Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice

Proanthocyanidins (PAs) are major phytochemicals in rice, and accumulate abundantly in red pericarp (RP) rice. Consumers and rice breeders are increasingly showing interest in PAs because of their beneficial health effects; however, PA biosynthesis in rice is not well-understood. Therefore, to gain insights into this process, we performed comparative transcriptome analysis of grains harvested at 14 days after flowering (DAF; i.e., the stage at which active PA biosynthesis occurs without pericarp color change) and 28 DAF (the stage of late seed development with pericarp color change) from RP and white pericarp rice. In RP rice at 14 DAF, the expression levels of six structural genes ( OsCHS , OsF3H , OsF3′H , OsDFR , OsANS , and OsLAR ), one modification gene ( OsUGT ), and one transport gene ( OsGSTU34 ) were significantly upregulated, along with the activation of Rc , the key regulator of PA accumulation in the pericarp. Functional enrichment analysis of 56 differentially expressed genes specifically upregulated in RP rice at 28 DAF revealed the presence of three laccase genes known to cause the browning reaction through oxidation. These results expand our understanding of PA biosynthesis in rice, and provide a genetic basis that will lead to further studies on the genes and underlying molecular mechanisms associated with this process.