Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2024 Abstracts

Understanding Plant/Environmental Interactions Using Single-Cell Approaches


Benjamin Cole1,5*, Thai Dao1, Karen Serano1,3,4,5, Margot Bezrutczyk1, Danielle Goudeau1, Rex Malmstrom1, Ronan O’Malley1, Axel Visel1,2, Henrik Scheller3,4,5


1DOE Joint Genome Institute; 2School of Natural Sciences, University of California–Merced; 3Joint BioEnergy Institute; 4Department of Plant and Microbial Biology, University of California–Berkeley; 5Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory


Biomass derived from plant feedstocks is a renewable and sustainable energy resource, but these resources are vulnerable to environmental stress such as water and nutrient limitations. Understanding how cells work independently and in concert to regulate plant responses to their environment, including their surrounding microbial community, as well as abiotic stress will be crucial to improving their performance. This Early Career Research Project applies several cutting-edge single-cell and spatially resolved–transcriptome sequencing approaches to construct a comprehensive single-cell resource for plants and to better understand the complexity behind environmental responses among diverse cell types. To this end, researchers have profiled thousands of individual sorghum root cells grown under normal and phosphate-limited conditions. The team has also begun to profile Brachypodium root and leaf cells using single nuclei-RNA sequencing. Researchers are currently integrating this nascent data with additional single-cell data from other species, including maize. The project is also characterizing environmental stress using other advanced profiling methods, including spatial transcriptomics and spatial metabolomics, on plant-arbuscular mycorrhizae interactions. The team hopes to build a multispecies model of cell type–specific environmental responses.