Polymorphic regions of mitochondrial (mt) DNA displacement loop (D-loop) region from Japanese Black, Japanese Brown and Holstein breeds were analyzed by PCR mediated single strand conformation polymorphism (PCR-SSCP) method and PCR direct-sequencing to distinguish these breeds. The sample population comprised 25 Japanese Black cows, 16 Japanese Brown cows, 6 Holstein cows, which were showed 5, 4 and 3 types, respectively, by PCR-SSCP of polymorphic region (308 bp) in D-loop. It was difficult to distinguish among these breeds by this method, however, sequence differences could be detected briefly. We sequenced a portion of polymorphic region in D-loop (385 bp) of 4 Japanese Black cows, 2 Japanese Brown cows and 3 Holstein cows which were different SSCP types. The resulting sequences were compared to those in the literature for the European, African Zebu and Asian Zebu lineage. Each DNA sequences showed from 1 to 4 substitutions, respectively. However, the results showed no specific breed changes. A comparison of these results to those in the literature showed that the three breeds were same lineage as European and African breeds, but not to be of the same lineage with Asian Zebu. The polymorphic region in mtDNA D-loop was too variable in a breed to allow distinguishing among Japanese Black, Japanese Brown and Holstein.
