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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Physiology
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1343073
This article is part of the Research Topic Nitrogen Metabolism in Crops and Model Plant Species View all 8 articles

Nitrate and Ammonium, the Yin and Yang of Nitrogen Uptake: A Time-Course Transcriptomic Study in Rice

Provisionally accepted
Pierre-Mathieu Pélissier Pierre-Mathieu Pélissier 1,2Boris Parizot Boris Parizot 1,2Letian Jia Letian Jia 3Alexa De Knijf Alexa De Knijf 1,2*Vera Goossens Vera Goossens 4,5*Pascal Gantet Pascal Gantet 6Antony Champion Antony Champion 6Dominique Audenaert Dominique Audenaert 4,5*Wei Xuan Wei Xuan 3Tom Beeckman Tom Beeckman 1,2*Hans Motte Hans Motte 1,2*
  • 1 Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
  • 2 VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
  • 3 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
  • 4 Ghent University, Center for Bioassay Development and Screening (C-BIOS), 9052 Ghent, Belgium
  • 5 VIB Screening Core, 9052 Ghent, Belgium
  • 6 UMR DIADE, Université de Montpellier, IRD, CIRAD, 911 Ave Agropolis, 34394 Montpellier cedex 5, France

The final, formatted version of the article will be published soon.

    Nitrogen is an essential nutrient for plants and a major determinant of plant growth and crop yield. Plants acquire nitrogen mainly in the form of nitrate and ammonium. Both nitrogen sources affect plant responses and signaling pathways in a different way, but these signaling pathways interact, complicating the study of nitrogen responses. Extensive transcriptome analyses and the construction of gene regulatory networks, mainly in response to nitrate, have significantly advanced our understanding of nitrogen signaling and responses in model plants and crops. In this study, we aimed to generate a more comprehensive gene regulatory network for the major crop, rice, by incorporating the interactions between ammonium and nitrate. To achieve this, we assessed transcriptome changes in rice roots and shoots over an extensive time course under single or combined applications of the two nitrogen sources. This dataset enabled us to construct a holistic co-expression network and identify potential key regulators of nitrogen responses. Next to known transcription factors, we identified multiple new candidates, including the transcription factors OsRLI and OsEIL1, which we demonstrated to induce the primary nitrate-responsive genes OsNRT1.1b and OsNIR1. Our network thus serves as a valuable resource to obtain novel insights in nitrogen signaling.

    Keywords: Transcriptome, rice, co-expression network, Nitrogen, OsRLI1, OsEIL1

    Received: 22 Nov 2023; Accepted: 29 Jul 2024.

    Copyright: © 2024 Pélissier, Parizot, Jia, De Knijf, Goossens, Gantet, Champion, Audenaert, Xuan, Beeckman and Motte. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Alexa De Knijf, Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
    Vera Goossens, Ghent University, Center for Bioassay Development and Screening (C-BIOS), 9052 Ghent, Belgium
    Dominique Audenaert, Ghent University, Center for Bioassay Development and Screening (C-BIOS), 9052 Ghent, Belgium
    Tom Beeckman, Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
    Hans Motte, Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.