Additional file 1: Table S1.The origin, ecotypes and maturity groups of the soybean cultivars in this study. (DOCX 27 kb) Additional file 2: Table S2.Polymorphic SSR and SNP markers used for this study. (XLSX 230 kb) Additional file 3: Figure S1.The histogram of soybean flowering time in each environment. (a) The histogram of soybean flowering time in 2009. (b) The histogram of soybean flowering time in 2010. (c) The histogram of soybean flowering time in 2014 and 2015, respectively. (DOCX 5435 kb) Additional file 4: Figure S2.Population structure of 91 soybean cultivars using 63 SSR markers. (a) Estimation of the number of sub-populations. The left figure was a plot of ln (probability of data) vs. K ranging from 1 to 12 and the right figure was a plot of subpopulation number vs. delta K values. (b) Population structure of 91 soybean cultivars based on 63 SSR markers. The x-axis indicates the cultivars, and the y-axis indicates the Q value from STRUCTURE 2.3.1. The red color represents one sub-group, the green color represents another. (c) PCA of 91 soybean cultivars with the top two principal components. (d) Neighbor-joining tree of the 91 soybean cultivars. (DOCX 498 kb) Additional file 5: Figure S3.Genome-wide association scan for flowering time in different environments using SNPs. (a) The Quantile-Quantile Plot; (b) Manhattan plot for days to flowering. P-values (negative log-transformed) are shown in the plot relative to their position on each of the 20 chromosomes. The horizontal pink line indicates the genome-wide significant threshold (9.79 × 10−6). (DOCX 469 kb) Additional file 6: Figure S4.Manhattan plot for days to flowering in the association panel in different environments using SSRs. (a) Quantile-Quantile Plot (b) Manhattan plot for days to flowering. P-values (negative log-transformed) are shown in the plot relative to their genetic positions, the horizontal pink line indicates the genome-wide significant threshold (2.86 × 10−4). (DOCX 384 kb) Additional file 7: Table S3.The mean flowering time of the accession carrying different alleles. (DOCX 21 kb) Additional file 8: Figure S5.The plot of the interactions between significant loci with the flowering time and environment detected by the QTXNetwork. Red columns represent general QTX effects for all six environments. The green lines denote the n-th environment-specific effect. 1, SD + LT condition; 2, SP condition; 3, LD + LT condition; 4, SD + HT condition; 4–42, Gm04_4497001; 4–154, Gm04_42153936; 11–190, Gm11_36124908; 15–116, Gm15_11855585; 16–152, Gm16_30766209; 19–208, Gm19_44042544; 19–243, Gm19_47514601. (DOCX 407 kb) Additional file 9: Table S4.The significant loci associated with flowering time and related candidate genes. (DOCX 27 kb) Additional file 10: Table S5.The position of the loci and the corresponding candidate genes. (XLSX 18 kb)