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Additional file 1: Fig. S1.. correlation clustering run on the methylation percentages at CpGs10 covered in at least 22 samples per group. Fig. S2: heatmap run on CpGs discriminant between sperm and somatic cells. Fig. S3: annotation of fertility-related DMRs relative to different genome features. Fig. S4: average DNA methylation at individual LINE and LTR repeats after alignment of the RRBS sequences on a Repbase artificial genome. Fig. S5: pyrosequencing validation of the upstream region of LBX1 gene. Fig. S6: fertility, semen functional parameters and semen sample characteristics in correctly classified and misclassified bulls. Fig. S7: PCA run on the methylation percentages at DMCs, with or without the imputation of missing values. Fig. S8: semen functional parameters before and after correction for the batch effect.