The assembly of whole genomes by long-read sequencing has enabled the collection of resolved telomere-to-telomere (T2T) haplotypes, encouraging genome-wide approaches to study structural variations. Unlike comparative genomics approaches based on gene content or other types of annotation (transposable elements), the analysis of structural variants in genome-wide analysis is now commonly based on graph-oriented approaches. The pangenome graphs (PGG) are capable of storing the full genetic diversity of the genomes under study, achieving superior performance in read alignment, variant identification and genotyping for population studies. We propose to establish a pangenome graph for Zymoseptoria tritici with the available genomic sequences as well as 2 new assemblies of strains isolated on durum wheat (T. turgidum var. durum). Our goal is to evaluate the use of PGG instead of linear-reference genome for GWAS and GEA analyses and implement process to modify and improve the graph with upcoming new data. Establishing a shared reference PGG based on FAIR principles could be valuable to the community, such as the IPO323 reference genome. In addition, same analyses will be carried out with Pyricularia oryzae to validate the method and propose a common framework for other fungal species. We will present our first results on the establishment of graphs and the detections of variants compared to previous results obtained from single reference genome.