Comparative transcriptome profiling and co-expression network analysis reveals important genes regulating maize response to Southern corn rust

Southern corn rust (SCR) caused by Puccinia polysora Underw. (P. polysora) poses a serious threat to global maize (Zea mays L.) production. This study used six maize inbred lines (DTMA-45, DTMA-50, R99, N110, P767 and 15B020F3) as materials to systematically explore the response mechanism of maize to southern corn rust through phenotype identification, transcriptome sequencing, functional enrichment analysis, gene co-expression network analysis, and quantitative RT-PCR experiments. Phenotypic analysis shows that DTMA-50, R99 and P767 have strong resistance, while DTMA-45, N110 and 15B020F3 are more sensitive. Transcriptome analysis identified a large number of differentially expressed genes (DEGs), whereas gene ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that these genes are involved in multiple biological processes and metabolic pathways such as defense response, cytoskeleton organization, and plant hormone signaling transduction. Weighted gene co-expression network analysis (WGCNA) identified modules and key genes related to resistance, such as cell wall tissue related genes in the coral2 module and some genes in the ABC transporter and plant pathogen interaction pathways up-regulated in the resistant strain. Quantitative real-time PCR showed that ABCG11 (LOC100281487) and CCR1 (LOC103649447) genes are continuously up-regulated in the early stages of infection in the resistant line R99, which may play an important role in resisting fungal invasion. This study reveals the complex molecular mechanisms underlying maize's response to southern corn rust, offering important theoretical support and potential targets for maize disease resistance breeding.