Gene Expression Classification for Biomarker Identification in Maize Subjected to Various Biotic Stresses.

Abstract

Various diseases severely affect maize, leading to a significant reduction in yield and crop quality. Therefore, the identification of genes responsible for tolerance to biotic stress is important in maize breeding programs. In the present study, a meta-analysis on microarray gene expression of maize imposed to various biotic stresses, induced by fungal pathogens or pests, was performed to identify key tolerant genes. Correlation-based Feature Selection (CFS) was performed to attain fewer DEGs discriminating control and stress conditions. As a result, 44 genes were selected and their performance was confirmed in the Bayes Net, MLP, SMO, KStar, Hoeffding Tree, and Random Forest models. Bayes Net outperformed the other algorithms representing an accuracy level of 97.1831%. Pathogen recognition genes, decision tree models, co-expression analysis, and functional enrichment were implemented on these selected genes. A robust co-expression was observed among 11 genes responsible for defense response, diterpene phytoalexin biosynthetic process, and diterpenoid biosynthetic process in terms of biological process. This study could provide new information on the genes responsible for resistance to biotic stress in maize to be implicated in biology or maize breeding.