168 It was assumed that the down-regulated genes were related to inhibition of anthocyanin metabolism or had a negative effect on the anthocyanin biosynthesis pathway. Among the six down-regulated genes, Os06g0170500 showed levels of expression in all developmental stages of the Dongjin cultivar. Table 2 shows the primer list of the 15 candidate genes. Two genes were omitted due to small differences with control rice. Each primer used to amplify the candidate genes. Conclusions There has been increased interest in the use of black rice due to the numerous health benefits associated with the anthocyanin pigment. In this study, we identified putative transcription factors involved in anthocyanin biosynthesis in black rice cultivars using a newly designed 135 K Oryza sativa microarray. We performed a four-stage analysis to evaluate anthocyanin biosynthesis in black rice: first, we tested for the presence of commonly expressed genes between different rice cultivars, second, functional classifi- cation categories were identified by COGs and GO analysis, third, transcription factors were identified by the hyper-geometric analysis method, and finally, selected unknown and hypothetical genes were verified by RT- PCR. Among the 137 transcription factor genes identified, 24 genes were unknown and hypothetical genes. Among these, 17 genes differed between the white cultivar and the two black rice cultivars at all the seed developmental stages. The 17 candidate genes consist of 10 and 7 genes were up- and down-regulated gene, respectively. These genes may play a regulatory role in anthocyanin produc- tion, or are related to anthocyanin metabolism during flavonoid biosynthesis. Results of RT-PCR analysis largely coincided with the expression profiles obtained through the microarray experi- ments. While these genes still require further investigation and validation, these results demonstrate the potential of this method using newly designed microarrays. This study provides valuable insight into pigmentation production and will greatly facilitate future breeding of anthocyanin-rich hybrid varieties of rice. Acknowledgements This work was supported in part by the National Academy of Agricultural Science, Bio-green 21 Program of Rural Development Administration, and with a grant from the Crop Functional Genomics Center of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology, Seoul, Korea. 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