Genomic basis for biologically effective ploidy reduction. A. Site-specific ploidy reduction in one or more subgenomes is a proportional consequence of site-specific deletion within the alternate subgenomes. Site-specific ploidy may be reduced from the octoploid (8x) to the hexaploid (6x), tetraploid (4x), or diploid (2x) levels. B. Alignment of Illumina short reads to the ‘Hawaii 4’ v1.1 reference genome reveals a ~1.5 kb region of localized read depth reduction, indicative of ploidy reduction, in octoploid F. ×ananassa ‘Winter Dawn’, corresponding to the site of a ~1.5 kb deletion in diploid F. iinumae relative to the F. vesca diploid reference genome. The deletion is absent in diploid F. mandshurica, a close relative of F. vesca. Visualized in Integrated Genome Viewer (IGV, Broad Institute).