Lifecycle transcriptomics of field-droughted sorghum reveals rapid biotic and metabolic responses

Nelle Varoquaux*, Benjamin Cole*, Cheng Gao*, Grady Pierroz, Christopher R. Baker, Dhruv Patel, Mary Madera, Tim Jeffers, Joy Hollingsworth, Julie Sievert, Yuko Yoshinaga, Judith A. Owiti, Vasanth R. Singan, Stephanie DeGraaf, Ling Xu, Matthew J. Blow, Maria J. Harrison, Axel Visel, Christer Jansson, Krishna K. Niyogi, Robert Hutmacher, Devin Coleman-Derr, Ronan O'Malley, John W. Taylor, Jeffery Dahlberg, John P. Vogel*, Peggy G. Lemaux*, Elizabeth Purdom*

Drought is the most important environmental stress limiting crop yields. The C4 cereal, Sorghum bicolor, is an important food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing pre- and post-flowering drought stress on two genotypes of S. bicolor across a tightly-resolved time series, resulting in a data set of over 350 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the stay-green phenotype. Finally, we discovered a large scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants' rhizosphere.

Transcriptomic data generated for this project

Raw reads files (fastq) and contact maps for each stage are available via GEO

   Sample type         GEO entry         Processed RNA-seq data         Differential expression and clustering analysis     
   Leaf      GSE128441      Count       Normalized       Metadata      DE and Clustering Results    Log fold change estimates   
   Root      GSE128441       Count       Normalized       Metadata      DE and Clustering Results    Log fold change estimates     

Public datasets used and analysed