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

• Published in: Developmental cell Vol. 57; no. 9; pp. 1177 - 1192.e6
• Main Authors: Reynoso, Mauricio A., Borowsky, Alexander T., Pauluzzi, Germain C., Yeung, Elaine, Zhang, Jianhai, Formentin, Elide, Velasco, Joel, Cabanlit, Sean, Duvenjian, Christine, Prior, Matthew J., Akmakjian, Garo Z., Deal, Roger B., Sinha, Neelima R., Brady, Siobhan M., Girke, Thomas, Bailey-Serres, Julia
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09-05-2022
• Subjects: chromatin; drought; Oryza sativa; roots; submergence; transcriptional regulatory networks; translatome; submergence; Oryza sativa; transcriptional regulatory networks; drought; translatome; roots; chromatin
• ISSN: 1534-5807; 1878-1551
• DOI: 10.1016/j.devcel.2022.04.013

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.
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•A translatome and chromatin atlas of rice root cell populations in nine environments•Cell-type population signatures can be maintained or perturbed across environments•Dynamic regulatory networks and transcription factor hierarchies of cell populations•Conditional plasticity of the cell cycle and barrier cell suberization and Fe uptake
Reynoso, Borowsky, Pauluzzi, et al. provide an atlas of gene activity of root cell populations of rice in varied agronomically relevant environments. They identify genomic cis- and trans-regulatory factors involved in stress responses that can facilitate breeding and engineering climate-resilient crops.