Figure 4

Scheme of identification of common deletion polymorphisms by parent (sire)--child (steer) heritability (P-C) error and validation by quantitative PCR. (A) Scheme of genoplot image in Illumina BeadStudio 3.2 software where SNP marker was located within copy number variation region. Steer and sire were marked as "X" and "O", respectively. The three dotted lines represent three SNP genotypes (A/A, A/B, and B/B). (B) Genoplot image showing P-C heritability error. The steer (child) is shown on the left side (copy number: 1×; CNV genotype: A/-; marked at "X") and its sire (parent) on the right (copy number: 1×; CNV genotype: B/-; marked at "O"). (C) Difference of SNP and CNV genotype in one pedigree. (D) Heritability error table. Nine P-C errors in one marker are displayed. The table shows the sample ID of steer (child) and sire (parent) and their SNP genotypes having heritability error. (E) Genoplot image of identified common deletion polymorphisms (marker name: ARS-BFGL-NGS-24778). Three types of copy number (2×, 1×, and 0×) are depicted. Individuals having hemizygous deletions (copy number: 1×) clustered into two distinct groups (color: cyan). Samples having null copy number are displayed with a black dot at the bottom. (F) Validation by qPCR around the ARS-BFGL-NGS-24778 marker. The individuals having homozygous (null) and hemizygous deletions in the genoplot image were spotted approximately in the same copy number position by qPCR.