Antagonistic chromatin regulation of LHY homologs by GmASH2R and GmNF-YC4 fine-tunes flowering time for soybean latitudinal adaptation

Soybean (Glycine max), a photoperiod-sensitive legume critical for global protein and oil supply, relies on precise flowering-time regulation for latitudinal adaptation. LATE ELONGATED HYPOCOTYL homologs (GmLHYs) promote flowering by repressing the floral inhibitor E1, but the mechanisms activating GmLHYs remain unclear. Additionally, COMPASS (Complex Proteins Associated with Set1) and COMPASS-like complexes, which catalyze histone H3 lysine 4 (H3K4) methylation, exhibit considerable functional divergence across species and are largely uncharacterized in legumes. Here, we show that GmASH2R1 and GmASH2R2 form a COMPASS-like complex with GmRBL and GmWDR5a that catalyzes genome-wide H3K4 mono-, di-, and tri-methylation, a function distinct from that in Arabidopsis thaliana. This complex directly activates GmLHYs expression by depositing H3K4me3 at their promoters, thereby accelerating flowering. Moreover, we uncover a tunable "Yin-Yang" module in which Nuclear Factor Y (NF-Y) subunits GmNF-YC4a and GmNF-YC4b interact with GmASH2R but act as transcriptional repressors. These NF-YC proteins compete for CCAAT-box binding at GmLHYs promoters, thereby antagonizing GmASH2R-mediated activation and fine-tuning flowering. Population analyses the GmASH2R1/2-GmNF-YC4a/b module may have been subject to antagonistic selection during domestication, and the specific allelic combinations could contribute to flowering time plasticity, consistent with adaptive diversification across latitudinal gradients. Our findings establish the COMPASS-like complex as a central activator of flowering in soybean and reveal an epigenetic-transcriptional mechanism fine-tuning flowering time to support environmental adaptation.