Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Glenn, Priscilla D.; McKinley, Brian A.; Barry, Kerrie; Schmutz, Jeremy; Mullet, John E.

doi:10.1111/tpj.70922

Title: Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Journal Article · Wed May 20 00:00:00 UTC 2026 · The Plant Journal

DOI: https://doi.org/10.1111/tpj.70922 · OSTI ID:3364448

^[1]; McKinley, Brian A. ^[1];

^[2];

^[3]; Mullet, John E. ^[1]

Department of Biochemistry and Biophysics Texas A&M University College Station Texas 77843 USA
Joint Genome Institute Lawrence Berkeley National Lab Berkeley California USA
HudsonAlpha Institute for Biotechnology Huntsville Alabama USA

SUMMARY Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA‐seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co‐expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co‐expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA‐seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day‐length, shading, water‐deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

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Research Organization:: Great Lakes Bioenergy Research Center (GLBRC) (GLBRC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018409

OSTI ID:: 3364448

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 4 Vol. 126; ISSN 1365-313X; ISSN 0960-7412

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

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