Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization

Table 1 Validated NARK regulation of soybean genes in R. irregularis-inoculated plants.

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

^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.

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