Identifying biotic stress-associated molecular markers in wheat using differential gene expression and machine learning techniques

Manar S. Ibrahim, Saifeldeen M. Ibrahim

Abstract


Wheat is an important crop for global food security and a key crop for many developing countries. Thanks to next-generation sequencing (NGS) technologies, researchers can analyze the transcriptome of wheat and reveal differentially expressed genes (DEGs) responsible for essential agronomic traits and biotic stress tolerance. In addition, machine learning (ML) methods have opened new avenues to detect patterns in expression data and make predictions or decisions based on these patterns. We used both techniques to identify potential molecular markers in wheat associated with biotic stress in six gene expression studies conducted to investigate powdery mildew, blast fungus, rust, fly larval infection, greenbug aphid, and Stagonospora nodorum infections. A total of 24,152 threshold genes were collected from different studies, with the highest threshold being 7580 genes and the lowest being 1073 genes. The study identified several genes that were differentially expressed in all comparisons and genes that were present in only one data set. The study also discussed the possible role of certain genes in plant resistance. The Ta-TLP, HBP-1, WRKY, PPO, and glucan endo-1,3-beta-glucosidase genes were selected by the interpretable model-agnostic explanation algorithm as the most important genes known to play a significant role in resistance to biotic stress. Our results support the application of ML analysis in plant genomics and can help increase agricultural efficiency and production, leading to higher yields and more sustainable farming practices.

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Gimenez E, Salinas M, Manzano-Agugliaro F. World wide research on plant defense against biotic stresses as improvement for sustainable agriculture. Sustainability. 2018;10(2):391.

Igrejas G, Branlard G. The importance of wheat. In: Wheat quality for improving processing and human health. Springer; 2020. p. 1-7.

Erenstein O, Jaleta M, Mottaleb KA, Sonder K, Donovan J, Braun HJ. Global Trends in Wheat Production, Consumption and Trade. In: Wheat Improvement. Springer; 2022. p. 47-66.

Hayta S, Smedley MA, Clarke M, Forner M, Harwood WA. An efficient Agrobacterium-mediated transformation protocol for hexaploid and tetraploid wheat. Current Protocols. 2021;1(3):e58.

Zhou Y, Zhao X, Li Y, Xu J, Bi A, Kang L, et al. Triticum population sequencing provides insights into wheat adaptation. Nature genetics. 2020;52(12):1412-22.

Poudel PB, Poudel MR. Heat stress effects and tolerance in wheat: A review. Journal of Biology and Today’s World. 2020;9(3):1-6.

Jasrotia P, Kashyap PL, Bhardwaj AK, Kumar S, Singh G.Scope and applications of nanotechnology for wheat production: A review of recent advances. Wheat Barley Res. 2018;10(1):1-14.

Zhou G, Soufan O, Ewald J, Hancock RE, Basu N, Xia J. NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic acids research. 2019;47(W1):W234-41.

Kumar Kushwaha S, Vetukuri RR, Odilbekov F, Pareek N, Henriksson T, Chawade A. Differential gene expression analysis of wheat breeding lines reveal molecular insights in yellow rust resistance under field conditions. Agronomy. 2020;10(12):1888.

Wang T, Li B, Nelson CE, Nabavi S. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. BMC bioinformatics. 2019;20(1):1-16.

Paul S, Duhan JS, Jaiswal S, Angadi UB, Sharma R, Raghav N, et al. RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response. 2022.

Yang X, Tan B, Liu H, Zhu W, Xu L, Wang Y, et al. Genetic diversity and population structure of Asian and European common wheat accessions based on genotyping-by-sequencing. Frontiers in Genetics. 2020;11:580782.

Velu G, Crespo Herrera L, Guzman C, Huerta J, Payne T, Singh RP. Assessing genetic diversity to breed competitive biofortified wheat with enhanced grain Zn and Fe concentrations. Frontiers in Plant Science. 2019;9:1971.

Devesh P, Moitra P, Shukla R, Pandey S. Genetic diversity and principal component analyses for yield, yield components and quality traits of advanced lines of wheat. Journal of Pharmacognosy and Phytochemistry. 2019;8(3):4834-9.

Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, et al. NCBI GEO: mining millions of expression profilesdatabase and tools. Nucleic acids research 2005;33(suppl_1):D562-6.

Zhang X, Wang Z, Hu L, Shen X, Liu C. Identification of potential genetic biomarkers and target genes of periimplantitis using bioinformatics tools. BioMed Research International. 2021;2021.

Udhaya Kumar S, Thirumal Kumar D, Bithia R, Sankar S, Magesh R, Sidenna M, et al. Analysis of differentially expressed genes and molecular pathways in familial hypercholesterolemia involved in atherosclerosis: a systematic and bioinformatics approach. Frontiers in Genetics. 2020;11:734.

Liu S, Wang Z, Zhu R, Wang F, Cheng Y, Liu Y. Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2. JoVE (Journal of Visualized Experiments). 2021;(175):e62528.

Sivasakthi P, Sabarathinam S, Vijayakumar TM. Network pharmacology and in silico pharmacokinetic prediction of Ozanimod in the management of ulcerative colitis: A computational study. Health Science Reports. 2022;5(1).

