Transcriptomics analyses of genes regulating anthocyanin production in black rice

We used a 135K rice microarray to identify genes involved in anthocyanin biosynthesis and metabolism in black rice. Using our multi-interaction screening method, we then screened 427 expression genes, 754 orthologous genes, and 416 pathway-network related genes associated with anthocyanin bio-synthesis. Finally, we identified eight candidate genes by comparing pathway-expression genes, including ortholog-ontology genes. To verify the candidate genes, each was mapped to the black rice genome, and functional predictions were confirmed via phylogenetic reconstructions using the candidate genes and their homologous proteins. While the eight genes identified by our method require further characterization and validation, our study demonstrates the power of multi-interaction screening after the initial identification of genes with microarrays.