Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

• Type of Material: Article
• Authors: Mauricio A. Reynoso, University of California Riverside; Alexander T. Borowsky, University of California Riverside; Germain C. Pauluzzi, University of California Riverside; Elaine Yeung, University of California Riverside; Jianhai Zhang, University of California Riverside; Elide Formentin, University of California Riverside; Joel Velasco, University of California Riverside; Sean Cabanlit, University of California Riverside; Christine Duvenjian, University of California Riverside; Matthew J. Prior, University of California Riverside; Garo Z. Akmakjian, University of California Riverside; Roger Deal, Emory University; Neelima R. Sinha, University of California Davis; Siobhan M. Brady, University of California Davis; Thomas Girke, University of California Riverside; Julia Bailey-Serres, University of California Riverside
• Language: English
• Date: 2022-05-09
• Publisher: Elsevier
• Publication Version: Final Published Version
• Copyright Statement: © 2022 The Authors. Published by Elsevier Inc.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): https://doi.org/10.1016/j.devcel.2022.04.013
• Title of Journal or Parent Work: Developmental Cell
• Volume: 57
• Issue: 9
• Start Page: 1177
• End Page: 1192.e6
• Grant/Funding Information: Funding support for this work: NSF PGRP grants IOS-1238243 and 1856749 to R.B.D., N.R.S., S.M.B., and J.B.-S.; NSF PGRP IOS-1810468 to T.G. and J.B.-S.; NSF DGE-1922642 to A.T.B. and J.B.-S.; and USDA NIFA 1026477 to A.T.B; ANPCyT PICT 2018-00503 and PICT 2019-01970 to M.A.R.
• Keywords: chromatin; submergence; Oryza sativa; transcriptional regulatory networks; translatome; drought; roots
• Research Categories: Biology, Cell; Biology, Plant Physiology

Abstract

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.