Genome-wide comparative analysis of the JmjC gene family in Setaria italica and Setaria viridis reveals transcriptional divergence and stress-responsive candidates

Introduction Histone demethylation mediated by Jumonji C (JmjC) domain-containing proteins is a pivotal epigenetic mechanism governing plant development and stress adaptation. However, a comprehensive characterization of this family in foxtail millet ( Setaria italica ) and its wild progenitor, green foxtail ( Setaria viridis ), remains lacking. Methods In this study, we performed a genome-wide identification of 24 SiJMJ and 23 SvJMJ genes, classifying them into five conserved subfamilies. Comparative genomics, promoter cis-element analysis, transcription factor binding site prediction, and expression profiling under various abiotic stresses were conducted to characterize their evolutionary and functional divergence. Results Comparative genomics revealed extensive collinearity and structural conservation between the two species, yet significant divergence in promoter cis-elements and transcription factor binding sites suggested potential regulatory remodeling during domestication. Expression profiling indicated distinct tissue-specific patterns, particularly in apical meristems and germination. Under abiotic stresses, SiJMJ17 was significantly upregulated under saline-alkali and cold stresses, whereas SiJMJ1 exhibited specific upregulation under waterlogging and herbicide treatments. Discussion These findings elucidate the evolutionary history of the Setaria JMJ family and highlight candidate demethylases for enhancing stress resilience in C4 cereal crops through epigenetic engineering.