Y-encoded, species-specific DNA in mice: evidence that the Y chromosome exists in two polymorphic forms in inbred strains

We have investigated the structure of the murine Y chromosome by first developing a novel method for specifically cloning Y-encoded DNA and then generating a library enriched for Y-specific DNA sequences. Three randomly chosen Y DNA clones were studied and found to share several interesting properties: all three are members of small Y-specific multisequence families; all three are mouse-specific; and all three probes detect Y-encoded restriction fragments that are polymorphic. Examination of polymorphic Y chromosome restriction fragments in male DNA from nine different inbred strains suggests that only two polymorphic forms of Y chromosomal DNA exist among inbred strains of mice.