Using a bioinformatics approach, we developed 18 variable number of tandem repeat markers for Aspergillus oryzae for use in population genetic studies. Repeat sequences in the genome sequences of A. oryzae were identified by a tandem repeat finding program. Length polymorphisms at 18 loci were examined in 41 strains of A. oryzae. The total number of alleles per locus ranged from two to 20. Investigation of cross-species amplifications with A. sojae and A. tamarii showed success. The variable number of tandem repeat markers will be used to determine the population structure of these three Aspergillus species used in brewing.
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