Avian

Genetic Characterization of the Chicken TAPBP Gene and Its Haplotypic Association with BF2 in the Major Histocompatibility Complex

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Abstract

In chickens, the TAPBP (Tapasin) gene encodes the key chaperone in the peptide-loading complex, linking TAP1/TAP2 and BF2 genes to stabilize and edit peptides for optimal MHC class I binding. Genetic variation in TAPBP is expected to affect peptide loading efficiency and MHC class I repertoire formation, making TAPBP haplotype identification important for understanding functional diversity in the chicken MHC-B region. This study aimed to characterize the TAPBP gene in Korean native chickens (KNC), identify novel allelic variants, and assess whether identical MHC-B haplotypes for BF2 gene share corresponding TAPBP counterparts. 36 KNC samples were analyzed, representing six populations: Gray-brown, Black, Red-brown, White, Yellow-brown, and Yeonsan Ogye. gDNA was extracted from blood samples and analyzed using the BSNP panel developed by Fulton et al. (2016) and the LEI0258 marker. Homozygous samples for both BSNP haplotypes and LEI0258 allele sizes were grouped. Sanger sequencing of TAPBP exons 3-8 was performed, and assembled sequences (Geneious Prime v2024.0.7) were compared with reference MHC-B and TAPBP haplotypes. Haplotype and nucleotide diversity were analyzed using R, with haplotype diversity calculated via the "ape", "pegas", and "seqinr" packages, and nucleotide diversity estimated using "ape" and "pegas". Haplotype diversity was assessed at both nucleotide and amino acid levels by defining sequence groups based on pairwise identity thresholds of 99-100%. The calculated haplotype diversity for TAPBP was 0.92698, indicating high variation. Overall nucleotide diversity was 0.00892, with exon 5 showing the highest diversity (0.010587). Comparison with reference haplotypes revealed multiple TAPBP nucleotide and amino acid sequence groups, reflecting substantial haplotypic diversity in KNCs. Several TAPBP sequences were identical to reference TAPBP haplotypes, including Tapasin*02 and *12, at both the nucleotide and amino acid levels. Due to the limited number of reference TAPBP haplotypes, TAPBP diversity was also assessed using MHC-B haplotypes. Complete sequence identity was observed for the B9 haplotype at the nucleotide level. At the amino acid level, B2, B5, B6, B8, B9, B11, B12, B19, B23, and B24 had identical MHC-B haplotype sequences, with complete identity between B6 and B24, B12 and B19, and among B5, B8, and B11. A total of seven novel variants were identified across exons 3-6, of which two were nonsynonymous. BF2 gene sequencing previously conducted on these samples confirmed 100% identity to the reference B6 and B9 haplotypes. These identical MHC-B haplotype samples were then used to assess the association between the BF2 and TAPBP genes. Notably, all BF2 B9 haplotypes corresponded to their TAPBP B9 counterparts, while BF2 B6 haplotypes showed non-identical TAPBP sequences, suggesting allelic diversification within the same haplotype. In conclusion, although the TAPBP gene showed strong conservation with few novel polymorphisms, haplotype-specific patterns suggest potential differences in BF2-TAPBP compatibility, which may ultimately influence peptide-loading efficiency.

Keywords: 2026

How to Cite:

Fernando, R., Agulto, T., Cho, E., Kim, J., van Hateren, A. & Lee, J., (2026) “Genetic Characterization of the Chicken TAPBP Gene and Its Haplotypic Association with BF2 in the Major Histocompatibility Complex”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286178. doi: https://doi.org/10.31274/wcgalp.23871

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