Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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Exploratory study for single cell-type RNA-sequencing of the Sorghum bicolor stem

Tuesday, September 3, 2019
Principal Investigator: 
Amy Marshall-Colon
Lead Institution: 
University of Illinois at Urbana-Champaign
Closed Date: 
Sunday, November 3, 2019
Project ID: 

Sorghum bicolor is an important bioenergy crop because it is nutrient and water use efficient, 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 oils or oil precursors, 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 gene expression and regulation. A high-resolution temporal and spatial transcriptome of sorghum stem cell-types would provide unprecedented insight into differential gene expression and regulation. An improved understanding of tissue and cell-type gene networks will accelerate the identification of gene targets for engineering for crop improvement. Recent advances in laser capture microdissection and RNA-sequencing have made single cell and single cell-type transcriptome studies feasible. The purpose of this proposal is to develop a protocol for stem cell-type RNA-sequencing. This proposal is mutually beneficial to BRC and EMSL researchers by increasing our collective expertise in molecular and biochemical approaches for sorghum. The pilot study proposed here will allow our collective team to troubleshoot potential problems and optimize a protocol for sorghum stem tissue analyses. EMSL has a unique combination of expertise and instrumentation for method development and testing, which is not available at our academic institutions. The proposed project will provide preliminary results needed for a larger-scale proposal to develop a cell-type specific sorghum stem gene expression atlas that would be an impactful resource for the BRC, specifically CABBI BRC and GLBRC.