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

Dev Cell. 2022 May 9;57(9):1177-1192.e6. doi: 10.1016/j.devcel.2022.04.013. Epub 2022 May 2.


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.

Keywords: Oryza sativa; chromatin; drought; roots; submergence; transcriptional regulatory networks; translatome.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / metabolism
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Oryza* / metabolism
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • Water / metabolism


  • Chromatin
  • Plant Proteins
  • Water