3.5 DEGs from anthocyanin biosynthesis and its associated regulatory complex
All the major identified unigenes involved in the phenylpropanoid pathway, such as PAL , cinnamate 4-hydroxylase (C4H ) and 4-coumarate CoA ligase (4CL ), were up-regulated upon both red and blue light treatments (Figure 6). Caffeoyl CoAO -methyltransferase (cCoAoMT ) expression was found to be at a relatively higher level in blue light compared to red light treatment also with similar expression levels identified in peroxidases and cationic peroxidases (Prx , cPrx) genes leading to lignin biosynthesis via the p -coumaryl alcohol branch pathways (Figure 6).
All the anthocyanin biosynthetic pathway structural genes were up-regulated both in red and blue light (Figure 6). The key biosynthetic enzyme gene CHS was found with a log2 fold increase of 3,3 and 3 between red and blue treatment, respectively. Expression of CHIand F3H was found to be at a higher level in red light treatment when compared with the blue light treatment. The changes in expression levels of F3 ʹH , DFR and ANS genes were found to be slightly higher in blue light treatment whereas the key gene involved in the delphinidin branch pathway, F3 ʹ5 ʹH , and the specific gene for anthocyanin biosynthesis, UFGT , were found to be highly up-regulated in the response towards red light (Figure 6).
R2R3 MYBs (8 unigenes) and bHLHs (6 unigenes) were found among the top 500 DEGs. All the identified TFs of MBW complex from top DEGs and corresponding gene ID with IPS domains are provided in the Table S9. SQUAMOSA-MADS box (TDR-type) TFs, such as AGAMOUS(AGL 80, 21,15, 61,62) and MADS (2,3), were significantly up-regulated in red light treatment and down-regulated under blue light treatment (Figure 6). In contrast, blue light up-regulated DEF2and PHE2 type MADS box transcription factors and red light down-regulated SPL4 type TFs (Figure 6), which are all linked to regulating circadian rhythm and flowering. The expression level ofMYBA1, the key regulatory gene of anthocyanin biosynthesis, was up-regulated by both red and blue light treatments, whereasMYBPA1.1 was found comparatively higher level in red light treatment. Most of the eight R2R3-MYB genes categorized as DEGs expressed very similarly in both the light treatments exceptMYBPA1.1, MYBPA3 and MYBC2 which were found slightly lower levels in blue light treatment (Figure 6). All the bHLH TFs categorized under DEGs (bHLH6 (MYC2), bHLH130, bHLH137, bHLH147, bHLH68 andbHLH79 ) were found up-regulated in both light treatments and expressed in similar levels.