Natural variation in GmRVE4d facilitates soybean latitudinal adaptation by regulating GmPRR5a-dependent flowering and maturity

Timely flowering and maturity are crucial for plant reproduction and environmental adaptation. As a core molecular system for plants to perceive environmental cues, the circadian clock integrates cyclic photothermal signals with intrinsic developmental programs, exerting a pivotal regulatory role in these processes. Soybean is a short-day thermophilic crop sensitive to photoperiod and temperature, but the molecular mechanism of the circadian clock in soybean photothermal adaptation remains largely elusive. Herein, we performed genome-wide association study (GWAS) combined with deep learning approach with maturity variations in soybean, and first identified GmRVE4d, a homologue of the circadian clock gene REVEILLE, which significantly associated with maturity in different photothermal conditions. Genetic analysis revealed that GmRVE4d underwent domestication-related artificial selection, and its favorable allele GmRVE4dH3 was characterized. Further functional analyses demonstrate that GmRVE4d directly binds to the promoter of GmPRR5a, the soybean ortholog of Arabidopsis circadian clock central component PSEUDO-RESPONSE REGULATOR5 (PRR5), and represses its transcriptional expression, thereby delaying soybean flowering and maturity. Thus, GmRVE4d is a novel negative regulator of soybean flowering and maturity that functions by directly repressing GmPRR5a expression, and is a promising molecular target for improving soybean photothermal adaptation and expanding cultivation latitudes through molecular breeding.