Northern corn leaf blight (NCLB) is a destructive foliar disease of maize that results from infection with the
fungal pathogen, Exserohilum turcicum. Annual yield losses incurred from NCLB in South Africa may exceed 50 % when
environmental conditions optimal for disease development prevail. In order to study the genetic diversity of E. turcicum, 13
microsatellite markers and mating type PCR primers were developed. Thirty-two primer pairs were designed from the E.
turcicum genome sequence to flank microsatellite regions. A multiplex PCR assay amplifying both mating type
idiomorphs was designed from the MAT1-1 and MAT1-2 gene sequences, and a protocol for multiplex PCR amplification
of MAT loci was optimized. Initial screening identified 13 microsatellite regions that were polymorphic in 9 isolates of
E. turcicum. To test the efficacy of the markers, 26 isolates of E. turcicum from 6 South African provinces, including 2
isolates from sorghum, were genotyped. A total of 90 alleles across 13 loci were obtained and the gene diversity ranged
from 0.074 to 0.929. Cross-species amplification withE. rostratum was obtained for one SSR marker (SSR27). The
MAT markers were specific to E. turcicum and could be used to differentiate isolates of E. turcicum and E.
rostratum. The markers developed in this study will be useful to elucidate the population genetic structure, genetic
diversity and mode of reproduction of E. turcicum on maize and sorghum.