Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse

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 the insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3,214 horses (187 genotyped) we used a generalized linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1,368 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 ELA class II (equine leuckocyte antigens) 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 of 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 of 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 the estimation of overall and regional inbreeding effects.