Fig. 2

Genome-wide association study for the non-classic Swiss marking pigmentation phenotype in 65 JT goats based on a linear mixed model and genomic control. The Manhattan plot shows the association results of 14,412,316 biallelic SNPs on autosomes 1–29 with the coat color phenotype in 65 JT goats (48 solid black vs. 17 non-classic Swiss markings). The chromosomes are plotted in different colors. The P-values were obtained by using a mixed-model association approach and the genomic control and then transformed to –log10 (P-values). The horizontal dashed line indicates the genome-wide Bonferroni-corrected significance level