by chromosomes 3B (7) and 3A(6), where wheat genomes A, B and D have 30, 35 and 27 genes, respectively. Five different amino acids motifs have been revealed among studied wheat amino acid sequences. The gene annotation tools used to infer studied amino acid gene annotation. Amino acid sequences belongs to lectin, kinase, tyrosine-protein kinase (STK), thaumatin, and cysteine-rich repeats representing 2, 9, 8, 19, 23 genes respectively, in addition to 31 hypothetical genes. The proteins chemical content have been assessed through 16 different amino acid chemical and physical characteristics


Wheat; Pathogens; Pathways; Fungal;Phylogenetic; RFLP

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FAOSTAT. 2017; Available from:

Figueroa M, Hammond-Kosack KE, Solomon PS. A review of wheat diseases—a field perspective. Mol Plant Pathol. 2018;19(6):1523–36.

Kumar P, Yadava RK, Gollen B, Kumar S, Verma RK, Yadav S. Nutritional contents and medicinal properties of wheat: a review. Life Sci Med Res. 2011;22:1–10.

Farg E, Arafat SM, El-Wahed MA, El-Gindy AM. Estimation of evapotranspiration ETc and crop coefficient Kc of wheat, in south Nile Delta of Egypt using integrated FAO-56 approach and remote sensing data. Egypt J Remote Sens Sp Sci. 2012;15(1):83–9.

McVey D V, Nazim M, Leonard KJ, Long DL. Patterns of virulence diversity in Puccinia triticina on wheat in Egypt and the United States in 1998-2000. Plant Dis. 2004;88(3):271–9.

Al-Naggar AMM, Sabry SRS, Atta MMM, El-Aleem OMA. Field Screening of Wheat (Triticum aestivum L.) Genotypes for Salinity Tolerance at Three Locations in Egypt. Ecol Res Intern(JAERI). 2015;4(3):88–104.

Skoracka A, Rector BG, Hein GL. The interface between wheat and the wheat curl mite, Aceria tosichella, the primary vector of globally important viral diseases. Front Plant Sci. 2018;9.

Kushalappa AC, Yogendra KN, Karre S. Plant innate immune response: qualitative and quantitative resistance. CRC Crit Rev Plant Sci. 2016;35(1):38–55.

Lehmann S, Serrano M, L’Haridon F, Tjamos SE, Metraux J-P. Reactive oxygen species and plant resistance to fungal pathogens. Phytochemistry. 2015;112:54–62.

Alsamman AM, Ibrahim SD, Hamwieh A. KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping. Bioinformatics. 2019;

Habib PT, Alsamman AM, Hamwieh A. BioAnalyzer: Bioinformatic Software of Routinely Used Tools for Analysis of Genomic Data. Biotechnology. 2019 ;10:33–41.

Awan Z. Plant Molecular Biology Databases. Highlights Biosci. 2019;1–7.

Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2010;39(suppl_1):D52--D57.

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, et al. The Ensembl genome database project. Nucleic Acids Res. 2002;30(1):38–41.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402.

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37 :W202--W208.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–9.

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–80.

Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Elsevier current trends; 2000.

Wang J, Li L, Qi H, Du X, Zhang G. RestrictionDigest: A powerful Perl module for simulating genomic restriction digests. Electron J Biotechnol. 2016; 19(3):36–42.

You FM, Huo N, Gu YQ, Luo M, Ma Y, Hane D, et al. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008;9(1):253.

Gill SC, Von Hippel PH. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. 1989;182(2):319–26.

Pylaeva S, Brehm M, Sebastiani D. Salt Bridge in Aqueous Solution: Strong Structural Motifs but Weak Enthalpic Effect. Sci Rep. 2018;8.

Davis GD, Elisee C, Newham DM, Harrison RG. New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnol Bioeng. 1999;65(4):382–8.

Righetti PG. Determination of the isoelectric point of proteins by capillary isoelectric focusing. J Chromatogr A. 2004;1037(1–2):491–9.

Broome BM, Hecht MH. Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol. 2000;296(4):961–8.

Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, et al. The eukaryotic linear motif resource--2018 update. Nucleic Acids Res. 2017;46(D1):D428--D434.

Giraud-Panis M-J, Ye J, Gilson E. TRFH domain: at the root of telomere protein evolution? Cell Res. 2018;28(1):7–8.

Liu BA, Shah E, Jablonowski K, Stergachis A, Engelmann B, Nash PD. The SH2 domain--containing proteins in 21 species establish the provenance and scope of phosphotyrosine signaling in eukaryotes. Sci Signal. 2011;4(202):ra83--ra83.

Williams JG, Zvelebil M. SH2 domains in plants imply new signalling scenarios. Trends Plant Sci. 2004;9(4):161–3.

Pires JR, Hong X, Brockmann C, Volkmer-Engert R, Schneider-Mergener J, Oschkinat H, et al. The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p. J Mol Biol. 2003;326(5):1427–35.

Meng X, Zhang S. MAPK cascades in plant disease resistance signaling. Annu Rev Phytopathol. 2013;51:245–66.

De Hoff PL, Brill LM, Hirsch AM. Plant lectins: the ties that bind in root symbiosis and plant defense. Mol Genet genomics. 2009;282(1):1–15.

Lannoo N, Van Damme EJM. Lectin domains at the frontiers of plant defense. Front Plant Sci. 2014;5:397.

Van Damme EJM, Lannoo N, Peumans WJ. Plant lectins. In: Advances in botanical research. Elsevier; 2008. p. 107–209.

Wang Y, Bouwmeester K. L-type lectin receptor kinases: New forces in plant immunity. PLoS Pathog. 2017;13(8):e1006433.

Wawra S, Fesel P, Widmer H, Timm M, Seibel J, Leson L, et al. The fungal-specific $β$-glucan-binding lectin FGB1 alters cell-wall composition and suppresses glucan-triggered immunity in plants. Nat Commun. 2016;7:13188.

Llorente F, Alonso-Blanco C, Sánchez-Rodriguez C, Jorda L, Molina A. ERECTA receptor-like kinase and heterotrimeric G protein from Arabidopsis are required for resistance to the necrotrophic fungus Plectos-phaerella cucumerina. Plant J. 2005;43(2):165–80.

Fu D, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen X, et al. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science (80). 2009;323(5919):1357–60.

Wan J, Zhang X-C, Neece D, Ramonell KM, Clough S, Kim S, et al. A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell. 2008;20(2):471–81.

Misra RC, Kamthan M, Kumar S, Ghosh S, others. A thaumatin-like protein of Ocimum basilicum confers tolerance to fungal pathogen and abiotic stress in transgenic Arabidopsis. Sci Rep. 2016;6:25340.

Ali G, Hu X, Reddy ASN. Overexpression of the Arabidopsis thaumatin-like protein 1 in transgenic potato plants enhances resistance against early and late blights. bioRxiv. 2019;621649.

Marcato R, Sella L, Lucchetta M, Vincenzi S, Odorizzi S, Curioni A, et al. Necrotrophic fungal plant pathogens display different mechanisms to counteract grape chitinase and thaumatin-like protein. Physiol Mol Plant Pathol. 2017;99:7–15.

Patiño B, Vázquez C, Manning JM, Roncero MIG, Córdoba-Cañero D, Di Pietro A, et al. Characterization of a novel cysteine-rich antifungal protein from Fusarium graminearum with activity against maize fungal pathogens. Int J Food Microbiol. 2018;283:45-51.

Maróti G, Downie JA, Kondorosi É. Plant cysteine-rich peptides that inhibit pathogen growth and control rhizobial differentiation in legume nodules. Curr Opin Plant Biol. 2015;26:57–63.

Mokhtar MM, Adawy SS, El-Assal SE-DS, Hussein EHA. Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.). PLoS One. Public Library of Science; 2016;11(7):e0159268.

Adawy SS, Mokhtar MM, Alsamman AM, Sakr MM. Development of annotated EST-SSR database in olive (Olea europaea). Int J Sci Res. 2015;4(9):1063–73.



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