A total of 118 SNPs with p < 9.79 × 10−6 and 11 SSRs with p < 2.86 × 10−4 were associated with the phenotypic values when GLM was performed (no loci was detected in 2009). The markers were further clumped based on the linkage disequilibrium blocks defined using the method described previously  and resulted in 87 QTLs for flowering time (Table 3). The proportion of genotypic variance explained by QTLs ranged from 13 to 35% among different environments (Table 3, Additional file 5: Figure S3, Additional file 6: Figure S4). The number of detected loci in each environment was different. There were 27, 23, 24, 24, 23, 45, 52 and 36 loci significantly associated with flowering in the LD + LT, LD + HT SP, SU, 14SP, 14SU, 15SP and 15SU, respectively. In addition, a total of 30 loci were detected in both pot experiments and field experiments, suggesting the soybean flowering were controlled by both environment-sensitive loci and environment-insensitive loci.Table 3The loci associated with flowering time and their phenotypic variation explained by the GLM modelMarkerChrPositionLD + LTLD + HTSPSU14SP14SU15SP15SUKnownDistanceReport QTLsa genes(100Kbp)Gm01_53278791Gm01532787910.130.13First flower 16-1Gm01_53675540Gm01536755400.17 N Gm02_10536842Gm02105368420.140.130.13First flower 16–2Gm02_11998056Gm02119980560.19First flower 16–2 Pod maturity 19–1Gm02_22829006Gm02228290060.160.150.16First flower 13–4;First flower 13–2Sat_135Gm02403662150.340.35First flower 13–2Gm03_1077329Gm0310773290.16 N Gm03_5502496Gm0355024960.140.130.15 N Gm03_36634361Gm03366343610.160.14Pod maturity 16–4;Flower number 1–2Gm03_38526701Gm03385267010.13Flower number 1–2Gm04_4497001Gm0444970010.160.160.150.170.130.160.13 GmCOL3a 2.78First flower 22–1Gm04_38840391Gm04388403910.16 N Gm04_42951376Gm04429513760.14Flower number 1–3Gm04_46390533Gm04463905330.14 N Gm05_682648Gm056826480.14 N Gm05_1705841Gm0517058410.13 N Gm05_26685967Gm05266859670.130.13 N Gm05_38636402Gm05386364020.130.130.14 N Gm05_40349605Gm05403496050.160.190.16 N Gm06_2086304Gm0620863040.17 N Gm06_2253042Gm0622530420.180.15 N Satt422Gm0672276380.19Pod maturity 26–1Gm07_3143196Gm0731431960.13First flower 4–2Gm08_11052135Gm08110521350.13Days to maturity 1-g1Gm08_40882335Gm08408823350.170.140.15 N Gm09_2327785Gm0923277850.160.150.15 N Gm09_24238724Gm09242387240.130.140.13First flower 3–4Gm09_39822766Gm09398227660.14Photoperiod insensitivity 5–2Gm09_43508261Gm09435082610.130.170.190.13 N Gm10_2317882Gm1023178820.140.150.140.15Days to flowering 1-g18;Days to maturity 1-g14Gm11_1161553Gm1111615530.17 N Gm11_3950213Gm1139502130.150.140.140.14Pod maturity 24–6Gm11_4519147Gm1145191470.150.17NGm11_5065170Gm1150651700.20.130.140.14Node number 3–3Gm11_6512939Gm1165129390.13 N Gm11_6901726Gm1169017260.15Flower number 1–5;Pod number 1–5Satt197Gm1188794800.30.29First flower 11–1;Pod maturity 17–1Gm11_10847172Gm11108471720.180.140.210.210.230.270.280.23Pod maturity 18–2Gm11_11572077Gm11115720770.170.180.150.180.240.16 N Gm11_16492046Gm11164920460.190.160.150.150.15First flower 11–2;First flower 