Comparative Transcriptomics Reveals the Molecular Mechanisms of Maize in Response to Downy Mildew Disease Caused by Peronosclerospora philippinensis (Weston) Shaw

Abstract

Maize is the Philippines’ second most valuable crop based on overall value and total area planted. Still, maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogen Peronosclerospora philippinensis (Weston) Shaw, causing annual losses in maize production. The use of resistant varieties remains the most effective method of control together with integrated pest and disease management strategies. To date, there are no commercially available maize breeding lines or hybrids deployed in the country while the effectiveness of the fungicide metalaxyl versus DM has declined. Hence, it is necessary to initiate pre-breeding and breeding programs to understand the mechanism of resistance of maize against DM. To comprehend the underlying mechanisms of the presence of the disease, we performed an RNA-Seq comparative transcriptomic approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize. 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 multi-faceted defense strategies govern the molecular basis of DM resistance in maize. These include multi-process regulations such as transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Finally, transcriptome-wide variants (SNPs and indels) and their impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.