Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Defining Transcriptomic Dynamics in Sorghum in Multiple Abiotic Stresses


Dae Kwan Ko1,2,3* ([email protected]), Federica Brandizzi1,2,3and Timothy J. Donohue3,4


1MSU-DOE Plant Research Laboratory; 2Michigan State University; 3Great Lakes Bioenergy Research Center (GLBRC); and 4University of Wisconsin–Madison



Increasing crops’ resilience to the changing climate is critical to sustaining the bioeconomy on a large scale. Crop resilience is orchestrated by gene reprogramming events in response to environmental stresses. To better understand how gene expression changes are coordinated in sorghum, an important bioenergy crop, in response to climate stress, researchers performed a time-course transcriptome profiling under three major abiotic stress conditions followed by co-expression network analyses. These analyses provide new insights into the gene regulatory dynamics in response to stress but also fundamental resources for genetic engineering and molecular breeding.


The growth, development, and productivity of crops are challenged by abiotic stresses such as drought, heat, and salinity, whose severity is projected to increase steadily and irreversibly in the future. To survive and thrive in the environment, plants rapidly execute gene expression changes for necessary cellular and metabolic functions. Despite its significance in basic research and field applications, a comprehensive landscape of the abiotic stress-responsive transcriptome changes in bioenergy crops remains elusive to date. The use of dynamic time-course data on multiple abiotic stress-responsive transcriptomes in shoots and roots of sorghum (Sorghum bicolor (L.) Moench) with support of DOE Joint Genome Institute (JGI) allowed dissection of the complex stress-, tissue-, and phase-specific gene responses through a streamlined gene network modeling. The team established a series of co-expression modules of abiotic stress-responsive genes in shoots and roots, separately, where marker genes for various phytohormones are significantly enriched. The expression dynamics in the transcriptome data facilitated gene regulatory network mapping that identified potential candidate transcription factors (TFs) upstream of tissue-specific phytohormone network hub genes. The team proposes that in sorghum, the dynamic regulation of phytohormone marker genes in the abiotic stress-responsive co-expression network modules is coordinated by the master TFs in a tissue-specific manner. This knowledge can be used to boost bioenergy crop productivity and agricultural sustainability through genetic, chemical, and biotechnology engineering.

Funding Information

This material is based upon work supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Biological and Environmental Research (BER) Program under Award Numbers DE-SC0018409. The work conducted by the U.S. Department of Energy Joint Genome Institute ( is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.