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Table 3 Putative phenylpropanoid/flavonoid gene sets upregulated more than 2-fold in the seed coats of black (iRT) soybean compared to the brown (irT) isolinea,b.

From: Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes

      SAM
Gene Family Probe Sets Name Target Description Black/brown fold change P-value d-score
Phenyl-propanoid/Flavonoid pathway GmaAffx.80720.1.S1_at DFR2* Dihydroflavonol-4-reductase 62.45 0.000002 24.70
  GmaAffx.42116.1.S1_at CHS4*/CHS5* Chalcone synthase (LOC732575) 10.99 0.000020 8.45
  GmaAffx.42116.1.S1_x_at    8.06 0.000026 7.124398
  Gma.1163.1.S1_at ANS2*/ANS3* Anthocyanidin synthase 6.77 0.000018 8.77
  Gma.17141.1.S1_at F3H-like Moderately similar to A. thaliana putative flavonone 3-β-hydroxylase clone U20744 (74%) 6.43 0.004849 2.03
  Gma.7423.2.S1_a_at 4CL-like 4-coumarate-CoA ligase-like protein 2.80 0.005815 1.96
  Gma.5621.1.S1_at G4DT* Pterocarpan 4-dimethylallyltransferase 2.36 0.009232 1.80
  Gma.8472.1.S1_at 4CL2* 4-Coumarate-CoA ligase 2 2.27 0.000108 4.60
Glycosyl-transferase GmaAffx.71999.1.S1_at UGT78K2 Glycosyltransferase 3.09 0.000124 4.50
  Gma.1002.2.S1_at UGT78K1* UDP-glucose:flavonoid 3-O-glucosyltransferase 2.81 0.000229 4.03
O-methyl-transferase Gma.9647.1.S1_at OMT-like O-methyltransferase, putative 2.58 0.000098 4.74
  GmaAffx.57777.1.S1_at OMT5 Caffeoyl-CoA O-methyltransferase 5 2.48 0.000157 4.33
Glutathione S-transferase GmaAffx.71212.1.A1_at GST26 Glutathione S-transferase 234.11 0.000003 21.22
  Gma.5139.1.S1_at GST21 Glutathione S-transferase 2.05 0.000656 3.09
  1. aExpression values were obtained using RMA (Irizarry et al., 2003).
  2. bSee Table S2 for the complete list of upregulated genes.
  3. *Previously characterized flavonoid biosynthesis genes.