Transcriptomic analysis reveals time-of-day-specific genes and gene regulatory networks in response to chilling stress in sorghum

Sorghum is a versatile crop with many uses, ranging from human consumption to biofuel production. In the U.S., sorghum experiences heat stress during flowering in the summer. Several strategies have been developed to reduce yield loss caused by heat stress. One of the most reliable strategies is ‘heat escape’, in which early-season planting shifts the crop’s reproductive phase to occur before heat stress exposure. However, this heat escape strategy is limited due to sorghum’s sensitivity to early-season chilling. In sorghum, early-season chilling stress negatively affects seed germination, emergence, and seedling vigor. Candidate chilling-tolerant genes in sorghum have been proposed, but the molecular mechanisms of the candidate genes in chilling stress response have not been well established. We hypothesized that many transcriptional responses critical for sorghum’s response to low temperature have been missed by not examining gene expression at multiple times throughout the day. Here, we investigated the effect of chilling stress and time of day on transcriptional responses using 3′ RNA-Seq. We found that time-of-day gated gene expression in response to chilling stress results in various transcriptional response patterns, each with unique biological processes. Weighted gene correlation network analysis (WGCNA) identified modules of transcripts that are specifically responsive to nighttime chilling. Candidate regulatory transcription factors (TFs) of the chilling stress response in sorghum were identified through gene regulatory network analysis. Our results demonstrate that the time of day samples are collected substantially affects our understanding of chilling tolerance, and suggest that a full capture of the network of chilling stress responses requires an examination of multiple times of day. By profiling transcription across different times of day under chilling conditions, we identify regulatory programs that can be leveraged to expand early-planting windows.