Trace of native cattle in Japanese Holstein assessed by mitochondrial DNA sequence polymorphism

On the basis of sequence variation in the displacement loop region of mtDNA, 588 Japanese and North American Holstein cows were classified into 5 mitochondrial haplotypes, which were found in Japanese Black cattle. One of the haplotypes (named type 1), which was present at the highest frequency in Japanese Black cattle, was not observed in either European or African cattle. This haplotype is characterized by 2 single-nucleotide polymorphisms. One is called the type B polymorphism, and it refers to a base change from T to C at nucleotide 16042 of the mitochondrial genome (T160042C). The other is called the type I polymorphism, and it refers to the base change as G16093A. The proportion of the Japanese Holstein population with both polymorphisms was 18.3%, whereas none of the North American cows had this genotype. Because the mitochondrial types were inherited maternally, it is clear that a considerable number of Japanese Holstein cows are descended from native Japanese cattle. Polymorphisms B and I accounted for no variance in the estimated breeding value for milk production among cows from the Hyogo herd (582 cows) or the Chiba region herd (758 cows). This result suggests that most autosomal genes of native animals have been successively replaced by those of pure Holstein after grading up of over 15 generations, even though resulting animals have native animal-oriented mitochondrial types and may still have some number of the native autosomal genes.