Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depression for insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3214 horses (187 genotyped), we used a generalised linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1368 records). In addition to the classical pedigree information, we used the single-step approach that enabled joint use of pedigree and genomic information to estimate inbreeding depression overall genome and equine leucocyte antigen (ELA) class II region. Significant inbreeding depression was observed in all models fitting overall inbreeding coefficients (odds ratio between 1.018 and 1.074, P < 0.05) with the exception of Kalinowski’s new inbreeding (P = 0.0516). The increase of ELA class II inbreeding was significantly associated with increased prevalence of IBH (odds ratio 1.018; P = 0.027). However, when fitted jointly with the overall inbreeding coefficient, the effect of ELA class II inbreeding was not significant (odds ratio 1.016; P = 0.062). Overall, the higher ELA class II and/or overall inbreeding (pedigree or genomic) was associated with increased prevalence of IBH in Old Kladruber horses. The single-step approach provides an efficient use of all the available pedigree, genomic, and phenotype information for estimation of overall and regional inbreeding effects.

中文翻译：

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近交和区域马白细胞抗原纯合性与老克拉德鲁伯马昆虫叮咬过敏流行的关系

近交衰退是由近亲交配引起的性能下降。在牲畜种群中，近交衰退传统上是通过表型对谱系近交系数的回归来估计的。这种估计可以通过利用基因组近亲繁殖系数来改进。在这里，我们估计了老克拉德鲁伯马中昆虫叮咬过敏症 (IBH) 流行率的近交抑制，这是世界上最常见的过敏性马病。在 3214 匹马（187 只基因分型）的深度谱系中，我们使用广义线性混合模型，其中 IBH 表型来自 1996 年至 2009 年间检查的 558 匹马（1368 条记录）。除了经典的血统信息，ELA ) II 类区域。 除了 Kalinowski 的新近交 ( P  = 0.0516)外，在拟合整体近交系数的所有模型中都观察到了显着的近交衰退（优势比在 1.018 和 1.074 之间，P < 0.05 ）。的增加ELA II类近亲繁殖与IBH的患病率增加了显著相关联（比值比1.018; P  = 0.027）。然而，当与整体近交系数一起拟合时，ELA II 类近交的影响不显着（优势比 1.016；P  = 0.062）。总体而言，较高的ELA 等级 II和/或整体近亲繁殖（谱系或基因组）与老克拉德鲁伯马 IBH 的患病率增加有关。一步法可以有效利用所有可用的谱系、基因组和表型信息，以估计整体和区域近亲繁殖效应。