Molecular Characterization of BoLA-DRB3 Exon 2 Reveals Sequence Polymorphism and Phylogenetic Relationships in Bali Cattle (Bos javanicus domesticus)

Abstract

Polymorphisms within the major histocompatibility complex (MHC) class II, particularly the BoLA-DRB3 locus, play a critical role in immune function and disease resistance in cattle. However, the genetic diversity of this locus in Bali cattle (Bos javanicus domesticus), an indigenous Indonesian genetic resource, remains poorly characterized. This study aimed to investigate genetic diversity at the BoLA-DRB3 locus in Bali cattle through sequence polymorphism and phylogenetic analyses. Blood samples were collected from eight male Bali cattle maintained at the Denpasar Breeding Center and Forage Research Station (BPTU-HPT Denpasar) for Bali Cattle, Bali Province, Indonesia. High-quality DNA was successfully obtained from all animals, and six samples were selected for Sanger sequencing based on DNA quality. The BoLA-DRB3 exon 2 region was amplified using a newly designed primer pair, generating the expected 496-bp PCR product. Sequence alignment and phylogenetic analyses were performed using Clustal Omega, BioEdit, and MEGA XII. Sequence analysis identified several single nucleotide polymorphisms (SNPs) among the analyzed samples, indicating the presence of genetic variation within the BoLA-DRB3 locus. Phylogenetic reconstruction clustered the Bali cattle sequences with the same major clade as Bos indicus and Bos taurus reference sequences, with a mean genetic distance of 0.055 among the analyzed samples. These findings provide preliminary evidence of genetic variation in the BoLA-DRB3 of Bali cattle and establish a foundation for future studies investigating the association of BoLA-DRB3 polymorphisms with immune function, disease resistance, and adaptive genetic potential in this indigenous breed

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