RNA-Seq analysis reveals the role of MYB12, MYB111 and MBW complex repressors in regulation of flavonoid biosynthesis in stigmas of saffron (Crocus sativus L.) flowers

RNA-Seq analysis of quiescent apical buds and developing stigmas of saffron crocus revealed a differential patterning of expression of flavonoid biosynthesis during stigma development in saffron crocus. While CsC4H, Cs4CL, CsCHS, and CsCHI showed high expression during transition of the stigmas from yellow to orange stage, CsF3H, CsF3'H, CsFLS, and CsGT1 showed high expression during transition of the stigmas from orange to red stage. Compared to CsDFR, CsFLS showed significantly higher transcript abundance in stigmas at all stages of development. MBW complex repressors, viz., CsETC1 and CsSPL9 showed highest expression in red and scarlet stigmas, respectively. Correlation analysis between TFs and flavonoid biosynthetic genes showed a positive correlation of CsMYB12 and CsMYB111 with CsCHS and CsFLS and a negative correlation of CsETC1 with CsANS, CsLAR, CsUF3GT, and CsUGT73B4 in the stigmas. SPL9 also revealed negative correlation with CsDFR and CsANR. In silico analysis indicated an unstable MBW complex because of weak interaction between CsMYB12, CsMYC2 and CsTTG1 and high expression of CsETC1 and CsSPL9 in red and scarlet stigmas. The unstable nature of MBW complex in the stigmas could suppress the expression of CsDFR, CsANS, and CsUF3GT, thereby allowing higher expression of flavonol biosynthetic genes.