ABSTRACTThe potential for sexual reproduction inAspergillus oryzaewas assessed by investigating the presence and functionality ofMATgenes. Previous genome studies had identified aMAT1-1gene in the reference strain RIB40. We now report the existence of a complementaryMAT1-2gene and the sequencing of an idiomorphic region fromA. oryzaestrain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of theMAT1-1andMAT1-2genotypes among 180 strains assayed, including industrialtane-kojiisolates. Strains used for sake and miso production showed a near-1:1 ratio of the MAT1-1 and MAT1-2 mating types, whereas strains used for soy sauce production showed a significant bias toward the MAT1-2 mating type. MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and gene expression was compared by DNA microarray and quantitative real-time PCR (qRT-PCR) methodologies under conditions in whichMATgenes were expressed. Thirty-three genes were found to be upregulated more than 10-fold in either the MAT1-1 host strain or the MAT1-2 gene replacement strain relative to each other, showing that both theMAT1-1andMAT1-2genes functionally regulate gene expression inA. oryzaein a mating type-dependent manner, the first such report for a supposedly asexual fungus.MAT1-1expression specifically upregulated an α-pheromone precursor gene, but the functions of most of the genes affected were unknown. The results are consistent with a heterothallic breeding system inA. oryzae, and prospects for the discovery of a sexual cycle are discussed.