Identification and diversity of bovine major histocompatibility complex class II haplotypes in Japanese Black and Holstein cattle in Japan.

Bovine leukocyte antigen (BoLA), the major histocompatibility complex of cattle, is one of the most polymorphic gene clusters. We genotyped a population of 109 Japanese Black and 39 Holstein cattle to analyze their BoLA class II haplotypes, BoLA-DRB3 locus, 5 BoLA-DQA loci, and 5 BoLA-DQB loci. We identified 26 previously reported DRB3 alleles, 22 previously reported and 3 new DQA alleles, and 24 previously reported and 6 new DQB alleles. A dendrogram was constructed based on the predicted amino acid sequences of the α1 or β1 domains encoded by BoLA-DQA or -DQB alleles, which revealed that DQA alleles were clustered into 5 loci, whereas DQB alleles could not be clearly assigned to specific DQB loci. The BoLA-DRB3-DQA-DQB haplotypes were sorted by sequential analytical processes, and 42 distinct haplotypes, including 11 previously published haplotypes and 31 novel haplotypes, were defined. Strong linkage disequilibrium was present in the BoLA genes. We also compared DRB3-DQA1 haplotype frequencies between 507 Japanese Black and 143 Holstein cattle. Thirty-nine DRB3-DQA1 haplotypes were identified, including 29 haplotypes from Japanese Black and 22 haplotypes from Holstein cattle. The majority of the haplotypes could be identified in both breeds, although several haplotypes were identified in only a single breed. This is the first report presenting a detailed study of the BoLA class II haplotype in Japanese Black and Holstein cattle in Japan.