Comparative Transcriptome Analysis Identifies Candidate Coordinated Defense Mechanisms in Corn Stalk Rot Resistance

Corn stalk rot (CSR) is a devastating soil-borne disease, but the transcriptional basis of constitutive resistance remains unclear. Here, we performed comparative transcriptome analysis of the CSR-resistant maize cultivar Qi319 (JR) and the CSR-susceptible maize cultivar Ye478 (JS) under pathogen-challenged conditions. A total of 6009 differentially expressed genes (DEGs) (3074 upregulated, 2935 downregulated in JR) were identified, with JR exhibiting a higher proportion of low-expression genes. Functional enrichment based on all the DEGs identified significant overrepresentation of flavonoid biosynthesis, Cutin/wax biosynthesis, alpha-linolenic acid metabolism (jasmonic acid synthesis), and starch/sucrose metabolism pathways. Weighted gene co-expression network analysis (WGCNA) identified candidate hub genes, including Zm00001d006069, Zm00001d043607 (hexokinase6), and Zm00001d044122 (anthocyaninless1), potentially associated with regulatory roles. qRT-PCR validated the differential expression of key genes. Subcellular localization assays further showed that Zm00001d044122 (anthocyaninless1) and Zm00001d006069 were mainly localized to the nucleus and plasma membrane, respectively. Collectively, this study provides a transcriptomic landscape associated with CSR resistance and suggests candidate coordinated physical, chemical, hormonal, and metabolic defense pathways. The identified hub genes are candidate targets for marker-assisted selection and genetic improvement. However, pathway-level interpretations are transcriptome-based hypotheses and require metabolite profiling and functional validation.