Metabonomic Profiling and Gene Expression Analysis Reveal Anthocyanin Biosynthesis Mechanisms Underlying Tissue-Specific Color Variation in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis )

Detailed profiles of anthocyanins and their underlying biosynthetic mechanisms in tissues exhibiting distinct purple pigmentation in purple-heading Chinese cabbages remain poorly characterized. Here, we performed an integrated transcriptional and metabolomic analysis of anthocyanin metabolism. A total of 68 anthocyanins were identified, including 34 cyanidin-, 9 delphinidin-, 3 malvidin-, 9 pelargonidin-, 9 peonidin-, and 4 petunidin-derived compounds, along with two procyanidins. Cyanidin-3-O-glucoside (4.285 to 12.799 mg kg–1), delphinidin-3-O-(2‴-O-p-coumaroyl)rutinoside-7-O-glucoside (0.020 to 11.088 mg kg–1), and delphinidin-3-O-sophoroside (0.432 to 14.396 mg kg–1) were predominant anthocyanins. Tissues proximal to the growing point (flower buds, siliques) are clearly separated from those close to underground (rosette leaves, roots). The conjoint and coexpression analysis revealed that BrMYB2, BrMYBL2.1, and BrEGL3.1 might affect the expression of BrPAL4.0, Br4CL4.2, BrCHSs, BrDFR1, BrANS1, BrUFGTs, BrATs, and BrGSTs, thereby modulating anthocyanin biosynthesis; besides, BrPAL3.2, BrCHS5, BrF3′H, BrUGT84A1.1, BrTT2, and BrTT8 also governed the production of procyanidin B2 in siliques.