Candidate genes in red pigment biosynthesis of a red-fleshed radish cultivar (Raphanus sativus L.) as revealed by transcriptome analysis

Abstract Among radish (Raphanus sativus L.) groups, a special cultivar is characterized by its high content of red pigment (RP) in both skin and flesh. However, little is known about the molecular mechanisms of the RP formation. This paper characterized the transcriptomes of the RP cultivar and other two in different colours to investigate genetic basis of the RP biosynthesis. The gene expression analysis showed that 1634/1848 genes were significantly up-regulated/down-regulated in the RP cultivar, in comparison with those of the other two, respectively. The up-regulated ones included several anthocyanin structural genes, such as chalcone isomerase (CHI), chalcone-isomerase 1 (CHI-1), flavanone 3-hydroxylase (F3H), dihydroflavonols 4-reductase (DFR), flavonol synthase 3 (FLS3), anthocyanidin synthase (ANS), as well as some carotenoid biosynthesis genes including LUT2, CYP707A1, BGLU18 and CYP707A3. Additionally, the molecular evolution analysis identified 191 putative fast evolving genes in the RP cultivar, which may regulate the RP synthesis processes by influencing the expression levels of anthocyanin structural genes. Overall, our study provides valuable RNA-Seq data of the RP radish cultivar group to deepen our understandings of the molecular mechanisms in its RP biosynthesis.