Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Identification and comparative analysis of novel major histocompatibility complex-B haplotypes in Indonesian native chickens

  • Roshani Fernando (Department of Animal Science, Chungnam National University) ;
  • Trisha Nicole Agulto (Department of Animal Science, Chungnam National University) ;
  • Prabuddha Manjula (Department of Animal Science, Uva Wellassa University) ;
  • Minjun Kim (Department of Animal Science, Chungnam National University) ;
  • Eunjin Cho (Department of Bio-AI Convergence, Chungnam National University) ;
  • Jaewon Kim (Department of Animal Science, Chungnam National University) ;
  • Fatmawati Mustofa (Department of Animal Science, Universitas Diponegoro) ;
  • Dyah Maharani (Department of Animal Breeding and Reproduction, Universitas Gadjah Mada) ;
  • Jun Heon Lee (Department of Animal Science, Chungnam National University)
  • Received : 2025.11.03
  • Accepted : 2026.02.08
  • Published : 2026.06.01
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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.

Keywords

Acknowledgement

This research was funded by a grant from the National Research Foundation, Republic of Korea (grant number RS-2025-16072125).

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