Maize stalk rot is one of the common and most devastating diseases in major maize production areas in China. Under natural conditions, maize stalk rot is mostly caused by the synergistic infection of various pathogens. The purpose of this study was to screen elite maize germplasms resistant to the synergistic infection with F. graminearum and F. verticillioides. Meanwhile, QTN associated with resistance to the infection by synergistic infection of two Fusarium species and the candidate resistance genes were identified, which will provide gene resources and theoretical reference for molecular breeding of maize variety resistant to synergistic infection of different pathogens.

Using a maize natural population as experimental materials, the maize stalk rot phenotypes were investigated upon simultaneous infection with F. graminearum and F. verticillioides. Furthermore, GWAS analysis was conducted to identify significant resistance SNP and to predict candidate genes for stalk rot resistance.

Through the phenotypic analysis of stalk rot caused by synergistic infection under both field and laboratory conditions, it was found that inbred lines from different sources and subgroups showed significant phenotypic variation. More specifically, the field assay results showed that the inbred lines collected from China were more resistant and that from USA were more susceptible to synergistic infection. Moreover, the inbred lines of tropical and subtropical subgroup were more resistant, whereas the inbred lines of Mixed subgroup more susceptible. The seedling assay results under laboratory condition showed that the lines collected from USA were more resistant, whereas that from CIMMYT were more susceptible. The lines of SS subgroup were more resistant, and that of Mixed subgroup were more susceptible. By integrating field and laboratory phenotypic data, 29 and 16 lines with higher levels of resistance to synergistic infection were screened out respectively, and 6 resistant lines were identified under both conditions. Moreover, based on the field phenotype GWAS, 18 QTNs associated with the resistance were identified, and 93 candidate genes associated with stalk rot resistance to synergistic infection were mined. Among these candidate genes, four genes showed haplotype variation, whose expression levels were up-regulated in disease-resistant lines.

Using the natural population of maize with great diversity in genetic background, 6 resistant lines to the synergistic infection with Fusarium spp. were identified under two conditions, which can be used as potential germplasm resources for maize stalk rot resistance in the future. Four candidate genes that might be involved in the resistance to synergistic infection were identified by GWAS, which will provide genetic resources for the breeding maize varieties with enhanced resistance to stalk rot caused by F. graminearum and F. verticillioides.