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The dominant hemimelia (Dh) mutation causes various developmental abnormalities in mice. Most -Dh/+ males, crosses between DDD females and DH-Dh/+ males, have lethal abnormalities during the neonatal period. This is a consequence of synergism among three independent gene loci; that is, the Dh allele on chromosome (Chr) 1, the DDD allele on an X Chr-linked locus, and a Y Chr-linked locus in some strains. With regard to the Y Chr derived from Mus musculus musculus (M. m. musculus), the Y Chrs of C57BL/6J and BALB/cA caused lethality, but the Y Chr of C3H/HeJ did not, suggesting that not all M. m. musculus Y Chrs are the same. In the present study, whether Y Chrs derived from M. m. domesticus and M. m. castaneus could cause lethality was investigated. Among seven inbred strains, including AKR/J, DDD, RF/J, SJL/J, SWR/J, TIRANO/Ei, and CAST/Ei, Y Chrs of AKR/ J, DDD, SJL/J, SWR/J, and TIRANO/Ei caused lethality, but Y Chrs of RF/J and CAST/Ei did not. It was unlikely that the mitochondrial genome of the DDD strain contributed to the lethality. The X Chr-linked locus could not compensate for the role of the Y Chr-linked locus. These results suggest that not all M. m. domesticus Y Chrs are the same.