Identification of genes involved in soybean flowering time may give us a better understanding of the genetic mechanism underlying the environmental regulation on soybean flowering time (Table 3, Fig. 6, Additional file 9: Table S4, Additional file 10: Table S5). The loci Gm04_4497001, Gm16_30766209 and Gm19_47514601 were identified to be associated with flowering time using both TASSEL and QTXNetwork software. Of the four important flowering genes Glyma04g06240 (GmCOL3a), Glyma16g26660 (GmFT2a), Glyma16g26690 (GmFT2b) and Glyma19g41210 (E3 or GmPhyA3) which were within 300 kb of the significant SNPs, Glyma04g06240 (GmCOL3a) is located at 277.4 kb downstream of the peak SNP Gm04_4497001. CONSTANS (CO) is the key transcriptional activator of the gene that encodes the “florigen” protein FLOWERING LOCUS T (FT) in Arabidopsis . Glyma16g26660 and Glyma16g26690 were close to the significant SNP Gm16_30766209, with physical distances of 19.9 kb and 14.3 kb, respectively. Glyma16g26660 and Glyma16g26690 are the key flowering time genes GmFT2a and GmFT2b, and GmFT2a is identified as the key flowering integrator in soybean . Gm19_47514601 is located between exon 2 and exon 3 of Glyma19g41210 (E3 or GmPhyA3), which encodes the phytochrome A (PHYA) protein , a far-red receptor involved in stabilizing the flowering activator CONSTANS (CO) protein during the late afternoon . The peak SNP, Gm20_3880320, detected in the SP condition was located 61.6 kb upstream of the gene Glyma20g03988, a homolog of PFT1 (phytochrome and flowering time regulatory protein 1) in Arabidopsis, which was an activator of flowering in a photoperiod pathway . In the LD + HT condition, the peak SNP, Gm20_43146832, is 169.2 kb upstream of the gene Glyma20g35020, a homologous gene encoding COP1-interacting protein, which is a regulator of light-regulated genes and a potential direct downstream target of COP1 for mediating light control of gene expression . Gm11_33034954 was the peak SNP in SU conditions, and 215.2 kb upstream of the flower gene Glyma11g31940, which was predicted to encode auxin response factor 8. The peak SNP, Gm11_10847172, detected in the SU, 14SP, 14SU and 15SP four conditions was located 294.25 Kb upstream of the gene Glyma11g15504, a homolog of CONSTANS protein, which has not been reported in soybean. These results indicate that our methods of association mapping and genetic effect analysis across different photo-thermal conditions were efficient in detecting the major and significant genomic regions (QTL) and genes regulating soybean flowering time. The markers associated with these loci can be utilized as markers for marker-assisted breeding for improving soybean adaptation.Fig. 6The positions of flowering time-related loci and their corresponding candidate genes. The positions of candidate genes were marked in black, the loci were shown in red, and the known flowering genes were underlined. The position of the first locus on each chromosome was set as zero, and the left number showed the relative in the genome, 1 = 100 kb