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Fig. S1 Conditional indeterminate domain 10 (idd10) phenotypes and complementation test.

Fig. S2 Root growth of indeterminate domain 10 (idd10) mutants in modified Murashige–Skoog (MS) salts medium.

Fig. S3 Complementation assay and ammonium-mediated gene induction in the indeterminate domain 10-green fluorescent protein (IDD10-GFP) overexpression line.

Fig. S4 Electromobility shift assays (EMSAs) identify an indeterminate domain 10 (IDD10)-binding sequence in the AMT1;2 promoter.

Fig. S5 Expression of four N-linked metabolic genes in three independent overexpression lines.

Fig. S6 Locations of indeterminate domain 10 (IDD10)-binding motifs present in the promoters of ferredoxin-nitrite reductases (NiRs) and cytokinin dehydrogenase or the introns of glutamine synthetase 2 (GS2) and trehalose-6-phosphate synthase, and electromobility shift assay (EMSA) of IDD10-binding affinity.

Fig. S7 Effects of glutamine dosage on the ammonium transporter AMT1;2 and glutamate dehydrogenase 2 (GDH2).

Fig. S8 Ammonium contents in wild-type and indeterminate domain 10 (idd10) roots.

Fig. S9 The indeterminate domain 10 (idd10) root coiling phenotype is independent of external pH.

Table S1 List of ammonium-responsive genes affected by indeterminate domain 10 (IDD10)

Table S2 Sequences of real-time PCR primers

Table S3 Primer sequences