Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice.
Mauricio A Reynoso, Alexander T Borowsky, Germain C Pauluzzi, Elaine Yeung, Jianhai Zhang, Elide Formentin, Joel Velasco, Sean Cabanlit, Christine Duvenjian, Matthew J Prior, Garo Z Akmakjian, Roger B Deal, Neelima R Sinha, Siobhan M Brady, Thomas Girke, Julia Bailey-Serres
Author Information
Mauricio A Reynoso: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina.
Alexander T Borowsky: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Germain C Pauluzzi: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Elaine Yeung: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Jianhai Zhang: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Elide Formentin: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy.
Joel Velasco: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Sean Cabanlit: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Christine Duvenjian: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Matthew J Prior: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Garo Z Akmakjian: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Roger B Deal: Department of Biology, Emory University, Atlanta, GA 30322, USA.
Neelima R Sinha: Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.
Siobhan M Brady: Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
Thomas Girke: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
Julia Bailey-Serres: Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands. Electronic address: serres@ucr.edu.
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
