Detection of candidate R genes and single nucleotide polymorphisms for downy mildew resistance in maize inbred lines by association analysis

Downy mildew (DM) is a plant disease that strongly limits maize production. The resistance (R) genes for this disease have been identified and characterized and serve as important tools for plant disease evaluation. In this study, partial genes for PIC15, PO145579, and zmcf5 were identified and analyzed in a panel of 60 public and private maize inbred lines using bioinformatics and statistics tools. These candidate R genes exhibited an average nucleotide diversity value of 0.015. The negative Tajima’s D values for these genes suggested that purifying selection has played a role in the evolution of maize DM resistance genes. In addition, linkage disequilibrium among these genes occurred across an extent of ~ 200 bp. Using association analysis methods, a general linear model, and a mixed linear model, five polymorphisms within the partial PIC15 and PO145579 genes were detected and associated with DM disease. These are new polymorphisms that have not previously been reported in association with DM disease traits. Therefore, correlations between these new polymorphisms and DM disease in these germplasm collections could advance the development of a functional marker for marker-assisted selection of DM disease resistance in maize breeding programs.