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

Single-Cell Omics to Examine the Cell Type-Specific Gene Regulatory Programs of Mucilage Production in Sorghum bicolor


Rafael E. Venado1, Saptarshi Pyne1, Matias Kirst2, Sushmita Roy1, and Jean-Michel Ané1*


1University of Wisconsin–Madison; and 2University of Florida


Specific accessions of sorghum (Sorghum bicolor) develop aerial roots and produce carbohydrate-rich mucilage. The presence of mucilage suggests potential nitrogen-fixing microbial associations that contribute to nitrogen nutrition, as reported in a maize (Zea mays) landrace. However, the specific cell types and their underlying gene regulatory programs that produce mucilage are poorly understood. To understand the molecular basis of mucilage production, researchers developed a protocol to isolate nuclei of the cells collected from aerial roots that produced mucilage. The isolated nuclei were then sequenced using the 10X Genomics chromium technology. The preliminary single-nucleus dataset of circa 7,000 cells detected cell types in the aerial root based on the expressions of known marker genes. In parallel, the team has been developing novel analytical pipelines to identify cell types, cellular lineage structure, and cell-type-specific gene regulatory networks (GRNs). Using the team’s approach to published single-cell RNA-seq datasets, researchers were able to recapitulate putative GRN components and regulators for the cell fate specification. Applying these approaches to the sorghum single nucleus datasets should advance understanding of mucilage production in the aerial root. This opens the possibility of identifying and validating candidate genes for breeding this important trait.