A field-focused systems approach reveals mRNA covalent modifications linked to sorghum growth and development under drought stress

Covalent RNA modifications (RCMs) are post-transcriptional changes to the chemical composition of RNA. RCMs influence mRNA stability, regulate transcription and translation efficiency, and play critical roles in the growth and development of eukaryotes. However, their role in plants remains poorly understood, particularly as they relate to performance in the field under stress conditions. In this study, we grew a panel of six diverse sorghum (S. bicolor) accessions in the field during the summer in central Arizona and examined their physiological and molecular responses to drought and heat stress over time. We then explored the molecular features that contributed to plant performance under stress. To do so, we combined genomic, transcriptomic, epitranscriptomic, physiological, and metabolomic data in a systems-level approach. Co-expression network analyses uncovered two modules of interest, one controlled primarily by a single stress-responsive transcription factor, SbCDF3, and the other by an RCM, dihydrouridine. While the CDF3 module largely contained a set of stress response and photosynthesis-associated genes that were positively correlated with plant performance, the dihydrouridine-associated module was largely comprised of photosynthesis and metabolism genes, including SbPPDK1, which is integral to C4 photosynthesis in the grasses. In addition, the transcript encoding the enzyme responsible for this RCM, dihydrouridine synthase (SbDUS2), was also present in this module, and its abundance was positively correlated with photosynthetic traits andSbPPDK1abundance. Given that this highly conserved RCM has never been characterized in plants, we examined loss of function mutants for the DUS2 enzyme in Arabidopsis, demonstrating decreases in plant growth and performance under heat stress in this background. Our work highlights both a key transcription factor, CDF3, for breeding in thePoaceae. In addition, for the xfirst time in plants, we reveal a role for the RCM dihydrouridine in modifying conserved, core metabolic and photosynthesis-associated transcripts in plants.