The most significant loci associated with flowering time varied under different photo-thermal conditions (Table 3, Fig. 3). Among SSR markers, Satt664 on Chr19 was the most significant locus associated with flowering time in the two LD conditions; Sat_135 on Chr02 was the most significant locus in the SP and SU conditions. Whereas, Sat_113 on Chr19 was the most significant locus in the 14SP, 14SU and 15SU conditions, respectively. Satt197 on Chr11 was the most significant locus with flowering time in the 15SP and 15SU conditions, respectively. Among SNPs, Gm11_10847172 was the locus most significantly associated with flowering time in the four conditions (SU, 14SP, 14SU and 15SP). Gm16_30766209 was the locus most significantly associated with flowering time in LD + LT and 15SU conditions, respectively. Gm20_43146832 on Chr20, Gm20_3880320 on Chr20 and Gm11_33034954 on Chr11 were the locus most significantly associated with flowering time in the LD + HT, SP and SU conditions, respectively. The significant SNPs were also detected in more than six environments, indicating that these loci may involve in regulation of flowering time in different photo-thermal conditions.Fig. 3Manhattan plot and linkage disequilibrium block in different environments. Linkage disequilibrium blocks associated with flowering time near Gm11_10847172, Gm11_33034954, Gm16_30766209, Gm20_3880320 and Gm20_43146832. Significance threshold is denoted by the orange line. The up panel was the Manhattan plots of negative log10-transformed P values vs. SNPs. The down panel was haplotype block based on pairwise linkage disequilibriumr2values. LD, 16 h; LT, low temperature (spring sowing); HT, high temperature (summer sowing); SP, Spring sowing season with natural day-length in 2010 pot experiment; SU, Summer sowing season with natural day-length in 2010 pot experiment; 14SP, Spring sowing in 2014 field experiment; 14SU, Summer sowing season in 2014 field experiment; 15SP, Spring sowing season in 2015 field experiment; 15SU, Summer sowing season in 2015 field experiment