Further analysis of the QTL detected by QTXNetwork confirmed the genetic variation underlying soybean flowering time across different environments. The expression of flowering time genes was influenced by environmental conditions, which is consistent with the results on Arabidopsis thaliana . Jia et al. (2014) identified gene × environment interaction of cotton yield traits via the software QTXNetwork and classified genetic loci into three types: constituted loci (having no interaction with the environment), environment-specific loci (detected only in one environment), and environment-sensitive loci (the effect of the loci being dependent upon the environment) . Our study identified the same types of loci with both additive and epistatic effects, and their interactions with the environment that controlled soybean flowering time. Our result is inconsistent with previous finding that soybean flowering time is mainly controlled by the additive effect . This inconsistency may result from different genetic backgrounds of materials used in different studies. Previous evidence showed that epistasis played an important role in controlling flowering time, and epistasis explained a portion of the ‘missing heritability’ in plants . In Arabidopsis, phytochrome A (PhyA) interacts with CO protein in the photoperiod pathway, and CO interacts with gibberellins to regulate the expression of FT in the GA pathway . Gm04_4497001 (CO) identified in the present study may be a core locus of epistasis interacting with other loci for controlling soybean flowering time. In our previous studies on soybean photo-thermal responses, we proposed that photoperiod determines whether soybean plant is reproductive or vegetative, whereas temperature controls its developmental rate, and the magnitude of temperature effects depends upon the developmental status of the plants (reproductive or vegetative) [53, 54]. Through the analysis of the interaction between genotypes and environments in the current study, we found that whether the additive × environment interaction effect on soybean flowering time was positive or negative was dependent on photoperiod, whereas the magnitude of additive × environment interaction effect was on temperature, which is consistent with the model of photo-thermal interactions on flowering time in soybean [53, 54].