title: The great diversity of major histocompatibility complex class II genes in Philippine native cattle.
abstract: Bovine leukocyte antigens (BoLA) are extensively used as markers for bovine disease and immunological traits. However, none of the BoLA genes in Southeast Asian breeds have been characterized by polymerase chain reaction (PCR)-sequence-based typing (SBT). Therefore, we sequenced exon 2 of the BoLA class II DRB3 gene from 1120 individual cows belonging to the Holstein, Sahiwal, Simbrah, Jersey, Brahman, and Philippine native breeds using PCR-SBT. Several cross-breeds were also examined. BoLA-DRB3 PCR-SBT identified 78 previously reported alleles and five novel alleles. The number of BoLA-DRB3 alleles identified in each breed from the Philippines was higher (71 in Philippine native cattle, 58 in Brahman, 46 in Holstein × Sahiwal, and 57 in Philippine native × Brahman) than that identified in breeds from other countries (e.g., 23 alleles in Japanese Black and 35 in Bolivian Yacumeño cattle). A phylogenetic tree based on the DA distance calculated from the BoLA-DRB3 allele frequency showed that Philippine native cattle from different Philippine islands are closely related, and all of them are closely similar to Philippine Brahman cattle but not to native Japanese and Latin American breeds. Furthermore, the BoLA-DRB3 allele frequency in Philippine native cattle from Luzon Island, located in the Northern Philippines was different from that in cattle from Iloilo, Bohol, and Leyte Islands, which are located in the Southern Philippines. Therefore, we conclude that Philippine native cattle can be divided into two populations, North and South areas. Moreover, a neutrality test revealed that Philippine native cattle from Leyte showed significantly greater genetic diversity, which may be maintained by balancing selection. This study shows that Asian breeds have high levels of BoLA-DRB3 polymorphism. This finding, especially the identification of five novel BoLA-DRB3 alleles, will be helpful for future SBT studies of BoLA-DRB3 alleles in East Asian cattle.
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan ; Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: S N
authors.initials: SN
authors.lastname: Takeshima
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Miyasaka
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Polat
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Kikuya
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Matsumoto
authors.affiliation: Philippine Carabao Center, Science City of Munoz, 3120 Nueva Ecija, Philippines.
authors.forename: C N
authors.initials: CN
authors.lastname: Mingala
authors.affiliation: Philippine Carabao Center, Science City of Munoz, 3120 Nueva Ecija, Philippines.
authors.forename: M A
authors.initials: MA
authors.lastname: Villanueva
authors.affiliation: Animal and Dairy Sciences Cluster, College of Agriculture, University of the Philippines - Los Baños, Los Baños 4030, Laguna, Philippines.
authors.forename: A J
authors.initials: AJ
authors.lastname: Salces
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Onuma
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan ; Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Aida
keywords: Allele frequency; BoLA, bovine MHC; BoLA-DRB3 allele; Cattle breed; HLA, human leukocyte antigen.; MHC, major histocompatibility complex; Major histocompatibility complex; PCR, polymerase chain reaction; Philippine; Population tree; SBT, sequence-based typing; Sequence-based typing