Identification and comparative analysis of novel major histocompatibility complex-B haplotypes in Indonesian native chickens

다국어 초록 (Multilingual Abstract)

Objective: The major histocompatibility complex (MHC) is central to immunological protection. This study represents the 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), with 24, 17, 30, 16, 14, and 20 birds from each population, respectively. Samples were genotyped using the MHC-B single-nucleotide polymorphism (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 have been identified to be shared: BSNP-IND14 (KJM and STL populations), BSNP-IND26 (KJM, NNK, and MRG populations), and BSNP-IND31 (KJM and MRG populations). Accordingly, all haplotypes obtained from the GAG and PLG populations were unique. Phylogenetic analysis of the results did not reveal a distinct pattern for any population; nonetheless, three subclades were identified, with all six populations represented in each clade. A 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 known standard haplotypes, indicating that all Indonesian haplotypes identified in this study are novel. Furthermore, the comparison of Indonesian MHC-B haplotypes to 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 may have variation in immune responses.

다국어 초록 (Multilingual Abstract)

Objective: The major histocompatibility complex (MHC) is central to immunological pro tection. This study represents the 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), with 24, 17, 30, 16, 14, and 20 birds from each population, respectively. Sam ples were genotyped using the MHC-B single-nucleotide polymorphism (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 have been identified to be shared: BSNP-IND14 (KJM and STL populations), BSNP-IND26 (KJM, NNK, and MRG populations), and BSNP-IND31 (KJM and MRG populations). Accord ingly, all haplotypes obtained from the GAG and PLG populations were unique. Phyloge netic analysis of the results did not reveal a distinct pattern for any population; nonetheless, three subclades were identified, with all six populations represented in each clade. A com parison of MHC-B haplotypes in Indonesian native chickens with MHC-B standard hap lotypes shows no distinct clades; however, three possible subclades were also identified.
Nevertheless, no Indonesian MHC-B haplotypes matched 100% with the known standard haplotypes, indicating that all Indonesian haplotypes identified in this study are novel. Fur thermore, the comparison of Indonesian MHC-B haplotypes to those from other Asian regions reveals that the majority of Indonesian haplotypes cluster with those from Bangla desh, suggesting a shared evolutionary background among South and Southeast Asian chickens.
Conclusion: This study identified unique MHC-B haplotypes in Indonesian native chick ens, suggesting that the observed populations are diverse in the MHC-B region and may have variation in immune responses.