Summary of flavonoid/phenylpropanoid gene and metabolite accumulations from black and brown soybean seed coats*. Transcripts upregulated and metabolites exclusive to the black (iRT) seed coat are shown in blue. Transcripts downregulated and metabolites absent in the black (iRT) seed coat but present in the nearly-isogenic brown (irT) seed coat are shown in red. 4CL, 4-coumarate-CoA ligase; OOMT, orcinol O-methyltransferase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3'H, flavonoid 3'-hydroxylase; F3'5'H, flavonoid 3',5'-hydroxylase; DFR, dihydroflavonol reductase; ANS, anthocyanidin synthase; UF3GT, UDP-glycose:flavonoid 3-O-glycosyltransferase; AOMT, anthocyanin O-methyltransferase; GST, glutathione S-transferase; FLS, flavonol synthase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; MATE, multidrug and toxic extrusion protein; IFR, isoflavone reductase; G4DT; pterocarpan 4-dimethylallyltransferase. *For the complete lists of differentially regulated transcripts see Table S2 and Table S5, and for a complete list of differentially accumulated metabolites see Table 2.