(A) A 10-Mb region with a strong selective signature signal was zoomed in (BTA 6: 84–93 Mb). Association mapping results from imputed WGS variants on CM resistance (dark blue) and MY (yellow) are shown in the upper panel; iHS results are shown in the lower panel (black). The CM resistance association peak occurs at the left side of the iHS peak, whereas MY association peak appears on the right side of the iHS peak. The red vertical line marks GC CNV. A 1-Mb region covering GC CNV, iHS lead SNP, and MY lead SNP are marked with translucent blue. (B) The extended haplotype homozygosity of the 1-Mb region marked in panel (A) is shown, together with four genes annotated in this region (top of the figure). The major haplotype shown in the upper part (black) branches outwards, implying recent positive selection acted upon this haplotype. The non-selected haplotypes, shown in the lower side (blue) rapidly break down from the iHS lead SNP. (C) Pairwise D’ and r 2 values between GC CNV, iHS lead SNP, and MY lead SNP in the ~4,000 daughter proven bulls. A screenshot made from Haploview software [ 111 ].