We also found that the direction of additive × environment interaction effect on soybean flowering time is dependent on photoperiod, whereas the magnitude of additive × environment interaction effect is dependent on temperature (Table 5, Additional file 8: Figure S5). For instance, the additive by environment interaction of Gm19_44042544 had a negative effect in the SD condition but positive in the LD condition, showing that the locus could enhance flowering time in the SD condition but delay flowering time in the LD condition. In contrast, the additive by environment interaction of Gm16_30766209 and Gm11_36124908 were positive in the SD condition but negative in the LD condition, suggesting that these loci could delay flowering time in the SD condition and accelerate flowering time in the LD condition. In response to photoperiod, the locus Gm19_44042544 showed opposite effect on flowering time compared with Gm16_30766209 and Gm11_36124908. On the other hand, for Gm16_30766209 and Gm11_36124908, the magnitude of delaying effect on flowering time was larger in the HT condition than in the LT condition, and the effect of Gm19_44042544 on the delay of flowering was also larger in the HT condition than that of the LT condition. These results indicate that high temperature could enhance both the positive or negative effects on flowering time in the SD conditions.