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Background  The flavan-3-ols catechin and epicatechin, and their polymerized oligomers, the proanthocyanidins (PAs, also called condensed tannins), accumulate to levels of up to 15 % of the total weight of dry seeds of  Theobroma cacao  L. These compounds have been associated with several health benefits in humans. They also play important roles in pest and disease defense throughout the plant. In Arabidopsis, the R2R3 type MYB transcription factor TT2 regulates the major genes leading to the synthesis of PA.    Results  To explore the transcriptional regulation of the PA synthesis pathway in cacao, we isolated and characterized an R2R3 type MYB transcription factor MYBPA from cacao. We examined the spatial and temporal gene expression patterns of the  Tc-MYBPA  gene and found it to be developmentally expressed in a manner consistent with its involvement in PAs and anthocyanin synthesis. Functional complementation of an Arabidopsis  tt2  mutant with  Tc-MYBPA  suggested that it can functionally substitute the Arabidopsis  TT2  gene. Interestingly, in addition to PA accumulation in seeds of the  Tc-MYBPA  expressing plants, we also observed an obvious increase of anthocyanidin accumulation in hypocotyls. We observed that overexpression of the  Tc-MYBPA  gene resulted in increased expression of several key genes encoding the major structural enzymes of the PA and anthocyanidin pathway, including  DFR  (dihydroflavanol reductase),  LDOX  (leucoanthocyanidin dioxygenase) and  BAN  ( ANR , anthocyanidin reductase).    Conclusion  We conclude that the  Tc-MYBPA  gene that encodes an R2R3 type MYB transcription factor is an Arabidopsis  TT2  like transcription factor, and may be involved in the regulation of both anthocyanin and PA synthesis in cacao. This research may provide molecular tools for breeding of cacao varieties with improved disease resistance and enhanced flavonoid profiles for nutritional and pharmaceutical applications.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0529-y) contains supplementary material, which is available to authorized users.

Tc-MYBPA is an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao