Comparative transcriptome profiling of two contrasting foxtail millet cultivars provides insights into molecular mechanisms underlying dehydration stress response

Abstract

Foxtail millet (Setaria italica L.) has emerged as a model system to understand its adaptation to environmental stresses in the past decade. However, studies on understanding the molecular mechanism underlying the adaptation to dehydration stress and the regulatory network involved in the process remain elusive. In the present study, RNA-seq was performed during dehydration stress in the tolerant (IC4) and sensitive (IC41) cultivars at different time points (0, 6, and 12 h). A total of 2467 and 3318 differentially expressed genes (DEGs) were identified in IC4, and 2535 and 5572 in IC41 at 6 h and 12 h compared to control (0 h), respectively. Gene ontology (GO) analysis revealed that the DEGs were enriched in water transport, response to water deprivation, oxidative stress, amino acid and sugar transport, lipid biosynthesis, and regulation of stomatal opening. Pathway analysis suggested a significant modulation of genes involved in the metabolism of glutathione and tryptophan and biosynthesis of flavonoid, ascorbate, arginine, and proline in IC4 compared to IC41. Genes encoding for DIVARICATA, SBP family protein (teosinte glume architecture 1), and SRS family proteins (LATERAL ROOT PRIMORDIUM 1 and SHI-RELATED SEQUENCE 1) were found to be exclusively upregulated in IC4 during dehydration stress. Gene co-expression networks constructed based on the expression data showed the key modules and hubs that play critical roles during dehydration stress. Altogether, the present study has identified key genes, pathways, and regulatory modules that would serve as a base for further studies to gain insights into the dehydration-responsive molecular circuitry in foxtail millet.