We have developed an in situ technique to label individual euchromatic chromosome arms in interspecific crosses between Mus musculus (MMU) and M. spretus (MSP). The MMU and MSP genomes diverged 2–3 million years ago and show an overall sequence divergence of approximately 1%. Comparative hybridization of MMU versus MSP DNA and subsequent spectral analysis of the euchromatic hybridization profiles discriminated between maternal (MMU) and paternal (MSP) chromosomes in F1 hybrids. Dispersed repetitive DNA elements were the preferred hybridization target of MMU DNA on maternal chromosomes and of MSP DNA on paternal chromosomes. Differences in centromeric satellite DNAs were detected by conventional fluorescence in situ hybridization and served as internal controls. Our experiments suggest that it is possible, in principle, to discriminate between paternal and maternal chromosomes on the basis of sequence differences.

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