List of genes in each module from Fig 7.

Morphological phenotype and gene expression differences are observed between genetically identical plants grown in the same environment. While we now have a good understanding of the source and consequences of transcriptional differences observed between cells, our knowledge is still very limited regarding variability between multicellular organisms. We characterised this variability using the high-affinity nitrate transporter gene NRT2.1 as a model for high inter-individual transcriptional variability. Thanks to a combination of live imaging and transcriptomics, we show that the differences in expression of this gene between plants are established in young seedlings and maintained for up to three weeks. However, the expression level of NRT2.1 in plants does not permit predicting its expression in the next generation. Our results also indicate that these expression differences could have phenotypic consequences on root growth and nitrate uptake mediated by NRT2.1. Finally, we observed enriched photosynthesis-related functions among genes whose expression correlates with NRT2.1 in individual seedlings. Our study thus demonstrates that a global coordination of the genes involved in the carbon/nitrogen (C/N) balance in plants is established in young seedlings, at different levels in each plant, and maintained over time. Our results also highlight the fact that not all transcriptional regulators of NRT2.1 were identified, and propose UNE10 as a transcription factor for further study focused on its possible involvement in this pathway. This work shows that thanks to single-plant analysis of gene expression, we can gain new knowledge on the mechanisms behind a phenotype of interest that is normally masked in studies performed on pooled plants.