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DOE OSTI · 3413470

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

Fu, Jie [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)]·James, Brandon [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)]·Hetti-Arachchilage, Madara [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)]·Lei, Yingjie [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); University of Illinois at Urbana-Champaign, IL (United States)]·McKinley, Brian [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)]·Kurtz, Evan [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)]·Barry, Kerrie [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)]·Moose, Stephen P. [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); University of Illinois at Urbana-Champaign, IL (United States)]·Mullet, John E. [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)]·Swaminathan, Kankshita [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)]·Marshall-Colon, Amy [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)]
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Abstract

Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified.

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59 BASIC BIOLOGICAL SCIENCESGene regulatory networkOrgan specificSorghumStemStem specificTranscription factor binding site

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Fu, Jie [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)], James, Brandon [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)], Hetti-Arachchilage, Madara [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)], Lei, Yingjie [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); University of Illinois at Urbana-Champaign, IL (United States)], McKinley, Brian [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)], Kurtz, Evan [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)], Barry, Kerrie [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Moose, Stephen P. [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); University of Illinois at Urbana-Champaign, IL (United States)], Mullet, John E. [Texas A&M University, College Station, TX (United States); DOE Great Lakes Bioenergy Resource Center, Madison, WI (United States)], Swaminathan, Kankshita [DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)], Marshall-Colon, Amy [University of Illinois Urbana-Champaign, IL (United States); DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)]. 2025-10-01. Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum. https://doi.org/10.1186/s12870-025-07303-1

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