Inheritance of a complex, multiallelic CNV at a segregating CNV locus. The Chr 12 locus harbors two unique CNVs: one specific to the HB3 parent (~161 kb, grey arrow) and the other to the Dd2 parent (~5 kb, blue arrow). 34 genes overlap with the HB3-type CNV and 3 genes with the Dd2-type CNV (which are common to both of the CNV types, demarcated by blue box). A) Heat map illustrates the increased relative probe signal intensities in the Dd2/progeny lines (red) in comparison to the reference HB3 parent. (B - D) Scatter plots represent the relative hybridization intensities as a log2 (test/HB3) for progeny inheriting Dd2-type CNV allele (B, inherited by 23 progeny) HB3-type CNV allele (C, inherited by 11 progeny) and a single progeny, that inherited both parental CNV alleles at this locus (D). (E) Linkage analysis with MS markers confirms a multiallelic region comprising an approximately 19 kb Dd2 allelic region interspersed within a larger HB3 allelic region overlapping the complex CNV in the progeny strain CH3-61.