Comparative transcriptomics reveals the molecular mechanisms of maize in response to downy mildew caused by Peronosclerospora philippinensis (Weston) Shaw

Maize is the Philippines second most valuable staple crop based on overall value and total area planted. Yellow maize, which is the most important type, is utilized as feed for poultry and swine. Still, local maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogen Peronosclerospora philippinensis (Weston) Shaw, causing substantial losses in maize production annually. To comprehend the underlying resistance mechanisms upon the presence of the disease, we performed an RNA-Seq comparative transcriptomics approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize inbred lines. Among the identified differentially expressed genes (DEGs), we detected 43 DEGs shared in both genotypes which may play roles in the basal defense response of maize upon DM infection. We also identified 68 DEGs exclusive to the susceptible genotype, providing insights into the molecular responses underlying successful DM disease progression in maize. Further, we detected 651 DEGs unique to the resistant genotype. This set of genes revealed that the molecular basis of DM resistance in maize is governed by multi-faceted defense strategies. These include multi-process regulations such as programmed cell death (PCD), regulatory proteins, and transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Out of 694 resistant DEGs detected, we narrowed down genes of interest, particularly those highly overexpressed and associated with disease resistance found in other crops. Finally, transcriptome-wide variants and their corresponding impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.