Rain-fed paddy rice is susceptible to water extremes – both flooding and drought - that reduce yields. A critical aspect of survival of water extremes is the regulation of gene networks and cellular processes in meristematic and differentiating cells. Even with new single-cell sequencing technologies, dynamics in gene regulation in these cell populations are difficult to monitor. To recognize key gene regulatory networks in developmentally plastic regions that are modulated by waterlogging, submergence, and moderate water deficit stress, we have used Translating Ribosome Affinity Purification (TRAP) and Isolation of Nuclei Tagged in specific Cell Types (INTACT), paired with the Assay for Transposase Accessible Chromatin (ATAC). Gene activity under controlled water extremes and post-stress recovery were contrasted with that of plants grown in the lab on plates as well as those cultivated in a paddy field. Using multiple methods of gene network modeling, we are identifying conditional and cell-population specific pathways, providing new insight into cellular and metabolic processes associated with response to and recovery from transient water extremes. I will share new data on our integration of quantitative information on constitutive and dynamic chromatin accessibility near transcription start sites, the occurrence of cis-regulatory motifs within these regions, and simultaneously active transcription factor genes enabled the recognition of network hubs specific to cell populations. These included networks activated by water deficit and reversed by re-watering. The data uncover dynamic gene regulatory networks controlling developmental plasticity in roots and more general acclimation mechanisms associated with flooding and water deficit resilience. Funded by US NSF-PGRP grants (IOS-1238243; IOS-1810468; IOS-1856749).
Julia Bailey-Serres is Distinguished Professor of Genetics, Director of the Center for Plant Cell Biology at the University of California, Riverside. She is a University of California MacArthur Foundation Chair. Bailey-Serres is known for her research on mechanisms of plant adaptive responses to environmental stresses. She is recognized for the in-depth dissection of the function of the SUBMERGENCE 1A gene, responsible for survival of rice plants under prolonged submergence as evidenced by its successful use in stabilizing rice grain yield in flood-prone regions of Asia. Her research has defined how plants sense and respond to deficiencies in oxygen and energy. She has pioneered technologies to uncover the activity of genes in specific cell types of multicellular organisms, through the capture of ribosomes and the associated mRNAs. Her current research focuses on mechanisms of metabolic and developmental plasticity to water extremes and nutrient deficiencies in rice, wheat and soybean provided by genes that have an impact in the field. The goal of these investigations is to provide molecular insight into genetic solutions that enhance global food security.
Bailey-Serres was born and raised in California, graduated from the University of Utah with a BS in biology and the University of Edinburgh with a PhD in botany. She began to work on flooding and gene regulation as a postdoctoral researcher at the University of California, Berkeley, an interest she has maintained as a faculty of the University of California, Riverside since 1990. She has mentored over 20 postdoctoral researchers, 20 doctoral students and 130 undergraduates. She currently leads the Plants3D graduate program that brings biologists and engineers together to translate discoveries to impact. Bailey-Serres is a fellow of the US National Academy of Sciences, American Association for the Advancement of Science and American Society of Plant Biologists. She serves as an Associate editor for several journals.