Genome scan for quantitative trait loci (QTL) for osteochondrosis in Hanoverian Warmblood horses using an optimised microsatellite marker set

The aim of this work was to establish a genome-wide microsatellite marker set for the horse in order to make possible whole genome scans for the identification of the chromosomal locations of quantitative trait loci (QTL) that significantly influence the development of equine osteochondrosis (OC). In a first step, a whole-genome scan panel was established consisting of 157 equine microsatellite markers. In order to test the suitability of the marker set for genome-wide QTL studies, 86 Hanoverian Warmblood horses were chosen for genotyping. Multiplex sets were established in order to increase efficiency of genotyping. The markers were equally spaced over all 31 autosomes and the X chromosome, and covered a total distance of 2081 cM, corresponding to 76.5% of the equine genome. The average distance between the markers used was 19.1 cM within the linkage groups. Due to the small number of markers and the missing assignment of the markers to linkage groups, the density of markers was low on ECA07 and ECA28. The average observed heterozygosity of the whole marker set was 65.7%, the average expected heterozygosity was 64.6%, and the average polymorphism information content (PIC), 60.3%. The average PIC of the chromosomes ranged from 46.7% to 73.7%. The majority of the 157 markers (n = 123, 78.34%) was highly informative, with a PIC > 50 %. Therefore, this new microsatellite marker set was classified as being well suited for whole-genome scans. In a second step, the marker set described above was used to genotype 123 foals affected either with OC or OCD or both, their respective dams, and 13 sires. The marker genotypes, the pedigree data and the phenotype data of the foals were analysed using non-parametric linkage analysis based on IBD mapping. Separate analyses were performed for OC (fetlock and/or hock), OCD (fetlock and/or hock), fetlock OC, fetlock OCD, hock OC, and hock OCD. The linkage analyses were performed for both sexes together and for each sex separately. In total, 27 chromosome-wide QTL for the different traits were found on 13 different equine chromosomes. Six of these QTL were present in both sexes, nine in male animals, and twelve in female animals. One chromosome-wide QTL was also found to be of genome-wide significance. The distribution of the QTL was heterogeneous with respect to sex and joint type. The QTL for fetlock OC/OCD and hock OC/OCD were located on different chromosomes, indicating that these traits may be inherited independently. The whole-genome scan carried out in this study was a first step towards the identification of candidate genome regions harbouring genes responsible for equine OC. Further investigations are necessary to verify the results obtained here and to refine the map positions of the QTL already identified for OC and OCD.