A novel iterative mixed model to remap three complex orthopedic traits in dogs

Abstract

Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic traits of dogs and all result in debilitating osteoarthritis. We reanalyzed previously reported data: the Norberg angle (a quantitative measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in 271 cases and 399 controls and their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed and random model with a circulating probability unification (FarmCPU) function, with marker-based principal components and a kinship matrix to correct for population stratification, was used. A Bonferroni correction at p<0.01 resulted in a P< 6.96 ×10-8. Six loci were identified; three for HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was described previously in the same dogs using a conventional mixed model. No loci were identified for RCCL in the previous report but the two loci for ED in the previous report did not reach genome-wide significance using the FarmCPU model. These results were supported by simulation which demonstrated that the FarmCPU held no power advantage over the linear mixed model for the ED sample but provided additional power for the HD and RCCL samples. Candidate genes for HD and RCCL are discussed. When using FarmCPU software, we recommend a resampling test, that a positive control be used to determine the optimum pseudo quantitative trait nucleotide-based covariate structure of the model, and a negative control be used consisting of permutation testing and the identical resampling test as for the non-permuted phenotypes.

Fig 1. The summary of genetic relationships among the breeds with the most individuals and the decay of linkage disequilibrium (LD).

Along the top three principal components of variation, the main breeds are genetically distinct (a, b). The extent of LD, measured as average pair-wise r², drops below 0.3 at 11 kb in multiple populations (c). The marker density plot shows the distribution of marker intervals and 80% of marker intervals are less than 30 kb (d). The genotype data used for principal component calculation and genetic relationship building comes from the biggest dataset for HD [11].

Fig 2

Manhattan plots, QQ plots and resampling test plots of GWAS for hip dysplasia (HD), elbow dysplasia (ED) and rupture of the cranial cruciate ligament (RCCL) (a, c and e). The dashed horizontal line depicts the Bonferroni-adjusted significance threshold (genome wide α level of 0.01). The QQ plot of association with the null distribution (expected) versus the observed associations is shown as insert. The Manhattan plot of the resampling test (b, d, and f) shows the y axis indicating the number of significant occurrences or associations [expressed as the–log(p)] in 1,000 replicated tests across the genome. Note the scale along the Y axis for the associated–log(p) value varies by plot.