Fig 1.
Phenotypes of rice seedling roots under.
(A) Photograph of 10-day-old rice seedlings. (B) Photograph of 7-day-old rice seedlings. (C and D) Fresh weight (FW) and dry weight (DW) of roots of 7-day-old seedlings. Scale bars = 5 cm. Data are mean ± SD; t-tests were used to identify significant differences, and different letters represent significant differences among different treatments (p < 0.05).
Fig 2.
(A) Photograph of roots grown for 7 days. Scale bar = 2 cm. (B-F) Measured parameters. ECR = embryonic crown root. Data are mean ± SD, n = 10; t-tests were used to identify significant differences, and different letters represent significant differences among different treatments (p < 0.05).
Fig 3.
Morphology, auxin responsiveness, and rhizosphere acidification.
(A) Micrographs of paraffin sections of radicles from 7-day-old seedlings. The approximate boundary of the elongation zone is marked by white arrowheads. (B) Micrographs of 7-day-old roots expressing DR-5::GUS, stained for GUS activity. In A and B, roots shown are the roots representative, selected from 10 seedlings in each treatment. Scale bars = 50 μm. (C) The pH of the culture solutions was measured every 2 days from the 3rd day after seed germination. Data are the mean ± SD; t-tests were used to identify significant differences; ** (p < 0.01) represent significant differences between each alleviation treatment and ammonium toxicity treatment.
Fig 4.
Composition, transport, and enzyme activity related to nitrogen status.
(A) The ammonium concentrations. (B and C) For the 15NH4+ transport assay, rice seedlings were grown for 7 days in 14NH4Cl (for B) or 15NH4Cl (for C) solution containing no other substance and then transferred to solutions containing 15NH4Cl (for B) or 14NH4Cl (for C) with the 3 alleviation treatments for 1 hour (see Materials and methods) before the root 15N content was measured. (D-H) Data are mean ± SD; t-tests were used to identify significant differences, and different letters represent significant differences among different treatments (p < 0.05).
Fig 5.
Differentially expressed genes (DEGs).
(A) Numbers of differentially expressed genes between given treatments and the control (H2O). (B) Venn diagram showing alleviation-related gene numbers in each alleviation treatment. The expression of these genes was differentially regulated by ammonium toxicity and restored to the control level by the 3 alleviation treatments.
Fig 6.
The weighted gene correlation network analysis.
(A) Hierarchical cluster tree showing coexpression modules identified by WGCNA. Each leaf in the tree represents 1 gene. The major tree branch comprises 15 modules labeled by different colors. (B) Venn diagram showing the interactions of genes in root-trait coupled modules and differentially expressed genes with expression that was recovered only by KNO3 under ammonium toxicity. (C) Module-trait association. Each row corresponds to a module. Each column corresponds to a trait. The color of each cell at the row-column intersection indicates the correlation coefficient from -1 (green) to 1 (red).
Fig 7.
The cell wall regulation network related to this synergism.
(A) A network involved in cell wall formation was constructed according to the literature (line) and predicted transcriptional regulation (dashed line). Blue boxes indicate genes or proteins; yellow ovals indicate chemicals; green boxes indicate biological processes. (B) Expression patterns of genes in this network under the treatments.