Genome-wide analysis of gene expression in sorghum furthers efforts to improve stem biomass

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.

Recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, including a groundbreaking study that identified gene expression patterns in the major cell types that make up the tissue of sorghum stems — the bulk of the plant’s total biomass — as well as potential cell-type-specific promoters and underlying regulatory gene networks.

But comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem-preferred expression patterns 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.

To address these gaps, a collaborative team from several U.S. Department of Energy (DOE)-funded research centers reanalyzed a published RNA-seq dataset to identify genes with organ-preferential expression and to infer representative organ functions across major developmental stages.

The analysis revealed that the sorghum stem exhibits distinct temporal functional signatures, which correlate with the developmental dynamics of stem-specific genes and their associated regulatory elements.

The researchers further identified a set of genes with ubiquitous stem-specific expression across diverse sorghum genotypes, suggesting their universal importance and broad potential for genetic engineering applications. Among them, SbTALE03 and SbTALE04 emerged as stem hub transcription factors (TF). Gene regulatory network analysis further indicated that these TFs participate in stage-specific transcriptional programs that maintain and regulate stem development.

Overall, this study presents a genome-wide analysis of organ-specific gene expression, functions, and regulatory networks in sorghum, with a focus on genes preferentially expressed in stems and their promoter motifs. These findings offer valuable candidates for further functional characterization and genetic engineering aimed at improving sorghum stem biomass and composition.

The work was led by researchers at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), a DOE-funded Bioenergy Research Center (BRC), in collaboration with the Great Lakes Bioenergy Research Center (GLBRC) and the Joint Genome Institute (JGI), a DOE-funded user facility. The first author is CABBI's Jie Fu, a Ph.D. candidate who worked on the study with the late CABBI Co-PI Amy Marshall Colon of the Department of Plant Biology at the University of Illinois Urbana-Champaign. The corresponding author is CABBI Co-PI Kankshita Swaminathan of the HudsonAlpha Institute of Biotechnology.

The full study was published in BMC Plant Biology.