Fig. 3.

Manhattan (a) and Q–Q (b) plots from GWAS for maternal calf survival at first calving and maternal calf survival at later calvings using Illumina BovineHD BeadChip in Holstein cattle. a Manhattan plot in which the genomic coordinates of SNPs are displayed along the horizontal axis, the negative logarithm of the association P-value for each SNP is displayed on the vertical axis, and the dark red line is the significance threshold line at the genome-wise false discovery rate of 5%. b Quantile–quantile (Q–Q) plot showing the late separation between observed and expected values. Genomic inflation factor is around 1 indicating that there is no population stratification