Table S1 QTL for Yield and Its Components Detected by CIM in the Rils and If2s in All

Appendix

Table S1 QTL for yield and its components detected by CIM in the RILs and IF2s in all environments

Trait / QTL / Chromosomesa / Environmentsb / Position
(cM) / Flanking markers / LOD / A / D / R2 (%) / D/Aa / GAb / Populations
SY / qSY-D2-1 / D2-1 / e4 / 0.01 / CIR381b–CIR246 / 2.83 / 1.67 / 6.29 / A / RILs
qSY-D2-2 / D2-2 / E6 / 8.99 / NAU2190–E14M4a / 2.69 / –2.9 / –0.01 / 7.15 / 0.00 / A / IF2
qSY-A3-1 / A3-2 / E4 / 0.01 / NAU3995–NAU1167 / 2.56 / –2.41 / 5.76 / 6.59 / –2.38 / OD / IF2
qSY-A5-1 / A5-2 / e4 / 16.47 / P1–N1U3273 / 2.7 / 1.91 / 5.98 / A / RILs
qSY-D5-1 / D5-2 / E1 / 0.01 / BNL3442–NAU4605 / 3.16 / 4.47 / 1.17 / 6.81 / 0.26 / PD / IF2
E6 / 7.01 / BNL3442–NAU4605 / 2.66 / 2.5 / 1.09 / 7.99 / 0.44 / IF2
qSY-D6-1 / D6 / E3 / 16.09 / TMG10–CIR407 / 3.85 / –4.9 / 3.03 / 8.3 / –0.62 / PD / IF2
E5 / 16.21 / TMG10–CIR407 / 2.59 / –2.61 / 2.05 / 5.88 / –0.78 / IF2
qSY-D8-1 / D8-2 / E5 / 0.01 / NAU3587–NAU3810 / 2.75 / –3.04 / 1.98 / 6.71 / –0.65 / PD / IF2
qSY-D8-2† / D8-3 / E6 / 14.01 / E21M8–NAU5263 / 3.9 / –2.5 / 2.16 / 8.47 / –0.86 / D / IF2
qSY-D9-1 / D9-1 / E1 / 0.01 / BNL686–NAU3100 / 3.87 / –5.7 / –2.62 / 8.17 / 0.46 / PD / IF2
e4 / 9.51 / NAU3100–E19M11 / 2.53 / –1.7 / 6.48 / RILs
qSY-D9-2 / D9-2 / E2 / 69.95 / BNL3031–NAU4554 / 2.6 / 3.27 / –3.33 / 6.62 / –1.02 / D / IF2
e5 / 76.01 / BNL3031–NAU4554 / 2.83 / 3.09 / 6.55 / RILs
qSY-D10-1† / D10-1 / E1 / 0.01 / BNL3646–E14M4b / 5.11 / –5.82 / 5.38 / 10.99 / –0.93 / D / IF2
qSY-A12-1 / A12-2 / E6 / 0.01 / NAU4020–NAU6643 / 2.59 / –2.86 / –0.52 / 7.52 / –0.18 / A / IF2
LY / qLY-D2-1 / D2-1 / e4 / 29.21 / NAU4238–NAU5467 / 3.76 / 0.75 / 7.64 / A / RILs
qLY-D2-2 / D2-2 / E6 / 16.99 / NAU2190–E14M4a / 3.56 / –1.72 / 0.04 / 13.28 / 0.02 / A / IF2
E2 / 7.99 / NAU2190–E14M4a / 2.91 / –1.91 / 0.06 / 8.62 / 0.03 / IF2
qLY-A3-1 / A3-2 / E4 / 0.01 / NAU3995–NAU1167 / 2.92 / –1.18 / 2.73 / 7.39 / –2.3 / OD / IF2
