Figure 3

PCR-based genotyping on a breed level (A) and individual level (B). A) Genotyping for the presence of SVs in breeds, represented by pooled samples. Except for SV50 and SV51, a small (see Table 4 for approximate sizes and breed encoding) PCR fragment that was absent in the reference was expected in some of the breeds that have the deletion. In SV50 and SV51, a slightly larger PCR fragment than that observed in the reference was expected in breeds that have the insertion. B) Genotyping for the presence of SVs in eight individuals of breeds in which the SV was detected in pooled samples. Except for SV50 and SV51, a small PCR fragment was expected in individuals homozygous for the deletion and SVs in which the reference genotype is too long for PCR. Heterozygous individuals in which both genotypes can be spanned (see Table 4) by PCR show two bands. In SV50 and SV51, both PCR fragments, which differ slightly in size, are expected in heterozygous individuals, whereas only the larger fragment is expected in individuals homozygous for the insertion.