Multi-Omics analysis of ubiquitin E2 genes in Setaria: evidence for the roles of E2 genes in various aspects of plant development and stress resistance

Ubiquitin E2 enzymes (E2s) are critical mediators in the ubiquitination cascade, a post-translational modification process that regulates protein stability, activity, localization, and degradation. Here, we analyzed the E2 gene family in foxtail millet (Setaria italica), integrating comparative genomics, transcriptomics, and functional studies. A total of 52 E2 genes were identified and classified into four subfamilies (UBC, UEV, SCE, and RCE) based on phylogenetic analysis across 49 species. Notably, foxtail millet exhibited significant gene expansion. Tissue-specific expression profiling revealed distinct roles of E2 genes in growth and development. Haplotype and quantitative trait loci (QTL) analyses demonstrated that several E2 genes, including SiUBC39, are associated with key agronomic traits such as plant height, flowering time, and stress tolerance.