Identification of new major histocompatibility complex-B haplotypes in chinese broilers

MHC in chicken demonstrates a great range of variations. This study was conducted to investigate the major histocompatibility complex-B (MHC-B) variability in three representative broiler breeds with large breeding populations in China namely Arbor Acres (AA), 817 broilers (817), and Jinling Partridge (JL). The three Chinese broilers were analyzed with a subset of 89 SNPs in the MHC-B SNP panel. The genotypes of these SNPs were obtained using multiplex PCR targeted amplicon sequencing. The haplotypes were analyzed through a combination of manual and computational haplotype reconstruction methods using PHASE program. The phylogenetic tree was constructed based on haplotypes using MrBayes program. A total of 67 haplotypes were identified within three broilers populations, among which three haplotypes from the AA and 817 populations shared the standard MHC-B SNP (BSNP) haplotype. No matching haplotypes were detected in the JL population. Phylogenetic analysis based on these SNPs did not reveal clearly defined population clusters. This study reveals a high level of genetic diversity within the MHC-B region, highlighting the importance of this functionally significant genomic region in the three broilers. However, the observed genetic patterns indicate a complex relatedness structure among the three populations. These findings indicate the need for further investigation to better understand the evolutionary dynamics and functional implications of MHC-B variation.