Methods and materials for modulating (e.g., increasing or decreasing) flavonoid levels in cacao plants are disclosed. For example, nucleic acids encoding flavonoid-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also provided are methods for accelerating breeding of Theobroma cacao plants of the porcelana variety with modulated levels of proanthocyanidin, its precursors and it polymers, useful in various medical and skin care products. Also provided are plants having modulated flavonoid levels and plant products produced from plants having modulated flavonoid levels.