qLY-D5-1 / D5-2 / E1 / 0.01 / BNL3442–NAU4605 / 2.88 / 1.9 / 0.25 / 6.17 / 0.13 / A / IF2
qLY-D6-1† / D6 / E3 / 15.09 / TMG10–CIR407 / 4.16 / –2.52 / 1.2 / 8.37 / –0.48 / PD / IF2
E5 / 16.21 / TMG10–CIR407 / 2.53 / –1.3 / 0.73 / 6.01 / –0.56 / IF2
qLY-D8-1 / D8-2 / E5 / 0.01 / NAU3587–NAU3810 / 2.69 / –1.45 / 0.75 / 6.8 / –0.52 / PD / IF2
qLY-D8-2† / D8-3 / E6 / 14.01 / E21M8–NAU5263 / 3.17 / –1.01 / 0.9 / 7.01 / –0.89 / D / IF2
qLY-D9-1 / D9-1 / E1 / 0.01 / BNL686–NAU3100 / 2.96 / –2.01 / –1.08 / 6.18 / 0.54 / PD / IF2
e8 / 9.51 / NAU3100–E19M11 / 3.06 / –0.75 / 6.67 / RILs
qLY-D10-1† / D10-1 / E1 / 0.01 / BNL3646–E14M4b / 4.57 / –2.31 / 2.15 / 9.62 / –0.93 / D / IF2
qLY-A11-1 / A11-2 / e4 / 0.01 / NAU5192–E17M8 / 3.36 / –0.7 / 6.94 / A / RILss
qLY-A12-1 / A12-2 / E6 / 1.01 / NAU4020–NAU6643 / 2.6 / –1.05 / –0.92 / 8.66 / 0.88 / D / IF2
qLY-A13-1 / A13 / E2 / 64.6 / NAU3398–NAU3393 / 3.26 / –1.34 / 1.43 / 7.52 / –1.07 / D / IF2
qLY-D13-1 / D13 / E4 / 5.31 / NAU985b–NAU4105 / 2.68 / –1.73 / 2.43 / 7.05 / –1.41 / OD / IF2
BP / qBP-D5-1 / D5-2 / E6 / 4.01 / BNL3442–NAU4605 / 2.74 / 0.49 / 0.29 / 7.81 / 0.58 / PD / IF2
E1 / 0.01 / BNL3442–NAU4605 / 4.48 / 1.27 / 0.2 / 9.2 / 0.16 / IF2
qBP-D6-1 / D6 / E2 / 10.27 / NAU5373–NAU3588 / 3.25 / 0.71 / 0 / 7.7 / 0.00 / A / IF2
E4 / 10.27 / NAU5373–NAU3588 / 4.39 / 0.86 / –0.21 / 8.97 / –0.24 / IF2
qBP-A7-1† / A7 / e1 / 0.01 / NAU1043–NAU3654 / 3.27 / 0.57 / 7.15 / A / RILs
qBP-D7-1 / D7 / E4 / 47.02 / NAU6468–NAU5152 / 3.71 / –0.75 / –0.43 / 8.62 / 0.57 / PD / IF2
qBP-D8-1† / D8-3 / E6 / 11.01 / E21M8–NAU5263 / 3.41 / –0.61 / 0.05 / 8.59 / 0.08 / A / IF2
qBP-D9-1 / D9-2 / e5 / 38.21 / BNL3140–NAU2658 / 2.93 / –0.53 / 6.19 / A / RILs
qBP-D9-2 / D9-1 / E1 / 0.01 / BNL686–NAU3100 / 3.3 / –1.17 / –0.64 / 6.5 / 0.55 / PD / IF2
qBP-D10-1 / D10-1 / E1 / 1.01 / BNL3646–E14M4b / 5.63 / –1.49 / 1.2 / 11.68 / –0.8 / D / IF2
qBP-D11-1 / D11 / E2 / 0.01 / NAU470–NAU5428 / 2.75 / 0.07 / –0.84 / 5.93 / –12.17 / OD / IF2
