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

Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum Biomass

Authors:

Wendell J. Pereira1* (wendellpereira@ufl.edu), Timothy Changa1, Chris Dervinis1, Kelly Balmant1, Sushmita Roy2, Wilfred Vermerris1, Matias Kirst1

Institutions:

1University of Florida; 2University of Wisconsin–Madison

Goals

Researchers plan to alter the genetic regulation of the cellular developmental programs that generate the vegetative tissues of sorghum, with the aim to increase the proportion of cells that are less recalcitrant to biomass deconstruction.

Abstract

Plant biomass is comprised of distinct cell types, which largely determine its physical and chemical properties, and hence, its recalcitrance to biomass processing aimed at generating fermentable sugars that microbes can convert to biofuels. The walls of parenchyma cells in the stalks of maize (Zea mays L.) and sorghum (Sorghum bicolor (L.) Moench) can be broken down using milder pretreatment conditions and with lower cellulase loadings than the lignified cells present in the outer rind of the stalk. The different cell types within the sorghum plant develop from undifferentiated meristem cells through variation in the spatio-temporal expression of regulatory genes that control structural genes. The understanding of the role of specific genes and their regulation in this developmental process is incomplete. Uncovering the function of the complete ensemble of genes involved in the differentiation and maturation of the cells that make up sorghum biomass creates the opportunity to manipulate its cellular composition, impacting its physical and chemical properties and, consequently, its value for bioenergy.

We are applying single-cell genome and transcriptome analysis of the sorghum shoot apex and stem to identify the function of genes involved in differentiating cells that determine biomass composition. Researchers have identified the internode in developing sorghum stems of 30-day-old plants that displays a developmental gradient, whereby the top of the internode is undifferentiated, and the bottom of the internode contains parenchyma, sclerenchyma, and proto-xylem cells. Nuclei isolated from dissected internodes have been subjected to single-nucleus RNA-sequencing using the 10×Genomics platform. Uniform Manifold Approximation and Projection (UMAP) was used to identify clusters of nuclei with similar expression profiles that are hypothesized to represent different stages of development of the different cell types. In the next phase, inferred cell lineage trajectories involved in the development of the cellular components of biomass will be explored to discover their regulators. Specific objectives are to: (1) define the function of each gene (including specific members within gene families) with respect to the development of the main cell types that determine sorghum biomass and its cell-wall composition; (2) construct the cellular lineages that give rise to each cell type that composes biomass (from the shoot apical and vascular cambium meristem cells to cells in the stem), and identify genes and cis-regulatory elements that contribute to the lineage progression; (3) categorize the function of gene and associated cis-regulatory components for their relevance in the control of cellular lineages that lead to each cell type; and (4) validate multiple targets in isolation and in parallel, to confirm their role in biomass development and their potential for enhancing biomass yield and its properties.

Funding Information

This research is supported by the DOE Office of Science, BER Program, grant no. DE-SC0023082.