Exploring the Effects of Nitrate and Ammonium on the Rice Root Transcriptome: a Systems Biology Approach

Nitrate (NO₃^-) and ammonium (NH₄⁺) are the two main forms of nitrogen available for plants in crop soils. Plants can adapt their root system architecture according to the availability of these nutrients, and NO₃^- and NH₄⁺ are known to have an important effect on lateral root density and primary root length. As an optimally developed root system contributes to an enhanced nitrogen use efficiency and hence an overall increase of yield, understanding the plant response at a molecular level to these two forms of nitrogen is of interest for modern agronomy.

For this purpose, we performed RNAseq analyses of the response to NO₃^-, NH₄⁺, or a combination of the two over a time-course in rice roots. In parallel, we also analyzed the transcriptional responses of the shoots since in the case of nutrient availability roots are known to interact with the aerial parts of the plant via the systemic signaling pathway. These experiments have resulted in a list of differentially expressed genes specific to an early response to nitrate, ammonium and their combination and of genes that are characteristic of steady state levels. Having several data-points considerably increased the resolution and allowed the construction of a gene co-expression network in which genes strongly co-regulated are clustered together into modules. Simultaneously, imaging the root system at the same conditions as the ones used during the transcriptomic analysis allowed the quantification of phenotypes such as the lateral root density, the root insertion angle, the lateral and primary root length and the total root surface in response to NO₃^- and NH₄⁺.

The phenotypic observations, the differentially expressed genes and the gene co-expression network information are eventually linked and analyzed to identify driver genes regulating the root system in response to NO₃^- and NH₄⁺, which will be of strong agronomical interest.