qBP-A13-1 / A13 / E2 / 65.63 / NAU3393–NAU4024 / 3.6 / –0.52 / 0.74 / 8.77 / –1.43 / OD / IF2
BW / qBW-D2-1 / D2-1 / E5 / 25.91 / NAU4238–NAU5467 / 3.67 / 0.12 / 0.04 / 8.9 / 0.39 / PD / IF2
E4 / 21.92 / NAU4238–NAU5467 / 2.77 / 0.1 / 0.12 / 7.8 / 1.22 / IF2
e1 / 28.92 / NAU4238–NAU5467 / 2.96 / 0.1 / 6.11 / RILs
qBW-D2-2 / D2-2 / E6 / 12.99 / NAU2190–E14M4a / 6.41 / –0.17 / 0.08 / 20.8 / –0.46 / PD / IF2
E1 / 15.99 / NAU2190–E14M4a / 3.93 / –0.15 / 0.06 / 13.72 / –0.37 / IF2
E3 / 11.99 / NAU2190–E14M4a / 3.07 / –0.15 / 0.14 / 10.62 / –0.93 / IF2
qBW-A3-1† / A3-2 / E1 / 19.12 / NAU4789–NAU4324 / 2.84 / –0.09 / 0.03 / 5.86 / 0.33 / A / IF2
E3 / 21.12 / NAU4789–NAU4324 / 3.22 / –0.13 / 0 / 7.52 / 0.00 / IF2
qBW-A4-1 / A4 / E3 / 17.32 / NAU1102–NAU3110 / 2.53 / –0.09 / 0.06 / 4.65 / –0.67 / PD / IF2
qBW-A5-1 / A5-1 / E1 / 1.39 / BNL3452–NAU879 / 3.51 / –0.07 / 0.13 / 7.21 / –1.96 / OD / IF2
qBW-A6-1 / A6 / E1 / 1.01 / NAU2684–NAU3859 / 3.32 / 0.11 / –0.12 / 8.36 / –1.14 / D / IF2
qBW-D6-1 / D6 / E5 / 13.71 / NAU3588–E18M8 / 2.6 / –0.02 / 0.15 / 6.53 / –7.24 / OD / IF2
qBW-D7-1 / D7 / E4 / 68.02 / NAU6468–NAU5152 / 2.96 / –0.13 / 0.06 / 6.84 / –0.51 / PD / IF2
E5 / 68.02 / NAU6468–NAU5152 / 2.52 / –0.19 / 0.04 / 5.11 / –0.22 / IF2
qBW-D8-1 / D8-2 / E3 / 11.01 / NAU3587–NAU3810 / 5.43 / –0.16 / 0.08 / 13.29 / –0.52 / PD / IF2
qBW-D8-2 / D8-3 / E3 / 14.01 / E21M8–NAU5263 / 3.06 / –0.04 / 0.16 / 5.85 / –4 / OD / IF2
E6 / 14.01 / E21M8–NAU5263 / 2.64 / –0.03 / 0.11 / 5.65 / –3.19 / IF2
qBW-D9-1 / D9-2 / E2 / 29.11 / JESPR110–NAU923 / 3.84 / –0.19 / 0.19 / 11.66 / –1.05 / D / IF2
qBW-A11-1 / A11-2 / e1 / 35.91 / NAU1233–NAU3260 / 2.95 / –0.1 / 6.8 / A / RILs
qBW-D11-1 / D11 / e7 / 20.32 / NAU5428–BNL1231 / 4.49 / –0.14 / 10.83 / A / RILs
e3 / 14.01 / NAU470–NAU5428 / 2.96 / –0.14 / 8.63 / RILs
qBW-A12-1 / A12-2 / E6 / 2.01 / NAU4020–NAU6643 / 2.67 / –0.11 / 0 / 8.39 / 0.00 / A / IF2
qBW-D12-1 / D12-1 / E1 / 0.01 / BNL3994–JESPR234 / 3.29 / –0.1 / 0.03 / 7.46 / –0.29 / PD / IF2
