Figure 1

Manhattan plots representing four genome wide association analyses for the binary BRDC case–control phenotype using (A) EMMAX-GRM, (B) GBLUP, (C) EIGENSTRAT and (D) Full versus reduced model regression (FvR) in the CA calves. In panel A, the plot for EMMAX-GRM case–control with covariates of sex and age is shown. For EMMAX-GRM, the first panel shows the –log₁₀P-values on the Y axis and the second panel shows the proportion of variance explained by effects at a single SNP. In panel B, the plot for GBLUP case–control with covariates of sex and age is shown. The Y axis shows the proportion of variance explained by a sliding window of 7 SNPs centered on the third SNP within each window. In panel C, the plot for EIGENSTRAT case–control principal component corrected input data (top 100 principle components) with covariates of sex and age is shown. The –log₁₀P-values are indicated on the Y axis. The blue line indicates the Wellcome Trust threshold for SNPs with modest evidence for association with BRDC susceptibility, and the red line indicates the threshold for SNPs with strong evidence for association with BRDC susceptibility. In panel D, the Manhattan plot for FvR case–control principal component corrected input data (top 53 principal components) with covariates of sex and age is shown. The first FvR panel shows the –log₁₀P-values on the Y axis, and the second panel shows corresponding F-test values for the Full versus Reduced Model Analysis.