In this study, the effects of flowering-time-related loci in different photo-thermal conditions have been evaluated. Some loci were detected in only one environment, others were in multiple environments. The number of loci and their associated effects varied across different photo-thermal conditions. Interestingly, none of the loci was associated with the flowering time in the SD treatment. In the previous Arabidopsis studies, there were few QTLs linked to flowering time of the plant grown in Sweden than Italian conditions. It was speculated that the Sweden condition may represent saturated vernalization conditions, which could reduce the variation in flowering time among genotypes and result in reducing or removing the expression of some genes . Similarly, soybean is a typical short day crop, we speculate that short day may also normalize soybean flowering time and remove contribution of some genes. The phenotypic variance of cultivars from different maturity groups became small in SD condition. Short days could reduce the effect of the dominant alleles of each dominant E genes on delaying flowering and maturity time in soybean .