(a) A schematic description of tandem duplication at the porcine KIT locus. A duplication unit is about 450 kb. A breakpoint at the junction between the two KIT copies is designated as duplicated, and another breakpoint at the distal end of the 2nd KIT copy is designated as normal. A splice donor mutation in intron 17, by which KIT becomes the fully dominant allele, is indicated by an arrow. The repeat elements around the breakpoint, L1MC1 and L1ME1, are described. The target points of pyrosequencing (Pyro_splice) for quantifying copies with the splice mutation and the quantitative oligonucleotide ligation assay (qOLA_CNV) for detecting total copy numbers are marked. (b) Nucleotide sequence around the breakpoint. While the breakpoint of the normal copy is on L1MC1, that of the duplicated copy is at the junction between L1MC1 and L1ME1. The common primer (BPT_Com) for the quantitative oligonucleotide ligation assay (qOLA_CNV) is marked in underlined italic letters and the two specific primers (BTP1 and BPT2) are indicated by underlined plain letters. The two nucleotides in a box, C and G, indicate the breakpoint and comparison point for qOLA_CNV in this study. Small letters g and c indicate the comparison point for measuring KIT CNV by pyrosequencing (Pyro_CNV) . (c) Schematic descriptions of KIT alleles. The two target points of pyrosequencing (Pyro_splice) for quantifying copies with the splice mutation, and qOLA_CNV for detecting total copy numbers are marked with arrows. A question mark in the IBE allele means an unidentified polymorphism causing the Belt phenotype. Discrimination between i and IBE is not possible at present.
Seo et al. BMC Genetics 2007 8:81 doi:10.1186/1471-2156-8-81