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

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


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

bSee Table S5 for the complete list of up-regulated genes.

*Previously characterized flavonoid biosynthesis genes.

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

Open Data