B1 insertions as easy markers for mouse population studies.

Few simple, easy-to-score PCR markers are available for studying genetic variation in wild mice populations belonging to Mus musculus at the population and subspecific levels. In this study, we show the abundant B1 family of short interspersed DNA elements (SINEs) is a very promising source of such markers. Thirteen B1 sequences from different regions of the genome were retrieved on the basis of their high degree of homology to a mouse consensus sequence, and the presence of these elements was screened for in wild derived mice representing M. spretus, macedonicus and spicilegus and the different subspecies of M. musculus. At five of these loci, varying degrees of insertion polymorphism were found in M. m. domesticus mice. These insertions were almost totally absent in the mice representing the other subspecies and species. Six other B1 elements were fixed in all the Mus species tested. At these loci, polymorphism associated with three restriction sites in the B1 consensus sequence was found in M. musculus. Most of these polymorphisms appear to be ancestral as they are shared by at least one of the other Mus species tested. Both insertion and restriction polymorphism revealed differences between five inbred laboratory strains considered to be of mainly domesticus origin, and at the six restriction loci a surprising number of these strains carried restriction variants that were either not found or very infrequent in domesticus. This suggests that in this particular group of loci, alleles of far Eastern origin are more frequent than expected.