Towards identification of individual homologous chromosomes: comparative genomic hybridization and spectral karyotyping discriminate between paternaland maternal euchromatin in Mus musculus x M-spretus interspecific hybrids

We have developed an in situ technique to label individual euchromatic chro mosome arms in interspecific crosses between Mus musculus (MMU) and M. spre tus (MSP). The MMU and MSP genomes diverged 2-3 million years ago and show an overall sequence divergence of approximately 1 %. Comparative hybridizat ion of MMU versus MSP DNA and subsequent spectral analysis of the euchromat ic hybridization profiles discriminated between maternal (MMU) and paternal (MSP) chromosomes in F-1 hybrids. Dispersed repetitive DNA elements were t he 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 serve d as internal controls. Our experiments suggest that it is possible, in pri nciple, to discriminate between paternal and maternal chromosomes on the ba sis of sequence differences.