Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici

•We have constructed Z. tritici ku70 and ku80 null mutants.•Gene targeting frequency in the ku null strains is greater than 85%.•Deletion of KU70 and KU80 does not affect in vitro growth or pathogenicity.•Sulfonylurea resistance was established as a new positive selection marker in Z. tritici.•Ternary vectors were constructed to enable yeast recombinational cloning in Z. tritici.