Aspergillus flavus exemplifies a pathogenic fungus that remains a significant contributor to the loss of corn (Zea mays) crops. The production of carcinogenic aflatoxins renders the crop hazardous for consumption and causes significant loss to farmers. Therefore, the prevention of A. flavus contamination continues to persist as a topic for research intervention. Host resistance to this pathogen provides a promising source of defense for the corn plant. Corn inbred line Mp313E was previously identified to exhibit significant resistance against the A. flavus fungal infection and aflatoxin contamination. Quantitative trait loci (QTL) mapping has previously established four major QTL locations associated with aflatoxin resistance in the corn inbred line Mp313E. Near-isogenic lines were developed containing these previously identified QTLs from backcrossing of inbred lines Mp313E (resistant donor parent) and Va35 (susceptible recurrent parent). Quantitative RT-PCR (qRT-PCR) was used to study gene expression patterns of 17 genes selected from plant-pathogen interaction pathways. Furthermore, genomic primer analysis was used for establishment of 15 candidate genes for marker- assisted breeding.