Fig. 4: GWAS for the rate of de novo ERVK[2-1-LTR] mobilization in the male germline of cattle.

a GWAS conducted using PCIP-determined mobilization rate in sperm samples of 430 Belgian Blue bulls and genotypes at ~10 million SNPs, revealing a very strong signal on chromosome 19. b GWAS conducted using the same population after correcting ERVK[2-1-LTR] mobilization rate for the effect of the chromosome 19 QTL. Seven additional (near) genome-wide significant effects were detected. Loci encompassing an ERVK[2-1-LTR] element are highlighted in red, others in light blue. c Zoom into the four loci encompassing an ERVK[2-1-LTR] element, shown as triangles (as opposed to circles for SNPs). Variants are colored according to their LD (r²) with the lead variant. The LD between the ERVK[2-1-LTR] element and the lead SNP was 1.00 (ERV = lead variant) for chromosome 19, 0.62 for chromosome 2, 0.84 for chromosome 4, and 0.94 for chromosome 21. All non-ERVK lead variants were imputed variants with imputation accuracy ≥ 0.95. Two-sided p-values were obtained with GEMMA as described in Methods. Experiment-wide 5% significance thresholds (dotted horizontal line in (a) account for the realization of 500,000 independent tests (see Methods). Source data are provided as a Source Data file.