Identification of Key Gene Network Modules and Hub Genes Associated with Wheat Response to Biotic Stress Using Combined Microarray Meta-analysis and WGCN Analysis

• Published in: Molecular biotechnology Vol. 65; no. 3; pp. 453 - 465
• Main Authors: Nemati, Mahdi, Zare, Nasser, Hedayat-Evrigh, Nemat, Asghari, Rasool
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.03.2023; Springer Nature B.V
• Subjects: Algorithms; Biochemistry; Biological Techniques; Biotechnology; biotic stress; Calories; Cell Biology; Chemistry; Chemistry and Materials Science; Crop production; data collection; DNA microarrays; foods; Gene Expression Profiling; gene expression regulation; Gene Regulatory Networks; Genes; Genetic engineering; Human Genetics; Humans; Meta-analysis; microarray technology; Modules; Molecular modelling; Original Paper; Plant Breeding; Protein Science; Statistical methods; stress tolerance; Stress, Physiological - genetics; Triticum - genetics; Triticum aestivum; Wheat; Hub genes; Microarray; Biological process; KEGG pathway; Co-expression network
• ISSN: 1073-6085; 1559-0305; 1559-0305
• DOI: 10.1007/s12033-022-00541-w

Wheat ( Triticum aestivum ) is one of the major crops worldwide and a primary source of calories for human food. Biotic stresses such as fungi, bacteria, and diseases limit wheat production. Although plant breeding and genetic engineering for biotic stress resistance have been suggested as promising solutions to handle losses caused by biotic stress factors, a comprehensive understanding of molecular mechanisms and identifying key genes is a critical step to obtaining success. Here, a network-based meta-analysis approach based on two main statistical methods was used to identify key genes and molecular mechanisms of the wheat response to biotic stress. A total of 163 samples (21,792 genes) from 10 datasets were analyzed. Fisher Z test based on the p -value and REM method based on effect size resulted in 533 differentially expressed genes ( p  < 0.001 and FDR  < 0.001). WGCNA analysis using a dynamic tree-cutting algorithm was used to construct a co-expression network and three significant modules were detected. The modules were significantly enriched by 16 BP terms and 4 KEGG pathways (Benjamini–Hochberg FDR  < 0.001). A total of nine hub genes (a top 1.5% of genes with the highest degree) were identified from the constructed network. The identification of DE genes, gene–gene co-expressing network, and hub genes may contribute to uncovering the molecular mechanisms of the wheat response to biotic stress.