Fig. 4

Manhattan plots showing − log10 (nominal p-values) corresponding to the null hypothesis that the effects of principal components that explain 99% of the variability due to the Sarda base gametes (BH^S) at each locus (43,390 SNPs) are zero. The dashed black lines indicate the 0.05 genome-wide significance threshold determined by permutations. MY milk yield; FY fat yield; PY protein yield; FP fat content; PP protein content