e8 / 0.01 / BNL3994–JESPR234 / 3.46 / –0.08 / 7.2 / RILs
qBW-A13-1 / A13 / E4 / 36.19 / OPAJ15–NAU1522 / 2.71 / –0.13 / 0.03 / 6.18 / –0.24 / PD / IF2
qBW-D13-1 / D13 / E3 / 16.73 / NAU4105–NAU6354 / 3.06 / –0.15 / 0.18 / 12.09 / –1.18 / D / IF2
qBW-LG01-1 / LG01 / E3 / 22.37 / NAU2135–NAU4310 / 6.44 / –0.14 / 0.13 / 12.97 / –0.88 / D / IF2
LP / qLP-A1-1† / A1-2 / E6 / 0.01 / NAU6251–NAU6309 / 3.58 / 0.42 / 0.04 / 6.93 / 0.10 / A / IF2
e3 / 0.01 / NAU6251–NAU6309 / 4.45 / 0.62 / 8.53 / RILs
e6 / 0.01 / NAU6251–NAU6309 / 3.31 / 0.41 / 5.83 / RILs
qLP-A1-2† / A1-1 / E3 / 2.01 / NAU4073–E4M9 / 2.69 / 0.03 / 1.34 / 23.46 / 42.19 / OD / IF2
E4 / 5.01 / NAU4073–E4M9 / 3.44 / 0.01 / 1.52 / 33.88 / 190.49 / IF2
e6 / 10.01 / NAU4073–E4M9 / 4.24 / 0.47 / 8.11 / RILs
qLP-D2-1† / D2-1 / E3 / 8.01 / CIR381b–CIR246 / 4.25 / 0.32 / 0.64 / 8.72 / 2 / OD / IF2
e3 / 2.01 / CIR381b–CIR246 / 3.16 / 0.54 / 6.65 / RILs
e4 / 29.21 / NAU4238–NAU5467 / 3.4 / 0.65 / 6.95 / RILs
e7 / 29.21 / NAU4238–NAU5467 / 4.37 / 0.56 / 8.44 / RILs
qLP-A5-1 / A5-1 / e3 / 1.39 / BNL3452–NAU879 / 3.78 / –0.55 / 7.19 / A / RILs
qLP-A5-2 / A5-2 / E1 / 4.43 / NAU2121–NAU6094 / 2.94 / –0.3 / 0.48 / 7.21 / –1.59 / OD / IF2
E6 / 9.43 / NAU2121–NAU6094 / 2.65 / –0.37 / 0.21 / 7.37 / –0.58 / IF2
qLP-A5-3 / A5-2 / E1 / 28.25 / NAU6109–E4M12 / 4.87 / –0.54 / 0.42 / 12.62 / –0.78 / PD / IF2
E5 / 35.91 / E9M14–NAU4951 / 3.85 / –0.5 / 0.2 / 9.72 / –0.39 / IF2
E6 / 22.76 / P1–NAU3273 / 5.21 / –0.5 / 0.21 / 12.29 / –0.41 / IF2
e4 / 22.76 / NAU3273–NAU6109 / 3.1 / –0.72 / 8.25 / RILs
qLP-D6-1† / D6 / E4 / 11.27 / NAU5373–NAU3588 / 3.65 / 0.52 / 0.35 / 9.29 / 0.68 / PD / IF2
E5 / 11.31 / NAU5373–NAU3588 / 2.85 / 0.13 / 0.58 / 7.81 / 4.34 / IF2
qLP-D7-1† / D7 / E3 / 0.01 / NAU6430–BNL2986 / 2.84 / –0.41 / 0.32 / 6.06 / –0.76 / PD / IF2
qLP-D8-1 / D8-2 / E1 / 0.01 / NAU3587–NAU3810 / 4.09 / –0.46 / –0.32 / 8.78 / 0.71 / PD / IF2
e2 / 0.01 / NAU3587–NAU3810 / 4.83 / –0.52 / 9.4 / RILs
e6 / 0.01 / NAU3587–NAU3810 / 5.06 / –0.52 / 9.5 / RILs
