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.

Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class IIBoLA‐DRB3 allele

“…Those same alleles were also detected in the Hereford × Jersey crossbreed at high frequencies (12.0% and 14.8%, respectively) (Table ). DRB3*4501 was rarely detected in other groups in this and other studies . Figure A also shows that Hereford was characterized by a low PC2 value, which was strongly influenced by the frequencies of BoLA‐DRB3*1601 and DRB3*3202 .…”

BOLA‐DRB3 gene polymorphisms influence bovine leukaemia virus infection levels in Holstein and Holstein × Jersey crossbreed dairy cattle

“…; Takeshima et al . ). In Holstein × Jersey animals (0–50% Holstein) five alleles reached >5% frequency ( DRB3*0101, *1101, *1201, *1501 and *2703 ), and the same alleles had high frequencies in the 75–100% Holstein group as well (Table ).…”

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

“…It is worth noting that a review of the IPD-MHC database showed that some variants had been previously detected in other Asian breeds (BoLA-DRB3*031:03, *058:01 and *064:02 in Chinese yellow cattle , BoLA-DRB3*013:03 in Korean Hanwoo cattle and BoLA-DRB3*049:01 in the Indian Red Sindhi); African Zebu breeds (BoLA-DRB3*038:01 in Ethiopian Arsi and BoLA-DRB3*013:03 in Sudanese Baggara) and other Asian Bos species, including BoLA-DRB3*013:03 in Indonesian Bos javanicus . In previous studies privative alleles were also identi ed in native breeds from Asia and South America [21,26,28]. In addition, some alleles detected in Creole cattle have also been detected in African breeds (Boran, N´Dama, Ethiopian Arsi, and Gudali) and Bos indicus (Brahman).…”

“…As a result of these studies there are 144 described BoLA-DRB3 alleles for bovines, and 303 subtypes listed in the Immuno Polymorphism Database (IPD-MHC) [30,31]. In addition, previous studies [16][17][18][19][20][21][22][23][24][25][26][27] have shown an even distribution of BoLA-DRB3 polymorphisms between the major bovine types (Bos taurus and B. indicus) and breeds. This is likely as a result of various factors including breed origin, arti cial or natural selection and geographical distribution.…”