The chicken major histocompatibility complex (MHC, also known as the BF-BL region of the B locus) is notably small and simple with few genes, most of which are involved in antigen processing and presentation. There are two classical class I genes, of which only BF2 is well and systemically expressed as the major ligand for cytotoxic T lymphocytes (CTLs). The other class I gene, BF1, is believed to be primarily a natural killer (NK) cell ligand. Among most standard chicken MHC haplotypes examined in detail, BF1 is expressed tenfold less than BF2 at the RNA level due to defects in the promoter or in a splice site. However, in the B14 and typical B15 haplotypes, BF1 RNA was not detected, and here, we show that a deletion between imperfect 32 nucleotide direct repeats has removed the BF1 gene entirely. The phenotypic effects of not having a BF1 gene (particularly on resistance to infectious pathogens) have not been systematically explored, but such deletions between short direct repeats are also found in some BF1 promoters and in the 5′ untranslated region (5′UTR) of some BG genes found in the BG region of the B locus. Despite the opposite transcriptional orientation of homologous genes in the chicken MHC, which might prevent the loss of key genes from a minimal essential MHC, it appears that small direct repeats can still lead to deletion.

鸡主要组织相容性复合体（MHC，也称为 B 基因座的 BF-BL 区域）特别小且简单，基因很少，其中大部分参与抗原加工和呈递。有两种经典的 I 类基因，其中只有 BF2 作为细胞毒性 T 淋巴细胞 (CTL) 的主要配体得到良好且系统的表达。另一个 I 类基因 BF1，被认为主要是自然杀伤 (NK) 细胞配体。在详细检查的大多数标准鸡 MHC 单倍型中，由于启动子或剪接位点的缺陷，BF1 在 RNA 水平上的表达量比 BF2 低十倍。然而，在 B14 和典型的 B15 单倍型中，未检测到 BF1 RNA，在这里，我们表明不完美的 32 个核苷酸同向重复之间的删除已完全删除了 BF1 基因。没有 BF1 基因的表型效应（特别是对感染性病原体的抵抗力）尚未得到系统探索，但在一些 BF1 启动子和 5' 非翻译区 (5'UTR) 中也发现了短同向重复序列之间的此类缺失。在 B 基因座的 BG 区域中发现了一些 BG 基因。尽管鸡 MHC 中同源基因的转录方向相反，这可能会防止最小必需 MHC 中关键基因的丢失，但小型同源重复似乎仍然会导致缺失。