Arbitrary primer PCR of dog DNA with estimates of average heterozygosity.

Arbitrary primer polymerase chain reaction (AP-PCR) detected anonymous DNA polymorphisms between individual representatives of seven breeds of dogs, between members of a single breed, and between members of a single family of dogs. Short arbitrary sequence PCR primers and promoter/protein motif sequence primers typically amplified 15-30 bands ranging from 200-2000 bp in length. The average heterozygosity of 10 line bred Belgian sheepdogs (H = 0.024 +/- 0.011, mean +/- 95% CI) was significantly lower than that of a panel of unrelated beagles (H = 0.057 +/- 0.018, mean +/- 95% CI, P < .01). The average heterozygosity of a seven-breed panel was intermediate between the two (H = 0.043 +/- 0.011, mean +/- 95% CI) and not significantly different than either panel. One motif sequence PCR primer pair yielded products that strongly differentiated between Belgian sheepdogs, beagles, and members of five other breeds. AP-PCR could be used to generate DNA fingerprints that distinguish between dog breeds, as well as to provide markers in this sparsely mapped genome.