Research Insights

Switchgrass, a C4 grass native to the US, is a high-yielding cellulosic bioenergy feedstock. Lowland switchgrass ecotypes produce high biomass yields but are largely cold-sensitive, which hinders expansion of their cultivation into Northern US regions where the lower yielding, but cold-tolerant upland ecotype is grown. Extensive efforts are dedicated to the rapid domestication of switchgrass, selecting for biomass yield, composition and environmental adaptation, to help meet the emerging demand for biofuels. To achieve this, a thorough understanding of the genetics of key traits and an ability to manipulate the underlying genes in a tissue or cell-type-specific manner is essential. This project aims to leverage single-cell genomics and natural variation in switchgrass to investigate mechanisms underlying cold tolerance and plant regeneration. By integrating single-cell genomics and spatial transcriptomics, we will generate a comprehensive resource detailing cell-type-specific transcripts and active cis-regulatory elements. Additionally, we are developing a cost-effective, open-source spatial transcriptomics platform specifically for plants, enabling 3D reconstruction of transcriptomes. Achieving these goals will provide the research community with a transformative resource and uncover genes and cis-regulatory elements critical for cold tolerance and plant regeneration. In the long term, this work will advance switchgrass genome annotation, improve causal gene identification for traits, refine transgene and cis-regulatory sequence design, and enhance the precision of genome-editing strategies across diverse accessions to engineer trait variation. To accomplish these goals, we propose three major objectives that will result in a high-resolution single-cell genomic atlas for switchgrass, development of open-source spatial transcriptomics applications for plants, identification of gene regulatory networks underlying cold tolerance and plant regeneration. Objective 1: Create a single-cell genomic atlas for switchgrass. Objective 2: Identify cell-type-specific transcripts and active cis-regulatory elements in upland (VS16), lowland (AP13) and isogenic switchgrass genotypes targeted at improving cold tolerance. Objective 3: Identify cell-type-specific transcripts and active cis-regulatory elements important for cell totipotency in regenerable calli as compared to non-regenerable calli. Successful completion of these objectives will result in a high-resolution and high-quality cell type-specific transcript and chromatin accessibility atlas for ten major switchgrass organs. This resource will enable the switchgrass community to multiply its impact to improve this important bioenergy feedstock. The use of single-cell genomics to explore cold tolerance and plant regeneration will provide an unprecedented view into how these processes occur at cell-type resolution thereby enabling development of varieties with expanded growth ranges, and advances in genome engineering strategies independent of genotype.

Funder: U.S. Department of Energy 

Amount: $2,183,886 

PI: Robert Schmitz, Franklin College of Arts and Sciences, Department of Genetics