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Table 4 Putative phenylpropanoid/flavonoid gene probe sets downregulated more than 2- fold in the black (iRT) compared to the brown (irT) soybean seed coata,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

Gene Family      SAM
  Probe Sets Name Target Description Black/brown fold change P-value d-score
Phenyl-propanoid/ Gma.17605.1.S1_at CHS1* Chalcone synthase 0.028 0.000007 -16.45
Flavonoid GmaAffx.92491.1.S1_s_at CHS9* Chalcone synthase 0.047 0.000005 -19.36
pathway GmaAffx.89828.1.S1_s_at IFR1-like Highly similar to isoflavone reductase homolog 1 (IFR1) (93%) 0.272 0.000132 -4.46
  Gma.8455.1.S1_at sf3'h1* Flavonoid 3'-hydroxylase 0.400 0.000646 -3.10
  GmaAffx.93221.1.S1_s_at OOMT-like Moderately similar to Rosa rugosa orcinol O-methyltransferase (OOMT-A) (72%) 0.410 0.003428 -2.17
  GmaAffx.34868.1.A1_at LAR1 Highly similar to Phaseolus coccineus leucoanthocyanidin reductase (LAR) (88%) 0.443 0.000016 -9.02
  Gma.4340.2.S1_a_at   Moderately similar to P. trichocarpa flavonoid O-methyltransferase-related (73.9%) 0.462 0.004180 -2.08
  Gma.10949.1.S1_s_at   Moderately similar to A. thaliana 3-chloroallyl aldehyde dehydrogenase/aldehyde dehydrogenase (NAD)/coniferyl-aldehyde dehydrogenase (ALDH2C4) (75.5%) 0.495 0.000273 -3.92
Transport GmaAffx.39265.1.S1_at MATE1 Weakly similar to A. thaliana antiporter/drug transporter MATE family protein (69.8%) 0.414 0.000265 -3.95
  1. aExpression values were obtained using RMA (Irizarry et al., 2003).
  2. bSee Table S5 for the complete list of up-regulated genes.
  3. *Previously characterized flavonoid biosynthesis genes.