Czech University of Life Sciences, Kamycka 129, Prague, 16500, Czech Republic.
Institute of Animal Science, Pratelstvi 815, Prague, 10400, Czech Republic.
Anim Genet. 2021 Aug;52(4):422-430. doi: 10.1111/age.13075. Epub 2021 May 10.
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.
近交衰退是指由于近亲交配导致的表现型降低。在牲畜种群中，传统上通过表型回归与系谱近交系数来估计近交衰退。利用基因组近交系数可以提高这种估计的准确性。在这里，我们估计了全球最常见的马过敏病——昆虫叮咬过敏（IBH）在老克德劳马中的发生率。在一个拥有 3214 匹马（187 匹被基因分型）的深度谱系中，我们使用了一个广义线性混合模型，该模型使用了 1996 年至 2009 年间检查的 558 匹马的 IBH 表型（1368 条记录）。除了经典的系谱信息外，我们还使用了单步方法，该方法可以联合使用系谱和基因组信息来估计整个基因组和马白细胞抗原（ELA）II 类区域的近交衰退。在所有拟合整体近交系数的模型中（1.018 到 1.074 之间的比值，P<0.05），除了 Kalinowski 的新近交系数（P=0.0516）外，均观察到显著的近交衰退。ELA II 类区域的近交增加与 IBH 发生率的增加显著相关（比值比 1.018；P=0.027）。然而，当与整体近交系数联合拟合时，ELA II 类区域的近交效应并不显著（比值比 1.016；P=0.062）。总体而言，较高的 ELA II 类和/或整体近交（系谱或基因组）与老克德劳马 IBH 发生率的增加相关。单步方法可有效利用所有可用的系谱、基因组和表型信息，以估计整体和区域近交效应。
