Septoria leaf blotch is one of the most devastating diseases of wheat worldwide. Understanding its genetic diversity and population structure is paramount importance in designing and sustainable management strategies to control the disease. Therefore, the present study was designed to detect and determine the genetic diversity and population structure of Z. tritici isolates collected from northern Ethiopia: Amhara and Tigray regional States using Simple Sequence Repeat markers(nine primers). In this study, a total of 24 single spore derived Septoria tritici isolates were subjected. Specific markers were used to confirm the isolates. The molecular study revealed a total of 242 bands, out of which 58.3% were found to be polymorphic. All loci across the populations were found to be highly (100%) polymorphic and informative with Polymorphic information contents ranging from 0.95 to 0.60. The genetic diversity across the entire populations ranged from 0.96 to 0.63 with overall mean of 0.87. Moreover, Analysis of molecular variance revealed that 95% (3.989) of the total genetic variation (4.19) was accounted within populations, leaving only 5% (0.2) for among populations. The smaller Fixation Index value (0.047) observed in the study indicates the presence of lower population differentiation as a result of higher gene flow (Nm =4.73) between the Z. tritici populations of Amhara and Tigray area. The unweight pair group with methods arithmetic average based cluster, Principal components of Analysis and Structure analysis poorly grouped the individuals into distinct clusters confirming the presence of population admixture due to the long distance movement of the sexual ascospores. The present study has observed higher genetic diversity in both populations, this indicates that both regions are hot spot for the pathogen study and also can serve as site for germplasm evaluation. The information is very relevant for wheat breeders and pathologists to design and implement integrated management strategies.

Keywords: Genetic diversity, Population structure, and Simple sequence repeats