Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C₄ plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. Particularly, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-seq was performed in two foxtail millet cultivars contrastingly differing in dehydration tolerance (IC403579; cv. IC4 – tolerant, and IC480117; cv. IC41 – sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4 and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.

Drought stress affects the growth and productivity of plants, where C ₄ plants can advantageously perceive and respond to the stress for their survival and reproduction. Epigenetic modifications play a prominent role in conferring drought tolerance in C ₄ plants; however, the molecular links between histone modifiers and their regulation are unclear. In the present study, we performed a genome-wide H3K9ac enrichment in foxtail millet ( Setaria italica ) and analyzed their role in regulating the expression of drought-responsive genes. The presence of H3K9ac on these genes were identified through the comparative analysis of dehydration tolerant (cv. IC4) and sensitive (IC41) cultivars of foxtail millet. A histone deacetylase, SiHDA9 , showed significant upregulation in the sensitive cultivar during dehydration stress. SiHDA9 overexpression in Arabidopsis thaliana conferred higher sensitivity to dehydration/drought stress than WT plants. We found that SiHDA9 physically interacts with SiHAT3.1 and SiHDA19. This complex is recruited through the SiHAT3.1 recognition sequence on the upstream of drought-responsive genes ( SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4 , and SiLHCB2.3 ) to decrease H3K9 acetylation levels. The modulations in H3K9ac levels cause repression of gene expression and induce drought-sensitivity in the sensitive cultivar. Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of drought stress response in foxtail millet.