qLP-A9-1 / A9 / E6 / 39.03 / NAU2666–NAU6668 / 3.57 / 0.22 / 0.55 / 10.46 / 2.5 / OD / IF2
E5 / 39.03 / NAU2666–NAU6668 / 2.69 / 0.14 / 0.56 / 8.27 / 3.89 / IF2
qLP-D9-1† / D9-2 / E1 / 24.11 / JESPR110–NAU923 / 2.77 / –0.45 / 0.3 / 7.25 / –0.68 / PD / IF2
E2 / 51.78 / NAU2658–BNL1672 / 4.28 / –0.63 / 0.17 / 10.33 / –0.27 / IF2
E6 / 49.78 / NAU2658–BNL1672 / 2.51 / –0.34 / 0.09 / 4.8 / –0.27 / IF2
qLP-A11-1 / A11-2 / e4 / 0.01 / NAU5192–E17M8 / 3.91 / –0.7 / 7.99 / PD / RILs
e7 / 0.01 / NAU5192–E17M8 / 4.97 / –0.59 / 9.57 / RILs
e5 / 4.01 / NAU5192–E17M8 / 3.05 / –0.53 / 7.73 / RILs
e8 / 4.01 / NAU5192–E17M8 / 3.1 / –0.18 / 7.84 / RILs
E6 / 19.74 / NAU5064–NAU1453 / 3.22 / –0.36 / 0.33 / 7.05 / –0.92 / IF2
E2 / 14.62 / NAU5064–NAU1453 / 3.39 / –0.18 / 0.63 / 6.49 / –3.53 / IF2
qLP-A11-2† / A11-2 / E3 / 18.74 / NAU538–NAU1595 / 2.61 / –0.43 / 0.35 / 5.73 / –0.81 / PD / IF2
E2 / 25.71 / NAU1595–NAU1233 / 6.55 / –0.72 / 0.5 / 16.64 / –0.69 / IF2
e5 / 20.71 / NAU538–NAU1595 / 3.43 / –0.52 / 7.4 / RILs
e8 / 20.74 / NAU538–NAU1595 / 3.48 / –0.18 / 7.49 / RILs
e3 / 22.71 / NAU1595–NAU1233 / 3.17 / –0.51 / 5.99 / RILs
e6 / 24.71 / NAU1595–NAU1233 / 3.17 / –0.44 / 7.29 / RILs
qLP-A11-3† / A11-2 / E6 / 33.91 / NAU1233–NAU3260 / 3.1 / –0.36 / 0.31 / 7.79 / –0.86 / D / IF2
E1 / 32.91 / NAU1233–NAU3260 / 3.29 / –0.4 / 0.5 / 9.33 / –1.26 / IF2
E3 / 30.91 / NAU1233–NAU3260 / 2.61 / –0.5 / 0.43 / 8.28 / –0.86 / IF2
e1 / 33.91 / NAU1233–NAU3260 / 3.75 / –0.58 / 9.2 / RILs
e5 / 33.91 / NAU1233–NAU3260 / 3.35 / –0.6 / 9.6 / RILs
e6 / 33.91 / NAU1233–NAU3260 / 4.93 / –0.56 / 11.73 / RILs
e8 / 33.91 / NAU1233–NAU3260 / 3.4 / –0.2 / 9.7 / RILs
qLP-D11-1 / D11 / e2 / 38.01 / E19M5–NAU6315 / 3.16 / 0.43 / 6.7 / A / RILs
qLP-A12-1 / A12-1 / E2 / 7.01 / NAU4047–NAU5466 / 3.46 / 0.61 / –0.15 / 9.37 / –0.25 / PD / IF2
qLP-A12-2 / A12-2 / E1 / 9.78 / NAU6643–CIR148 / 3.38 / –0.42 / –0.21 / 6.89 / 0.51 / PD / IF2
qLP-D12-1 / D12-1 / E2 / 8.01 / BNL3994–JESPR234 / 3.6 / –0.34 / 0.58 / 7.85 / –1.72 / OD / IF2