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, et al. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic acids research. 2021;49(D1):D605-12.

Liu GT, Wang BB, Lecourieux D, Li MJ, Liu MB, Liu RQ, et al. Proteomic analysis of early-stage incompatible and compatible interactions between grapevine and P. viticola.Horticulture research. 2021;8.

Duan Z, Lv G, Shen C, Li Q, Qin Z, Niu J. The role of jasmonic acid signalling in wheat (Triticum aestivum L.) powdery mildew resistance reaction. European journal of plant pathology. 2014;140(1):169-83.

Sun RJ, Xu Y, Hou CX, Zhan YH, Liu MQ, Weng XY. Expression and characteristics of rice xylanase inhibitor OsXIP, a member of a new class of antifungal proteins. Biologia plantarum. 2018;62(3):569-78

Tundo S, Mandalà G, Sella L, Favaron F, Bedre R, Kalunke RM. Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing. International Journal of Molecular Sciences. 2022;23(23):14994.

Hu C, Chen P, Zhou X, Li Y, Ma K, Li S, et al. Arms Race between the Host and Pathogen Associated with Fusarium Head Blight of Wheat. Cells. 2022;11(15):2275.

Wang Q, Shao B, Shaikh FI, Friedt W, Gottwald S. Wheat resistances to Fusarium root rot and head blight are both associated with deoxynivalenol-and jasmonate-related gene expression. Phytopathology. 2018;108(5):602-16.

Singh P, Song QQ, Singh RK, Li HB, Solanki MK, Yang LT, et al. Physiological and molecular analysis of sugarcane (VarietiesF134 and NCo310) during Sporisorium scitamineum interaction. Sugar Tech. 2019;21(4):631-44.

Erdayani E, Nagarajan R, Grant NP, Gill KS. Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat. Scientific reports. 2020;10(1):1-17.

Liu Y, Liu Y, Spetz C, Li L, Wang X. Comparative transcriptome analysis in Triticum aestivum infecting wheat dwarf virus reveals the effects of viral infection on phytohormone and photosynthesis metabolism pathways. Phytopathology Research. 2020;2(1):1-13.

Lata C, Prasad P, Gangwar O, Adhikari S, Thakur RK, Savadi S, et al. Temporal behavior of wheat–Puccinia striiformis interaction prompted defense-responsive genes. Journal of Plant Interactions. 2022;17(1):674-84.

Vishwakarma H, Junaid A, Manjhi J, Singh GP, Gaikwad K, Padaria JC. Heat stress transcripts, differential expression, and profiling of heat stress tolerant gene TaHsp90 in Indian wheat (Triticum aestivum L.) cv C306. PloS one. 2018;13(6):e0198293.

Al-Attala MN. The role of Some MYB genes in defense response of wheat against stripe rust pathogen. Egyptian Journal of Desert Research. 2019;69(3):113-29.

Liu Y, Yu TF, Li YT, Zheng L, Lu ZW, Zhou YB, et al. Mitogen-activated protein kinase TaMPK3 suppresses ABA response by destabilising TaPYL4 receptor in wheat. New Phytologist. 2022;236(1):114-31.

Sorahinobar M, Niknam V, Jahedi A, Ebrahimzadeh H, Moradi B, Behmanesh M, et al. Application of sodium salicylate up-regulates defense response against Fusarium graminearum in wheat spikes. Biologia plantarum.2019;63:690-8

Kang G, Li G, Yang W, Han Q, Ma H, Wang Y, et al. Transcriptional profile of the spring freeze response in the leaves of bread wheat (Triticum aestivum L.). Acta physiologiae plantarum. 2013;35(2):575-87.

Ekom DCT, Benchekroun MN, Udupa SM, Iraqi D, Ennaji MM, et al. Wheat Genetic Transformation as Efficient Tools to Fight against Fungal Diseases. Journal of Agricultural Science and Technology A. 2015;5(3):153-61.

He ZH, Li HW, Shen Y, Li ZS, Mi H. Comparative analysis of the chloroplast proteomes of a wheat (Triticum aestivum L.) single seed descent line and its parents. Journal of plant physiology. 2013;170(13):1139-47.

Sun W, Zhou Y, Movahedi A, Wei H, Zhuge Q. Thaumatin like protein(Pe-TLP)acts as a positive factor in transgenic poplars enhanced resistance to spots disease. Physiological and Molecular Plant Pathology. 2020;112:101512.

Patel P, Patil T, Maiti S, Paul D, Amaresan N. Screening of osmotic stress-tolerant bacteria for plant growth promotion in wheat (Triticum aestivum L.) and brinjal (Solanum melongena L.) under drought conditions. Letters in Applied Microbiology. 2022;75(5):1286-92.

Hegedus G, Kutasy B, Kiniczky M, Decsi K, Juhász Á, Nagy Á, et al. Liposomal Formulation of Botanical Extracts may Enhance Yield Triggering PR Genes and Phenylpropanoid Pathway in Barley (Hordeum vulgare). Plants 2022, 11, 2969. s Note: MDPI stays neutral with regard to jurisdictional claims in published ; 2022




DOI: https://doi.org/10.36462/H.BioSci.202203

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