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

Fu, Jie; McKinley, Brian; James, Brandon; Chrisler, William; Markillie, Lye Meng; Gaffrey, Matthew J.; Mitchell, Hugh D.; Riaz, Muhammad Rizwan; Marcial, Brenda; Orr, Galya; Swaminathan, Kankshita; Mullet, John; Marshall‐Colon, Amy

doi:10.1111/tpj.16690

Title: Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

Journal Article · 25 February 2024 · The Plant Journal

DOI: https://doi.org/10.1111/tpj.16690 · OSTI ID:2311910

^[1]; McKinley, Brian ^[2]; James, Brandon ^[3]; Chrisler, William ^[4]; Markillie, Lye Meng ^[4]; Gaffrey, Matthew J. ^[4]; Mitchell, Hugh D. ^[4]; Riaz, Muhammad Rizwan ^[5]; Marcial, Brenda ^[3]; Orr, Galya ^[4]; Swaminathan, Kankshita ^[3]; Mullet, John ^[2];

^[1]

Department of Plant Biology University of Illinois Urbana‐Champaign Urbana Illinois 61801 USA, DOE Center for Advanced Bioenergy and Bioproducts Innovation Urbana Illinois 61801 USA
Department of Biochemistry and Biophysics Texas A&,M University College Station Texas 77843 USA, DOE Great Lakes Bioenergy Resource Center Madison Wisconsin 53726 USA
DOE Center for Advanced Bioenergy and Bioproducts Innovation Urbana Illinois 61801 USA, HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806 USA
Pacific Northwest National Laboratory Richland Washington 99354 USA
Department of Plant Biology University of Illinois Urbana‐Champaign Urbana Illinois 61801 USA

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

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Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; SC0018409; SC0018420; AC05-76RL01830

OSTI ID:: 2311910

Alternate ID(s):: OSTI ID: 2426596; OSTI ID: 2426951

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 5 Vol. 118; ISSN 0960-7412

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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