Fig. 2

Discrimination of fertile and subfertile bulls based on fertility-related differentially methylated CpGs and regions. A, B principal component analysis (A) and correlation clustering (B) run on the DMCs identified after variant filtering between fertile (red) and subfertile (blue) bulls in the main cohort. A Although a certain degree of overlap exists between the groups, they clearly segregate along dimension 1. Confidence ellipses are represented. B The cluster on the left mostly contains subfertile bulls, while the cluster on the right mostly contains fertile bulls. C Heatmap showing the average DNA methylation values at 18 DMRs covered in all 100 samples. Each cell of the heatmap is colored according to the average methylation value in the corresponding sample (displayed in columns, with fertile and subfertile bulls shown in red and blue, respectively) and DMR (in rows, with DMRs hyper- and hypomethylated in subfertile bulls shown in red and black, respectively). For each DMR, the genomic coordinates and the gene containing the DMR (if any) are indicated on the right-hand side. Three different clusters of DMRs were obtained manually. Cluster 1 included 5 DMRs that were highly methylated in subfertile bulls, while cluster 2 included 9 DMRs with low methylation in fertile bulls