Integration of multi-omics data and comprehensive analysis of gene functions offer novel insights into the mechanism of flowering time stage in Elymus sibiricus

Elymus sibiricus stands out as a promising energy crop for cultivation on marginal lands, renowned for its high biomass production, superior fiber content and robust stress tolerance. Notably, the timing of its flowering plays a pivotal role in determining its biomass and seed yield. However, the mechanisms regulating flowering time stage in E. sibiricus remained enigmatic. In this study, we employed integrated proteomic and transcriptomic approaches to identify 1577 matched mRNA-protein pairs associated with flowering by contrasting two distinct flowering germplasms of E. sibiricus . Combined analysis highlighted essential roles for fatty acid degradation, circadian rhythm, and signal transduction pathways. The observed gene expression patterns suggested that fatty acid degradation might serve as a primary source of energy in late-flowering germplasm. Additionally, key genes such as EsFRS5 , EsCRK25 , and EsPIE1 from FAR1, SNF2, and RLK-Pelle_DLSV families, respectively, were identified as crucial contributors to the signaling pathway regulating flowering in E. sibiricus . Critically, we established the circadian rhythm framework in E. sibiricus and verified the role of EsFT and EsELF3 in regulating flowering. In conclusion, this study presents a comprehensive analysis of the transcriptome and proteome of E. sibiricus , revealing crucial flowering-related genes that serve as direct targets for precision breeding. • Fatty acid degradation supplied energy for flowering transition. • EsFRS5 , EsCRK25 , and EsPIE1 were key flowering regulators in E. sibiricus . • EsELF3 delayed flowering through repression of GI , FKF1 , PRR9 .