qLP-D12-2 / D12-3 / e6 / 7.89 / NAU460–NAU1298 / 3 / 0.38 / 5.29 / A / RILs
e2 / 7.91 / NAU460–NAU1298 / 3.55 / 0.43 / 6.51 / RILs
SI / qSI-D2-1 / D2-1 / E4 / 28.92 / NAU4238–NAU5467 / 3.11 / 0.18 / 0.06 / 6.76 / 0.33 / PD / IF2
E6 / 27.92 / NAU4238–NAU5467 / 3.19 / 0.13 / 0.05 / 5.83 / 0.36 / IF2
E5 / 29.21 / NAU4238–NAU5467 / 2.92 / 0.14 / 0.01 / 5.75 / 0.04 / IF2
E1 / 29.21 / NAU4238–NAU5467 / 6.24 / 0.23 / 0.03 / 13.63 / 0.13 / IF2
e4 / 13.86 / NAU6106–NAU4238 / 2.93 / 0.14 / 6.36 / RILs
e7 / 13.86 / NAU6106–NAU4238 / 3.01 / 0.12 / 6.31 / RILs
qSI-A3-1† / A3-2 / E6 / 20.12 / NAU4789–NAU4324 / 2.68 / –0.11 / –0.05 / 5.09 / –0.45 / PD / IF2
E3 / 17.34 / NAU1167–NAU4789 / 2.78 / –0.17 / –0.03 / 6.2 / –0.18 / IF2
qSI-D4-1 / D4-1 / E6 / 11.82 / JESPR220–NAU3546 / 7.94 / –0.21 / 0.09 / 15 / –0.41 / PD / IF2
E1 / 5.01 / NAU5236–JESPR220 / 3.85 / –0.2 / 0.07 / 11.72 / –0.33 / IF2
E2 / 4.01 / NAU5236–JESPR220 / 3.83 / –0.2 / 0.01 / 9.22 / –0.07 / IF2
E3 / 11.82 / JESPR220–NAU3546 / 9.51 / –0.31 / 0.21 / 21.39 / –0.68 / IF2
E5 / 11.82 / JESPR220–NAU3546 / 7.66 / –0.23 / 0.2 / 15.92 / –0.89 / IF2
qSI-A5-1† / A5-2 / E1 / 40.37 / NAU4951–NAU5077 / 5.35 / 0.23 / 0.03 / 11.81 / 0.13 / A / IF2
E2 / 40.37 / NAU4951–NAU5077 / 3.5 / 0.17 / 0.11 / 7.12 / 0.65 / IF2
E4 / 40.37 / NAU4951–NAU5077 / 3.99 / 0.22 / 0.01 / 8.64 / 0.05 / IF2
E5 / 29.31 / NAU4951–NAU5077 / 3.65 / 0.2 / 0 / 9.41 / 0.00 / IF2
E6 / 40.37 / NAU4951–NAU5077 / 6.48 / 0.2 / 0 / 11.78 / 0.00 / IF2
e8 / 25.24 / NAU3273–NAU6109 / 3.49 / 0.13 / 7.08 / RILs
qSI-A5-2† / A5-2 / E1 / 5.43 / NAU2121–NAU6094 / 4.09 / 0.15 / –0.23 / 12.19 / –1.57 / OD / IF2
qSI-D7-1 / D7 / E2 / 31.92 / BNL2986–NAU2820 / 4.22 / 0.2 / –0.2 / 11.02 / –1.01 / D / IF2
qSI-D9-1† / D9-2 / E1 / 17.01 / JESPR114–BNL1414 / 3.87 / 0.22 / –0.11 / 11.51 / –0.48 / PD / IF2
e7 / 16.69 / BNL1414–CIR194 / 3.25 / 0.13 / 6.73 / RILs
e4 / 16.98 / JESPR208–JESPR110 / 2.59 / 0.13 / 5.54 / RILs
e2 / 27.11 / JESPR110–NAU923 / 3 / 0.21 / 8.52 / RILs
