Genome-wide association analysis of patellar luxation in Flat-Coated Retrievers. (A) Association of individual SNPs with patellar luxation was analyzed with PLINK software by comparing allele frequencies in the cases (n = 45) and controls (n = 40). (B) Association analysis of individual SNPs using the Estimated Breeding Values (EBV) as phenotype using PLINK. (C) Multi-SNP association analysis was performed using the case/control patellar luxation status and iBAY software. (D) same as (C) using EBV as phenotype. The –10log of the P-values obtained of individual SNPs are plotted in (A) and (B), with the dotted lines indicating the Bonferroni threshold over 15,823 SNPs (α = 0.05). Multi-SNP association values are presented as Bayes factors in (C) and (D), with the dotted lines indicating the ‘substantial’ effect threshold according to guidelines by Kass and Raftery .