DNA fingerprinting with a set of synthetic oligonucleotides complementary to simple repetitive sequences was used to develop molecular markers for Ascochyta rabiei, the most important fungal pathogen of chickpea (Cicer arietinum). Two compatible mating type isolates (MatI and MatII) from the U.S. Pacific Northwest with the same low level of aggressivity were compared to highly virulent isolates from the Mediterranean region and Pakistan to find suitable mating partners for the production of a mapping population. After Hinf I or Taq I restriction, electrophoresis and in-gel hybridization with ten different simple repetitive oligonucleotides, all tested single-spored isolates exhibited unique fingerprint patterns. The analysis revealed that the two U.S. mating types share a considerable amount of genetic variability. A total of 77 polymorphic marker bands were detected. A higher number of polymorphic bands (up to 104) was observed between these isolates and those from different geographical regions. The isolates from the Mediterranean region and Pakistan shared a lower degree (between 80 and 90 bands) of detectable genetic diversity. These data permit selection of highly virulent crossing partners for the different mating types with a high degree of detectable polymorphism.

A sexual cross was performed to prove the Mendelian segregation of fingerprint bands for future linkage analysis. Additionally, the fingerprint data based on 268 informative characters combined with phenetic and phylogenetic algorithms allow determination of the genetic identity, relatedness and diversity of the different isolates. To confirm the phylogenetic data, two outgroupers Ascochyta fabae and Ascochyta pisi, were included. Results indicate that A. pisi is more closely related to A. rabiei than A. fabae.