The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species’ successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama. We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked. Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.

中文翻译：

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白尾鹿（Odocoileus virginianus）中两个MHC II基因（DOB，DRB）的特征。

主要的组织相容性复合体（MHC）负责检测和处理体内的外来病原体。尽管MHC基因的一般结构在哺乳动物物种中相对保守，但反刍动物之间的显着差异是由于染色体倒置将MHC II型基因分为两个子区域（IIa，IIb）。据报道，这些次区域之间的重组率很高，而且国内反刍动物缺乏联系。然而，尚未有研究检查野生反刍动物中这些亚区域之间的联系程度。白尾鹿（Odocoileus virginianus）是Cervidae家族的一种常见反刍动物，习惯上在其自然环境中受到病原体的困扰（例如Haemonchus contortus，Elaeophora）。由于MHC单倍型与疾病易感性之间存在关联，深入了解MHC多态性和MHC基因之间的联系可以进一步帮助该物种的成功管理。我们在MiSeq平台上从位于阿拉巴马州的封闭白尾鹿种群中测序了MHC-DRB外显子2（IIa）和MHC-DOB外显子2（IIb）。我们确定了12个新的MHC-DRB等位基因，并重新采样了7个等位基因，这与其他已发布的等位基因一起，使MHC-DRB外显子2的白尾鹿的已记录等位基因总数达到30。尾鹿发现非典型MHC基因的多态性（11个等位基因）明显较少。虽然发现MHC-DRB处于阳性，多样化选择之下，但发现MHC-DOB处于白尾鹿的纯化选择之下。我们发现MHC-DRB和MHC-DOB之间没有明显的连锁不平衡，这表明这些基因座不太可能紧密相连。总体而言，这项研究确定了12个新的MHC-DRB外显子2等位基因，并为白尾鹿确定了一个新的非经典MHC II基因（MHC-DOB）。我们还发现这两个基因座之间缺乏明显的连锁关系，这支持了反刍动物MHC II型基因区域内染色体倒置的先前发现，并表明白尾鹿可能在这些MHC区域之间具有类似于该区域的重组热点。被发现为金牛座。