Fine-Mapping and Functional Annotation of a Major QTL in Corn (Zea mays L.) for Downy Mildew Resistance Towards Precision Marker-Assisted Breeding

To date, no commercial variety of corn has good resistance against Philippine downy mildew disease. Based on quantitative trait loci (QTL) analysis, a QTL (RGA1-1) has been mapped tightly-linked to downy mildew resistance (DMR) and can readily be used in corn marker-assisted breeding (MAB). Cloning and sequence analysis of the RGA1-1 has validated it to be 91% similar to Zea mays E3 ubiquitin-protein ligase ATL31-like protein on chromosome 5. This is the first report of the possible contribution of ATL31-like protein in corn DMR. A sequence characterized amplified region (SCAR) marker was developed for RGA1-1 and used to fine-map the ATL31 ubiquitin ligase gene-region on corn chromosome 5. Further genetic linkage analysis has mapped the position of the SCAR marker within the interval of the QTL markers for onset of downy mildew systemic symptoms. This includes the major QTL on chromosome 5 that has been mapped for significant additive genetic effect and 23% R² against the most virulent strain of downy mildew, the Southern Mindanao pathogen strain. Using the published genome sequence database of corn, this gene region was further mined to characterize other associated QTLs for corn DMR. A total of 16 markers targeting 16 candidate R-genes were developed. These markers were screened for SNP between the parental genotypes, which will be used to fine-map the target QTL region and characterize the underlying gene networks and genetic effects towards precise marker-assisted breeding in corn for durable resistance against Philippine downy mildew.