J Appl Genetics (2011) 52:161–169 165 Fig. 1 GO analysis of anthocyanin production biosynthesis. The three process categories show the composition ratio of genes to pigments other than anthocyanin from the candidate gene list. Ultimately, 1,289 candidate genes were predicted to be related to anthocyanin biosynthesis and production. Transcription factors associated with anthocyanin We characterized the transcription factors associated with anthocyanin pigmentation using the hyper-geometric anal- ysis method. Table 1 shows the transcription factor groups predicted from the 1,289 candidate genes. We identified 10 groups that exhibit functionally diverse transcription factor activity involved in anthocyanin bio- synthesis. Of the 1,289 candidate genes, 137 (10.6%) were identified as putative transcription factors. The MYB and GT transcription factor families showed the highest expression levels with these groups accounting for approx- imately 37% of the predicted transcription factors. Other putative groups of anthocyanin production included the NAC families, basic helix-loop-helix (bHLH) and peroxi- some proliferator-activated receptor binding protein (PBP). Involvement of the Myb and GT families, NAC, bHLH and PBP transcription factors in colored tissues has been reported previously (Martin and Paz-Ares 1997; Yujie et al. 2010; Reddy et al. 1998; Borevitz et al. 2000; Sheng et al. 2005). These results illustrate the functional diversity of the transcription factor families and that these factors may be highly activated during anthocyanin pigmentation. MYB family members activate flavonoid pigmentation, are involved in specific steps of the anthocyanin pathway, and have evolved specific functions with different biochemical properties. The GT factors, GT-1 and GT-2, have been shown to interact with multiple sequences within the promoter of the Tdc gene and express a trans-acting factor possessing a GT- motif. GT-1-containing genes encoded factors such as the nuclear protein of light-responsive in rice. NAC factors play an important role in regulating the expression of flavonoid biosynthesis-related genes (Morishita et al. 2009). The bHLH factors function in determining red seed color in anthocyanin biosynthesis (Gonzalez et al. 2008). PBP factors may be closely related to the flower-specific Myb305 factor Table 1 Transcription factor groups (TFs) predicted by the cumulative hyper-genomic dis- tribution analysis method TFs MYB MYB-related GT family WRKY NAC bHLH PBF MADS AP2 PBP Etc. Description A life cycle activating related to metabolism of cell Flavonoid -biosynthesis related to Myb-like protein Nuclear factors related to trans-acting To biotic, abiotic stresses and development process Genes related to flavonoid biosynthetic pathway Anthocyanin biosynthesis and signaling The regulates cereal storage protein gene Determination of floral meristem and organ identity Ethylene responsive element binding factor Flower-specific gene related to Myb305 STF, GRF, bZIP, RAV and C2H2 factors Gene P-value 23 10 18 17 16 12 10 9 8 3 11 0.0413 0.0319 0.0325 0.0287 0.0317 0.0329 0.0108 0.0272 0.0305 0.0496 0.1258 Ratio 16.79 7.30 13.14 12.41 11.68 8.76 7.30 6.57 5.84 2.19 8.03