Structural complexity of the white flower locus in Chrysanthemum

The white flower trait in Chrysanthemum is attributed to the carotenoid cleavage dioxygenase 4a gene (CCD4a), 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 CCD4a locus utilising the whole genome sequence information of Chrysanthemum makinoi, a diploid white flower species, and found six homologous sequences of CCD4a, two of which being functional, and arranged in tandem in a 586-kb region on Chromosome 7. A qPCR analysis disclosed that white flower Chrysanthemum species possess at least two and as many as eight copies of CCD4a homologous sequences per monoploid genome, indicating high polymorphism of the CCD4a region. A detailed analysis of the structural diversity of the CCD4a region in Chrysanthemum could provide significant insights into the domestication trajectory of the cultivated chrysanthemum.