Phenotypic 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