Integrated comparative transcriptome and physiological analysis reveals the mechanisms underlying genotype variations in ammonium tolerance

Several mechanisms have been proposed to explain NH4+ toxicity. However, the core information about the biochemical regulation of plants in response to ammonium toxicity is still lacking. In this study, the tissue content of NH4+was found the main cause for NH4+ toxicity, and the cellular threshold was 50 µg/g. Furthermore, ammonium led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4+- tolerant ecotype Or-1. These results suggested that the NH4+-tolerant ecotype showed a more intense response to ammonium by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4+ uptake and NPE, but lower NH4+, indicating the tolerant ecotype maintained a low NH4+ level, mainly by promoting ammonium assimilation rather than inhibiting NH4+ uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton (2-OG) production capacity with higher levels of hexokinase (HK), pyruvate kinase (PK), and GDH activity to assimilate free NH4+. Taken together, the results revealed the threshold for ammonium toxicity and the core mechanisms utilized by plants in response to ammonium, which are consequently of ecological and agricultural importance Overall design: The seedlings were grown in a nitrate nutrient solution for 5 d, then transferred to 1 mM Ca(NO3)2 or 1 mM (NH4)2SO4 for 1 d. The total RNA was then extracted from the roots of the NH4+-tolerant and -sensitive ecotypes. Submitter states that missing raw files are due to file loss.