Table 1

Validated NARK regulation of soybean genes in R.

Gene locus

Affymetrix probe set(s)

Predicted gene function/Name

wt/nark (Affymetrix)^a

wt/nark_¬ (RT-qPCR)^b

Shoots

Roots

Shoots

Roots

Glyma15g15171

GmaAffx.30002.1.S1_at

Unknown

1.86

0.80

1.97

n.a.

Glyma18g17440

Gma.7686.1.S1_at

Ornithine acetyl transferase

0.17

0.12

0.028

0.0065

Glyma02g11150 [UniGen:EU669879]

GmaAffx.82595.1.S1_at GmaAffx.82595.2.S1_at

Stress-induced receptor-like kinase GmSIK1

0.22 0.30

0.02 0.08

0.25

0.23

Glyma17g09270

GmaAffx.68580.1.S1_at GmaAffx.46141.1.S1_at

DEAD box RNA helicase

0.71 0.74

0.65 0.71

0.54

0.60

Glyma10g35000

Gma.6487.1.A1_at

Unknown

1.37

0.44

n.a.

0.49

Glyma07g36986

Gma.17992.1.S1_at

Unknown

0.62

0.50

0.58

0.59

Glyma15g38010

Gma.3440.2.S1_at Gma.3440.2.S1_a_at

Annexin/GmAnn1a

0.37 0.43

0.82 0.79

0.30

0.90

Glyma03g36140

GmaAffx.40657.1.S1_at

NF-YA/GmNF-YA1a

0.70

0.56

0.84

0.63

Glyma19g38800

GmaAffx.40657.1.S1_at

NF-YA/GmNF-YA1b

0.70

0.56

0.76

0.62

irregularis-inoculated plants.

^aThe value gives the mean ratio between the mRNA accumulation in mycorrhizal plants of Bragg wild-type (wt) and of the nark mutant nts1007 19 days after inoculation determined by Affymetrix gene expression analysis (n = 3). Data for roots derived from non-inoculated root-parts of mycorrhizal plants. Bold numbers indicate values with P ≤0.1 (Student's t-test). Details are provided in Table S1 in Additional file 2.

^bThe value gives the mean ratio between the mRNA accumulation in mycorrhizal plants of Bragg-wild type (wt) and of both nark mutants 19 days after inoculation determined by RT-qPCR analysis in biological replicates different to those used for Affymetrix GeneChip analysis (n ≥8 of two to three independent experiments). Data for roots derived from non-inoculated root-parts of mycorrhizal plants. Bold numbers indicate values with P ≤0.05 (Student's t-test). n.a.: not analyzed.

Schaarschmidt et al. Genome Biology 2013 14:R62   doi:10.1186/gb-2013-14-6-r62