Identification and Comparative Analysis of Novel Major Histocompatibility Complex-B Haplotypes in Indonesian Native Chickens

Objective: The Major Histocompatibility Complex (MHC) is central to immune defense.This study represents the first assessment of MHC-B haplotype diversity in Indonesian native chickens.Methods: Six Indonesian native chicken populations were selected as study populations: Merawang (MRG), Pelung (PLG), Black Kedu (KJM), Sentul (STL), Nunukan (NNK), and Gaga (GAG); 24, 17, 30, 16, 14, and 20 birds from each population, respectively.Samples were genotyped using the MHC-B SNP panel.To explore haplotype diversity, the results were analyzed using PHASE 2.1 software. Results: Genotyping of six Indonesian native chicken populations revealed high haplotype diversity, with a total of 126 distinct haplotypes: 38, 25, 19, 21, 11, and 12 from the MRG, PLG, KJM, STL, NNK, and GAG populations, respectively.Three haplotypes were shared: BSNP-IND14, shared by the KJM and STL populations; BSNP-IND26, shared by the KJM, NNK, and MRG populations; and BSNP-IND31, shared by the KJM and MRG populations.Accordingly, all the haplotypes obtained from the GAG and PLG populations were unique.Phylogenetic analysis of the results did not reveal a distinct pattern for each population; however, three subclades were identified, with all six populations represented in each clade.Comparison of MHC-B haplotypes in Indonesian native chickens with MHC-B standard haplotypes shows no distinct clades; however, three possible subclades were also identified.Nevertheless, no Indonesian MHC-B haplotypes matched 100% with the reported standard haplotypes, indicating that all Indonesian haplotypes identified in this study are novel.Furthermore, the comparison of Indonesian MHC-B haplotypes with those from other Asian regions reveals that the majority of Indonesian haplotypes cluster with those from Bangladesh, suggesting a shared evolutionary background among south and Southeast Asian chickens.Conclusion: This study identified unique MHC-B haplotypes in Indonesian native chickens, suggesting that the observed populations are diverse in the MHC-B region and potentially have variation in immune responses.