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

Soybean (Glycine max), a photoperiod-sensitive legume critical for global protein and oil supply, relies on precise flowering-time regulation to achieve latitudinal adaptation. LATE ELONGATED HYPOCOTYL homologs (GmLHYs) promote flowering by repressing the floral inhibitor E1; however, the mechanisms that activate GmLHYs remain unclear. Although COMPASS (Complex of Proteins Associated with Set1) and COMPASS-like complexes catalyze histone H3 lysine 4 (H3K4) methylation, their functions have diverged considerably across species and remain largely uncharacterized in legumes. Here, we show that GmASH2R1 and GmASH2R2 form a COMPASS-like complex with GmRBL and GmWDR5a proteins that catalyzes genome-wide H3K4 mono-, di-, and trimethylation, revealing roles distinct from those of their counterparts in Arabidopsis thaliana. This complex directly activates GmLHY expression by promoting H3K4me3 deposition at GmLHY 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 proteins but act as transcriptional repressors. These NF-YC proteins compete for CCAAT-box binding at GmLHY promoters, thereby antagonizing GmASH2R-mediated activation and fine-tuning flowering time. Population analyses suggest that the GmASH2R1/2-GmNF-YC4a/b module may have been subject to antagonistic selection during domestication and that 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 that fine-tunes flowering time to support environmental adaptation.