Seminars

Plants need to adapt to a myriad of combined signals coming from i) their environment and ii) their own metabolism, to finely tune their development and phase transitions. Gene Regulatory Networks (GRNs) leading to these adaptations and signal integration are the central point of our research. Here I will show that by focusing on Nitrate (NO3-) regulated transcription factors (TFs) and their genome wide activity, using a technique called TARGET (Transient Assay Reporting Genome wide Effect of Transcription factors)¹, we were able to identify several important signaling cross-talks between NO3-, Phosphate (PO43-) ²,³and Reactive Oxygen Species (ROS) pathways⁴. These studies open perspectives at the same time on i) applied biotechnology [since we discovered genotypes with an enhanced NO3- transport activity]⁴, as well as on ii) basic understanding of large GRN function, dynamics, emerging properties, and topology in plants⁵. Finally I will present the recent method we developed the last 7 years, that now provides full epistatic maps that can be understood and 2D GWAS ⁶. This technique, by studying more than 60 billion marker interactions, helps to improve phenotypic predictions using machine learning techniques ⁶.

1.    Bargmann, B. O. R. Mol. Plant 6, 978–980 (2013)  DOI: .
2.    Medici, A. Nat. Commun. 6, 6274 (2015)  DOI: .
3.    Medici, A. Plant Cell 31, 1171–1184 (2019)  DOI: .
4.    Safi, A. J. Exp. Bot. (2021) doi:10.1093/jxb/erab114 DOI:  10.1093/jxb/erab114.
5.    Carré, C. NPJ Syst Biol Appl 3, 17 (2017)  DOI: .
6.    Carré, C. 2022.07.20.500572 (2022) doi:10.1101/2022.07.20.500572