<p>Enzootic bovine leukosis is the most common neoplastic disease in cattle caused by the bovine leukemia virus (BLV). Previous studies have shown that allele type in the DRB3 region of the bovine major histocompatibility complex (bovine leukocyte antigen: BoLA in cattle) is associated with resistance or susceptibility to infectious diseases. The Japanese brown (JBR) cattle have a genetic background of small population size, and thus, may exhibit different susceptibility to diseases compared with other cattle breeds. In the present study, we analyzed the diversity of the BoLA-DRB3 gene and attempted to clarify the genetic composition of the Kumamoto and Kochi strains belonging to the JBR.</p><p>Allele typing of the BoLA-DRB3 gene of 184 JBR detected 16 and 13 alleles in the Kumamoto and Kochi strains, respectively. The analysis of the observed (Ho) and expected (He) heterozygosity of the JBR based on allele frequencies, as well as Fis (using Ho and He), which indicates the inbreeding coefficient within a population, showed each population to have different BoLA-DRB3 gene diversities. Consequently, the degree of genetic difference among the populations (Fst) was analyzed based on the allele frequencies of the BoLA-DRB3 gene. The results showed the JBR populations to be genetically closer to the native Philippine and Myanmar cattle populations than the Japanese black, Japanese Shorthorn, Holstein or Jersey population. Furthermore, the proportions of cattle with at least on allele, which was reported to be associated with low proviral load (PVL) on infection of BLV, were 15.7% (20/127) and 63.1% (37/57) in Kumamoto and Kochi strain, respectively, and showed a significant difference. In the future, the direct evaluation of the BoLA-DRB3 gene allele types and PVL in BLV-infected individual cattle is warranted. In addition, the PVL of BLV-infected JBR of the Kumamoto strain is known to be lower than that of other breeds in Japan. Therefore, it is necessary to investigate the possibility of a different mechanism on PVL regulation from allele types.</p><p>The results of BoLA-DRB3 gene diversity and allele frequency analysis indicate that the JBR has a different genetic background from the Japanese black and the Shorthorn populations and possesses low PVL-associated alleles. Further studies are needed to analyze the relationship between PVL and BoLA-DRB3 gene in JBR to clarify the susceptibility of JBR to BLV.</p>