A combination of QTL mapping and GradedPool-Seq to dissect genetic complexity for Gibberella ear rot resistance in maize using an IBM Syn10 DH population

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most devastating maize diseases that reduces grain yield and quality worldwide. Utilization of host genetic resistance has become one of the most suitable strategies to control GER. In this study, a set of 246 diverse inbred lines derived from the intermated B 73 × Mo 17 doubled haploid population (IBM Syn10 DH) were used to detect quantitative trait loci (QTL) associated with resistance to GER. Meanwhile, a GradedPool-Seq (GPS) approach was performed to identify genomic variations involved in GER resistance. Using artificial inoculation across multiple environments, GER severity of the population was observed with wide phenotypic variation. Based on the linkage mapping, a total of 14 resistant QTLs were detected, accounting for 5.11 to 14.87% of the phenotypic variation, respectively. In GPS analysis, five significant single nucleotide polymorphisms (SNPs) associated with GER resistance were identified. Combining QTL mapping and GPS analysis, a peak-value SNP on chromosome 4 from GPS was overlapped with the QTL qGER4.2, suggesting that the colocalized region could be the most possible target location conferring resistance to GER. Subsequently, seven candidate genes were identified within the peak SNP, linking them to GER resistance. These findings are useful for exploring the complicated genetic variations in maize GER resistance. The genomic regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the combined strategy that can be used for quantitative traits in plant species.