Figure 2.

Conditioned analyses. To examine whether the associations detected on a chromosome were independent, a conditioned analysis was performed by including a genotype of the most significant SNP on the chromosome as a covariate in the model. Red and blue dots represent p values in –log₁₀ scale before and after conditioning, respectively. Large squares indicate the most significant SNP in the respective chromosomes. (A) BTA 14. (B) BTA 6. (C1) BTA 8. In BTA 8, Hapmap40466-BTA-82123 reached nearly genome-wide significance with conditioning on BTA-52694-no-rs (C1), while the association of BTA-52694-no-r became stronger with conditioning on Hapmap40466-BTA-8212 (C2, green dots). When conditioned on both SNP, associations of the surrounding SNP disappeared (C3, orange dots).