The environmental effect on the genetic variation of soybean flowering time had not been well documented . In our previous study, 71 of 91 cultivars originated from different latitudes in China were selected to analyse the effects of photoperiod and temperature and the interaction between photoperiod and temperature on flowering time . The results enhanced the understanding of the photo-thermal effects on flowering time at the phenotypic level. However, the effects of loci related to flowering time across photo-thermal conditions were not reported.