Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

This page lives in the old site. Check out our new site here.

Exploratory study to determine the spatial and temporal transcriptional landscape of the Sorghum bicolor stem

Tuesday, November 26, 2019
Principal Investigator: 
Amy Marshall-Colon
Lead Institution: 
University of Illinois at Urbana-Champaign
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 gene expression and regulation in sorghum stems. 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, including the potential identification of promoter elements that contribute to stem cell-type specific expression. 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 use a protocol, recently developed by EMSL and BRC researchers, for stem cell-type RNA-sequencing to explore the spatial and temporal transcriptome of sorghum stem cell-types. Specifically, four cell types over two developmental stages. This proposal is mutually beneficial to BRC 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 our academic institutions. The proposed project will provide preliminary results needed for a larger-scale proposal to develop a high-resolution atlas of sorghum stem gene expression over all developmental stages. The results of this exploratory proposal will be an important and impactful resource for CABBI BRC and GLBRC.