Genome-wide association studies for osteochondrosis in French Trotter horses1

Abstract

A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10(-5), this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10(-6)). By comparing QTL between traits at a decreased threshold (P < 5 × 10(-4)), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.

Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training

“…Therefore, it is possible that some of the polymorphisms reported as significant represent false positive hits. The same problem has already been reported by other authors (Lykkjen et al 2010;Teyssèdre et al 2010). Because of the relatively low heritability of the trait, SNP (and corresponding genes) of very high effects on the occurrence of OCD are not expected.…”

“…Different SNP were also found for cold blooded horses by Distl (2013). A French study identified osteochondrosis associated SNP on ECA03, ECA13, ECA14, ECA15 for the Standardbred Trotter (Teyssèdre et al 2010), whereas a Norwegian study found corresponding SNP on ECA05, ECA10, ECA27, and ECA28 (Lykkjen et al 2010). Breeds may differ in the linkage disequilibrium (Corbin et al 2012), but it is expected that breed-specific results will be more compatible.…”

A genome-wide association study of osteochondritis dissecans in the Thoroughbred

“…The closest to BIEC2-799865 was presented recently in a pre-print version of a study carried out in French Trotters and is located at 100-110Mb (Teyssèdre et al 2011). The relatively close proximity of the two QTL represents some correspondence between studies.…”

“…Three previous GWAS for OC in the horse have also identified QTL on ECA3 (Komm 2010;Lampe 2009;Teyssèdre et al 2010). The closest to BIEC2-799865 was presented recently in a pre-print version of a study carried out in French Trotters and is located at 100-110Mb (Teyssèdre et al 2011).…”

“…It is expected that this approach will allow the identification of common variants which could not be found using the traditional linkage based approach (Iles 2008). We are aware of four GWAS for OC that have been carried out in three different horse breeds to date: Lampe (2009) andKomm (2010) (using the same data), Teyssèdre et al (2010) and Lykkjen et al (2010). The number of QTL identified per study ranges from four (Lykkjen et al 2010) to 18 (Lampe 2009) with the range likely at least partly attributable both to differences in significance thresholds used and to differing phenotype definitions.…”