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Developing a protocol for spatial metabolomics to investigate cell types in the Sorghum bicolor stem

EMSL Project ID


Sorghum bicolor is an important bioenergy crop because it has high nutrient and water use efficiency, and produces a large quantity of biomass that can be processed into ethanol for biofuels. Many genomic resources exist for sorghum, and the transformation efficiency of different sorghum lines is increasing. Thus, sorghum is an ideal crop to research for improved biofuel and bioproduct production. One potential advancement would be to engineer sorghum stems to accumulate bioproducts, which would decrease the burden on conversion groups in the biofuel industry. Despite the wealth of sorghum sequencing data for gene expression and genetic variation, there is little information available about sorghum stem biology. Likewise, no studies have focused on single cell or single cell-type specific molecular biology in sorghum stems. The goals of this proposal are to i) understand the multilayer GRNs associated with cell specific stem carbon influx from leaves and subsequent utilization; and ii) exploit this information to engineer carbon partitioning such that mature stems become sinks for high value bioproducts like vegetative lipids and amino acids. A greater understanding of the genes that regulate traits and pathways of interest will accelerate the engineering of sorghum ideotypes with fine-tuned production of bioproducts in stems.
A high-resolution temporal and spatial transcriptome of the sorghum stem at two developmental stages has been obtained. This analysis revealed the differential expression of cell type specific genes at vegetative and reproductive stages. The resulting gene regulatory networks (GRNs) uncovered target genes for functional testing. Complementary proteomics and metabolomics would provide unprecedented insight into differential expression and regulation of genes and gene products that contribute to important phenotypes. EMSL’s recent advances in imaging mass spectrometry have made spatial metabolomics studies feasible. The purpose of the current proposal is to use EMSL’s protocols to expand our understanding of multilayer regulation stem cell types and the metabolic dynamics between adjacent cell types. The proposed research will include cryosectioning, standard "bulk" metabolomics and lipidomics, and spatial metabolomics through imaging MS. Spatial metabolomics data will be incorporated into GRN models to strengthen predicted interactions. This proposal is mutually beneficial to the researchers involved and EMSL researchers by increasing our collective expertise in molecular and biochemical approaches for sorghum, an important bioenergy crop. EMSL has a unique combination of expertise and instrumentation for method development and testing, which is not available at the academic institutions of the PIs. The proposed project will provide a molecular atlas of sorghum stems over development, and vastly increase our understanding of grass stem biology. The results of this exploratory proposal will be an important and impactful resource that will be shared freely among DOE funded BRCs.

Project Details

Project type
Exploratory Research
Start Date
End Date


Principal Investigator

Amy Marshall-Colon
University of Illinois at Urbana-Champaign


John Mullet
Texas A&M University

Kankshita Swaminathan
HudsonAlpha Institute for Biotechnology

Team Members

Brock Weers
Texas A&M University

Jie Fu
University of Illinois at Urbana-Champaign