The differential expression profiling of the fruit-specific genes between a blood orange (Citrus sinensis cv. Tarocco) and a blonde orange (Citrus sinensis cv. twenty-first century navel orange) was investigated by fruit transcriptome sequencing. The relative expression folds for Cs6g17570 and Cs5g31400 were significantly greater in the "Tarocco" fruits, but Cs9g04810 transcripts had no significant differences between two accessions by digital gene expression profiling. In particular, R2R3-MYB, bHLH-type, and WD40-repeat proteins (encoded by Cs6g17570, Cs5g31400, and Cs9g04810) were transcription factors with each conserved domain and interacted in vitro and in vivo. Moreover, the dihydroflavonol 4-reductase (DFR), a key enzyme involved into anthocyanin biosynthesis pathway, had greater transcription levels in Tarocco fruit and also in the transgenic Arabidopsis thaliana by Cs6g17570 ectopic expression. Furthermore, Cs6g17570 and Cs5g31400 in Tarroco were upregulated by cold induction and then had similar expression profiling during cold storage. In conclusion, Cs6g17570, Cs5g31400, and Cs9g04810 encoding proteins might be involved into anthocyanin regulation in Tarocco by MYB-bHLH-WD40 complex as well as in other fruit trees. Studies on the anthocyanin regulatory mechanism will aid in development of new biotechnological tools for Citrus breeding.
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