Role of homologous recombination (HR) in copy number fluctuation in the Chr 5 amplification. Linkage analysis of the CNV region revealed that of the progeny strains that exhibited copy number fluctuation at the Chr 5 locus, two CNVs were generated by HR between the two parental homologs. The predicted HR patterns and allele distributions in each progeny line A) QC23 and B) CH3-61, are shown with the associated MS marker. The region of the amplicon is highlighted by a black box, and the three MS markers that overlap with the CNV region are shown within the boxed region. D = Dd2 allele, H = HB3 allele.