Soybean is a major legume crop originating in temperate regions, and photoperiod responsiveness is a key factor in its latitudinal adaptation. Varieties from temperate regions introduced to lower latitudes mature early and have extremely low grain yields. Introduction of the long-juvenile (LJ) trait extends the vegetative phase and improves yield under short-day conditions, thereby enabling expansion of cultivation in tropical regions. Here we report the cloning and characterization of J, the major classical locus conferring the LJ trait, and identify J as the ortholog of Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). J depends genetically on the legume-specific flowering repressor E1, and J protein physically associates with the E1 promoter to downregulate its transcription, relieving repression of two important FLOWERING LOCUS T (FT) genes and promoting flowering under short days. Our findings identify an important new component in flowering-time control in soybean and provide new insight into soybean adaptation to tropical regions.

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Adaptability of soybean [Glycine max (L.) Merr.] to a wide range of latitudes is attributed to the natural variation in the major genes and quantitative trait loci (QTL) that control flowering time and maturity. Identification of novel genes and understanding their molecular basis is critical to improving soybean productivity. We identified a new locus conditioning days to flowering and maturity that was detected in hybrid progeny between cultivated and wild soybeans. A backcross was made between the recurrent parent Tokei 780 and two early-flowering recombinant inbred lines (rILs; from the cross Tokei 780 × Hidaka 4, a wild soybean accession, all of which possessed an identical genotype at the major four maturity loci, E1 to E4). The segregation patterns observed in the F 2 and F 3 progeny derived from the two crosses revealed that early-flowering was controlled by a single dominant gene. The gene was fine-mapped to a 245-kb interval between markers M5 and M7 on Gm16. A tagging marker ID1 was significantly associated with the variation in days to flowering (0.82, p < 0.01) and maturity (0.76, p < 0.01) in the F 2 population. The new early-flowering gene and its tagging marker are very useful for molecular breeding towards early maturity and stable productivity of soybean under high-latitude environments. The gene symbol E9e9 has been assigned. E9E9 results in early maturity and e9e9 results in late maturity.