8–4Gm11_17237725Gm11172377250.170.140.190.170.18Pod maturity 18–1Gm11_21023332Gm11210233320.15First flower 11–2;First flower 8–4Gm11_33034954Gm11330349540.170.190.210.130.250.260.24 N Gm11_33555216Gm11335552160.180.150.150.190.170.190.18 N Gm11_36174968Gm11361749680.160.140.160.160.150.170.18Pod maturity 22–2Gm12_5786241Gm1257862410.180.16Reproductive stage length 7–3;maturity 26–2Gm12_8435100Gm1284351000.14 N Gm12_13354287Gm12133542870.13 N Gm12_14231203Gm12142312030.15 N Satt586Gm13116399800.190.2First flower 11–4;Pod maturity 17–5Gm13_23509779Gm13235097790.140.150.14Photoperiod insensitivity 5–3Gm13_39307253Gm13393072530.15 GmCOL10b 2.25Days to flowering 1-g10Gm14_7302299Gm1473022990.150.140.170.190.15Flower number 1–6Gm14_44697544Gm14446975440.150.15 N Gm14_45457682Gm14454576820.140.14First flower 21–1Gm14_49107190Gm14491071900.140.150.140.270.210.19First flower 21–1Gm15_1265753Gm1512657530.170.150.140.13First flower 12–3;Flower number 1–7Gm15_13098003Gm15130980030.150.150.130.140.170.15First flower 12–3;Flower number 1–7Gm15_25411335Gm15254113350.17 N Gm15_35867161Gm15358671610.160.150.16 N Satt452Gm15389231520.170.20.180.18 N Gm15_45004801Gm15450048010.150.15 N Gm16_5773005Gm1657730050.14 N SSRFTGm16307416000.20.250.270.260.270.23 GmFT2a inter-geneGmFT2aGm16_30766209Gm16307662090.260.180.160.180.160.20.240.28 GmFT2a; 0.20;First flower 9–3 GmFT2b 0.14Gm16_35700223Gm16357002230.160.150.170.170.150.190.230.15First flower 13–8;Photoperiod insensitivity 5–4Gm17_37574384Gm17375743840.13 N Gm17_41063513Gm17410635130.13 N Gm18_4324818Gm1843248180.170.13Pod maturity 22–9Gm18_34401760Gm18344017600.180.170.16Photoperiod insensitivity 2–2Gm18_36929655Gm18369296550.180.20.140.140.16First flower 10–2Satt564Gm18476177950.210.260.210.240.22Flower number 1–9;Pod number 1–8Gm18_57126096Gm18571260960.130.150.140.140.14 N Gm19_5195925Gm1951959250.13 GmCOL2b 2.85 N Gm19_35449676Gm19354496760.14 N Gm19_39723056Gm19397230560.140.140.14First flower 15–2Sat_113Gm19421103320.290.280.290.290.29First flower 4–3;Pod maturity 24–10Satt664Gm19461097000.260.19 GmCOL11b 0.14Flower form 1–4bGm19_46761039Gm19467610390.160.15First flower 13–9;Flower form 1–4;First flower 16–4Satt229Gm19470490740.18First flower 20–2;First flower 13–9;Flower form 1–4Gm19_47514601Gm19475146010.14 E3 inter-geneFlower form 1–4;First flower 16–4;First flower 5–2;First flower 5–3Gm19_49786000Gm19497860000.15First flower 5–3;First flower 8–3;First flower 16–4;Flower form 1–4Satt571Gm2012918090.18Pod maturity 24–5Gm20_3880320Gm2038803200.220.20.170.160.180.18First flower 16–3Gm20_37857633Gm20378576330.140.150.14First flower 16–3;Flower form 1–3Gm20_43146832Gm20431468320.20.220.160.190.160.210.230.19 GmCRY2c 3.3Flower number 1–11Gm20_44260228Gm20442602280.130.140.140.15Flower number 1–11 aQTLs are from http://www.soybase.org; N indicates that there were no reported QTL near the loci related to flowering time; Chr: chromosome; LD + LT: 16 h and spring sowingin 2010; LD + HT: 16 h and summer sowingin 2010. 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