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.

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


aExpression values were obtained using RMA (Irizarry et al., 2003).

bSee Table S2 for the complete list of upregulated genes.

*Previously characterized flavonoid biosynthesis genes.

Kovinich et al. BMC Genomics 2011 12:381   doi:10.1186/1471-2164-12-381

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