Structural complexity of the white flower locus in <i>Chrysanthemum</i>

The white flower trait in <i>Chrysanthemum</i> is attributed to the carotenoid cleavage dioxygenase 4a gene (<i>CCD4a</i>), a key domestication gene that contributed to generation of various flower colours in modern chrysanthemum cultivars. This trait is believed to be controlled by a single dominant locus. We studied the structure of this <i>CCD4a</i> locus utilising the whole genome sequence information of <i>Chrysanthemum makinoi</i>, a diploid white flower species, and found six homologous sequences of <i>CCD4a</i>, two of which being functional, and arranged in tandem in a 586-kb region on Chromosome 7. A qPCR analysis disclosed that white flower <i>Chrysanthemum</i> species possess at least two and as many as eight copies of <i>CCD4a</i> homologous sequences per monoploid genome, indicating high polymorphism of the <i>CCD4a</i> region. A detailed analysis of the structural diversity of the <i>CCD4a</i> region in <i>Chrysanthemum</i> could provide significant insights into the domestication trajectory of the cultivated chrysanthemum.