Deciphering the Molecular Landscape of Bioenergy Sorghum Stems: Insights from Cell-Type-Specific Transcriptomics and Regulatory Networks

  • SorghumBase Team
  • 3 June 2024

Sweet sorghum, an annual crop with high biomass yield potential, low-input requirements, drought-resilience and deep-rooting, is a sustainable source of biofuel. By utilizing laser capture microdissection, researchers at University of Illinois Urbana-Champaign, Texas A&M University, DOE Center for Advanced Bioenergy and Bioproducts Innovation and Pacific Northwest National Laboratory isolated and analyzed transcriptome profiles from five major cell types present in sweet sorghum stems. Through transcriptome analysis, they identified genes with cell-type-specific expression patterns, revealing distinct metabolic and regulatory functions for each cell type. Additionally, the study uncovered cell-type-specific gene regulatory networks governing processes like secondary cell wall (SCW) formation, crucial for stem strength and biofuel production. 

By dissecting different cell types and examining their gene expression profiles, the researchers identified unique transcription factor families contributing to specific regulatory networks. Notably, the study highlighted the differential expression of genes involved in photosynthesis and carbohydrate metabolism across distinct cell types within the stem. Furthermore, the investigation into SCW biosynthesis unveiled cell-type-specific regulators and candidate genes influencing SCW accumulation patterns. Through bioinformatic analysis, the study elucidated both direct and indirect interactions between cell-type-specific transcription factors and their target genes, providing insights into the molecular mechanisms shaping sorghum stem architecture and function. The spatial transcriptomic dataset generated serves as a valuable resource for understanding sorghum stem biology and facilitating future research and engineering efforts aimed at enhancing bioenergy sorghum productivity.

This is the first high resolution insight into gene expression in mature internodes and lays the foundation for engineering specific cell types to produce novel bioproducts. – Marshall-Colon

The successful application of LCM on isolation of sorghum stem cell types opens a chance of obtaining a more comprehensive multi-omics atlas that extends beyond just transcriptomes. Our ongoing efforts have already yielded highly promising results. – Fu

SorghumBase examples: 

Figure 1: Phylogenetic Tree of Sorghum and Arabidopsis SCW Repression Genes. This figure presents a phylogenetic tree comparing sorghum genes with Arabidopsis genes that repress secondary cell wall (SCW) formation, focusing on the sorghum gene SbBHL6 (Sobic.001G494000). The analysis highlights evolutionary relationships and potential targets for enhancing sorghum biomass production for biofuel.

Reference:

Fu J, McKinley B, James B, Chrisler W, Markillie LM, Gaffrey MJ, Mitchell HD, Riaz MR, Marcial B, Orr G, Swaminathan K, Mullet J, Marshall-Colon A. Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems. Plant J. 2024 Feb 26. PMID: 38407828. doi: 10.1111/tpj.16690. Read more

 

Related Project Websites: 

Image 1: Spatial expression pattern of Sobic.001G106000 between shoot apex and nascent leaves in S.bicolor cv Wray at the vegetative stage, visualized by RNAScope in situ hybridization (ISH). Photo credit Dr. Brandon James, a member of Dr. Kankshita Swaminathan’s group at HudsonAlpha Institute for Biotechnology.