Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

Area of Science:

• Plant Biology
• Biotechnology
• Agricultural Science

Background:

• Bioenergy sorghum is a key crop for sustainable biofuels, biopower, and bioproducts due to its high biomass yield and resilience.
• Sorghum stems, comprising ~80% of biomass, accumulate sucrose valuable for bioethanol and biopolymer synthesis.
• Understanding cell-type specific gene expression in sorghum stems is crucial for engineering these valuable traits.

Purpose of the Study:

• To generate cell-type specific transcriptome profiles from bioenergy sorghum stems.
• To identify gene regulatory networks (GRNs) controlling cell-specific functions and biomass accumulation.
• To enable targeted engineering of sorghum stems for enhanced biofuel and bioproduct production.

Main Methods:

• Laser capture microdissection (LCM) was employed to isolate five distinct cell types from sweet sorghum (Wray) stems.
• Transcriptome sequencing was performed on isolated cell types to generate spatial transcriptomic data.
• Cell-specific data was integrated with known secondary cell wall (SCW) networks to identify relevant GRNs.

Main Results:

• Identified genes with cell-type specific and preferred expression patterns, revealing distinct cellular functions.
• Discovered unique transcription factor families and network motifs driving cell-specific regulatory landscapes.
• Uncovered GRNs differentially activating SCW formation in vascular sclerenchyma and epidermal cells.

Conclusions:

• The spatial transcriptomic dataset provides critical insights into sorghum stem cell functions and GRNs.
• This resource facilitates the engineering of bioenergy sorghum for improved biomass yield and composition.
• An interactive web application is available for exploring the comprehensive sorghum stem cell-type gene expression data.