Integrated multi-omics and functional dissection of RING-type E3 ubiquitin ligases in flowering-time control in...

Flowering time is a key adaptive and agronomic trait determining regional suitability and yield stability in plants. Although ubiquitin-mediated protein degradation regulates diverse developmental and stress responses, the role of RING-type E3 ubiquitin ligases in flowering-time control in plants remains relatively underexplored. Here, we conducted an integrated multi-omics analysis to investigate the contribution of RING-type E3 ligases to flowering-time regulation in Setaria italica. We identified 496 RING-type E3 ligases in the Setaria genome and revealed extensive family expansion driven by whole-genome duplication and lineage-specific duplication events. By integrating transcriptome profiling under contrasting photoperiods with flowering-time QTL mapping, we identified three candidate RING-type E3 ligases, including SGD1. Population genomics and haplotype analyses across 1,433 Setaria accessions uncovered functional polymorphisms in these genes associated with variation in flowering time and yield-related traits. Functional analyses demonstrated that SGD1 modulates both flowering time and grain yield by regulating the stability of the transcription factor SiSPL2, thereby reshaping downstream transcriptional networks related to photoperiod signaling and metabolism. Joint haplotype analyses further revealed additive effects between SGD1 and SiSPL2, providing a framework for haplotype-guided breeding. Together, our study highlights ubiquitin-mediated post-translational regulation as an important layer in flowering-time control and yield adaptation in cereal crops.