Fig. 4
Population genetic differentiation and functional analysis of SRS-based SVs. A Principal component analysis of the 39 cattle breeds/populations based on the SVs. B Linkage analysis between SVs and surrounding SNPs (300 SNPs flanking the SVs). C Manhattan plot of the DISV statistics between northern and southern Chinese cattle based on the SVs. The dashed blue line indicates the top 5% proportion of SVs with DISV. The red triangle represents the SVs belonging to the top 5% signals from both DISV and FST-SV and falling in the ATAC peaks. The distances of SVs from the genes are listed in brackets. D Significantly enriched KEGG pathways (corrected P < 0.01) for the genes that are structurally linked to the stratified SVs. E Distribution of the mean FST values of the SNPs (FST-SNPs) surrounding the selected SVs compared with all SVs in a 5-kb window. The dashed line indicates the top 1% cutoff of FST-SNP distributions around all SVs. F An example of a 41-bp insertion (INS) (BTA03: 93,224,919, Mongolian_v1) in the enhancer of the CPT2 gene with a high allele frequency difference (DISV = 0.897) and FST-SV (0.889) between northern and southern Chinese cattle. The numbers in brackets in the picks of ATAC-seq and ChIP-seq (H3K4me3 and H3k27ac) data indicate signal intensities