The alleles of the significant SNPs (Gm11_10847172, Gm11_33034954, Gm16_30766209, Gm20_3880320 and Gm20_43146832) had different effects on flowering time across different photo-thermal conditions (Fig. 4, Additional file 7: Table S3). 53 and 38 cultivars contained T allele and C allele for the SNP Gm11_10847172, respectively. The flowering time of the cultivars with minor allele C were delayed for 38.5 d, 19.8 d, 21.8 d, 10.6 d, 32.4 d, 17.2 d, 33.4 d and 15.9 d compared with that of the cultivars with T allele (major allele) under the LD + LT, LD + HT, SP, SU, 14SP, 14SU, 15SP and 15SU, respectively. Similarly, the cultivars carrying the minor allele G of the SNP Gm20_43146832 were 48.7 d, 32.8 d, 31 d, 14.5 d, 39.4 d, 20.3 d, 37.4 d and 16.8 d later in flowering time than the those carrying the major allele A in the LD + LT, LD + HT, SP, SU, 14SP, 14SU, 15SP and 15SU conditions, respectively. The same patterns of the association of the two alleles with flowering time were also observed at other three significant loci Gm11_33034954, Gm16_30766209 and Gm20_3880320. Generally, LD could extend the difference of the flowering time between the cultivars carrying different alleles, while high temperature (summer sowing) could reduce the difference of the flowering time between the cultivars (Fig. 4, Additional file 7: Table S3).Fig. 4Phenotypic variation between cultivars carrying different alleles of the SNPs significantly associated with flowering time in various environments. The box plot shows the significant difference of days to flowering of the cultivars carrying two alleles of the SNPs. The significant SNPs were Gm11_10847172, Gm11_33034954, Gm16_30766209, Gm20_3880320 and Gm20_43146832. The major allele of significant loci was marked by yellow, and the minor allele was marked by green. Significant differences tested by the student’s t-test are also given (***p < 0.001, **p < 0.01, *p < 0.05). 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