To understand better the differences related to manufacturers’ koji making methods, we evaluated the environment during koji making using trays or boxes, and assessed the qualities of the resulting koji at the measured locations. During koji making using boxes, spatial temperature in the box was lower than the koji temperature, whereas during koji making using trays, spatial temperature in the tray was similar to the koji temperature. Moreover, the spatial humidity in the tray was higher than that in the box. These differences were considered to affect the koji qualities. The water content in koji made using trays was higher than that in koji made using boxes. Enzyme activities, mycelium content, and mycelial growth level on rice（haze） in koji made using boxes were higher than those in koji made using trays. However, the glucoamylase to α-amylase activity ratio in koji made using trays was higher than that in koji made using boxes. This study showed the differences in the environment during koji making with trays and boxes.

In Mie Prefecture, five sake yeast strains（MK1, MK3, MK5, MK7, and MLA12） have been developed and are widely used by local breweries. We comprehensively investigated the genetic and brewing characteristics of these Mie sake yeast strains to reveal their properties in detail. Ploidy estimation revealed that MK1, MK3, MK5, and MLA12 were diploid, but MK7 was tetraploid. Genotyping of RIM15^5067ins indicated that all Mie sake yeast strains belong to the K7 group. The results of electrophoretic karyotype and whole-genome analysis indicated that MK1 and MK3 are in the K10 lineage, while MK5 and MK7 are in the K9 lineage. Chromosomal aneuploidy estimation revealed that MK3 had trisomy of Chr.3 and Chr.10, while MLA12 had trisomy of Chr. 3. The determination of the genotype of FAS2^G3748A and LEU4^C1652T revealed that MK3 had the FAS2 variant homozygously, MK7 and MLA12 had it heterozygously, and MLA12 had the LEU4 variant heterozygously. Compared brewing characteristics of small-scale sake brewing test roughly reflected their genomic background, and principal component analysis revealed the difference in brewing characteristics of each yeast strain. Moreover, products fermented by MK7 and MLA12 showed a unique character.