This study used a single-nucleotide polymorphism (SNP) panel to characterise the diversity in the major histocompatibility complex B region (MHC-B) in 12 chicken populations in Korea. Samples were genotyped for 96 MHC-B SNPs using an Illumina GoldenGate genotyping assay. The MHC-B SNP haplotypes were predicted using 58 informative SNPs and a coalescence-based Bayesian algorithm implemented by the PHASE program and a manual curation process. In total, 117 haplotypes, including 24 shared and 93 unique haplotypes, were identified. The unique haplotype numbers ranged from 0 in Rhode Island Red to 32 in the Korean native commercial chicken population 2 (“Hanhyup-3ho”). Population and haplotype principal component analysis (PCA) indicated no clear population structure based on the MHC haplotypes. Three haplotype clusters (A, B, C) segregated in these populations highlighted the relationship between the haplotypes in each cluster. The sequences from two clusters (B and C) overlapped, whereas the sequences from the third cluster (A) were very different. Overall, native breeds had high genetic diversity in the MHC-B region compared with the commercial breeds. This highlights their immune capabilities and genetic potential for resistance to many different pathogens.

这项研究使用单核苷酸多态性（SNP）面板来表征韩国12个鸡群主要组织相容性复合体B区（MHC-B）的多样性。使用Illumina GoldenGate基因分型分析对96个MHC-B SNP进行基因分型。MHC-B SNP单倍型使用58种信息性SNP和PHASE程序实现的基于聚结的贝叶斯算法以及手动管理过程进行预测。总共鉴定出117种单倍型，包括24种共有单倍型和93种独特单倍型。独特的单倍型编号范围从罗德岛红岛的0到韩国本地商业鸡种群2（“ Hanhyup-3ho”）的32。人口和单倍型主成分分析（PCA）表明，基于MHC单倍型没有明确的人口结构。三个单体型簇（A，B，C）这些人群中的隔离突出了每个群集中单倍型之间的关系。来自两个聚类（B和C）的序列重叠，而来自第三聚类（A）的序列非常不同。总体而言，与商业品种相比，MHC-B地区的本地品种具有较高的遗传多样性。这突出了它们对许多不同病原体的抵抗力的免疫能力和遗传潜力。