Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

To better understand the functional characterization of anthocyanin gene expression in black rice, we performed a detailed computational examination. The experiment was performed using the newly designed 135K Oryza sativa microarray to assess gene expression at three time points after the heading stage in Ds insertion lines. Transcription factors related to anthocyanin pigmentation biosynthesis were clustered. A total of 8,517 genes exhibited greater than 2.5-fold up- or downregulation in each comparison between three rice groups and three seed developmental stages. The resultant 82 transcription factor genes found to be associated with anthocyanin were classified into 12 groups. In addition, 12 unknown and hypothetical genes were identified from comparisons between the white cultivar and two black Ds insertion mutants tested. We identified 12 unknown and hypothetical genes involved in anthocyanin biosynthesis. These genes likely play either a regulatory role in the anthocyanin production process or are related to anthocyanin metabolism during flavonoid biosynthesis. While these genes require further characterization and validation, the results here underline the potential use of the newly designed microarray.