e8 / 27.11 / JESPR110–NAU923 / 3.75 / 0.15 / 9.7 / RILs
e5 / 35.51 / NAU923–BNL3140 / 3.5 / 2.08 / 8.1 / RILs
qSI-D10-1 / D10-2 / e2 / 0.01 / NAU4873–NAU4957 / 3.13 / –0.19 / 6.69 / A / RILs
qSI-A11-1† / A11-2 / E1 / 17.92 / NAU980–NAU3008 / 3.49 / 0.1 / –0.24 / 8.29 / –2.51 / OD / IF2
E3 / 17.92 / NAU980–NAU3008 / 3.2 / 0.15 / –0.17 / 6.31 / –1.16 / IF2
qSI-A12-1 / A12-2 / e5 / 2.01 / NAU4020–NAU6643 / 3.27 / 2.17 / 8.45 / A / RILs
qSI-D12-1 / D12-1 / e6 / 0.01 / BNL3994–JESPR234 / 3.45 / –0.15 / 7.08 / A / RILs
qSI-LG01-1 / LG01 / E1 / 12.37 / NAU2135–NAU4310 / 3.43 / 0.2 / 0.03 / 9.52 / 0.15 / A / IF2
LI / qLI-A1-1 / A1-1 / E1 / 10.01 / NAU4073–E4M9 / 3.21 / 0.2 / 0.35 / 29.52 / 1.74 / OD / IF2
qLI-D2-1 / D2-1 / E1 / 2.01 / CIR381b–CIR246 / 4.08 / 0.14 / 0.12 / 8.01 / 0.82 / D / IF2
E2 / 1.01 / CIR381b–CIR246 / 3.38 / 0.14 / 0.15 / 7.83 / 1.1 / IF2
E6 / 1.01 / CIR381b–CIR246 / 4.6 / 0.12 / 0.13 / 9.67 / 1.05 / IF2
E3 / 10.23 / CIR246–NAU6106 / 3.94 / 0.07 / 0.27 / 10.01 / 4.16 / IF2
e6 / 6.01 / CIR381b–CIR246 / 5.02 / 0.17 / 10.32 / RILs
e1 / 8.01 / CIR381b–CIR246 / 4.67 / 0.18 / 8.32 / RILs
e3 / 26.92 / NAU4238–NAU5467 / 2.83 / 0.17 / 6.38 / RILs
e4 / 26.92 / NAU4238–NAU5467 / 2.51 / 0.27 / 8.81 / RILs
e7 / 26.92 / NAU4238–NAU5467 / 4.41 / 0.22 / 12.3 / RILs
e8 / 29.21 / NAU4238–NAU5467 / 4.85 / 0.14 / 8.16 / RILs
qLI-D2-2 / D2-1 / E6 / 15.86 / NAU6106–NAU4238 / 2.63 / –0.07 / 0.15 / 5.42 / –2.33 / OD / IF2
E5 / 16.91 / NAU6106–NAU4238 / 3.32 / –0.13 / 0.14 / 6.8 / –1.13 / IF2
qLI-A3-1 / A3-2 / E4 / 0.34 / NAU1167–NAU4789 / 2.72 / 0.08 / 0.17 / 5.87 / 2.06 / OD / IF2
qLI-D4-1 / D4-1 / E1 / 3.01 / NAU5236–JESPR220 / 4.76 / –0.19 / 0.08 / 10.09 / –0.44 / PD / IF2
E3 / 11.82 / JESPR220–NAU3546 / 3.04 / –0.18 / 0.1 / 6.93 / –0.57 / IF2
E5 / 2.01 / NAU5236–JESPR220 / 3.5 / –0.14 / 0.04 / 7.95 / –0.31 / IF2
E6 / 3.01 / NAU5236–JESPR220 / 6.09 / –0.18 / 0.12 / 14.55 / –0.64 / IF2
e3 / 6.01 / NAU5236–JESPR220 / 3.22 / –0.18 / 7.14 / RILs
e8 / 6.01 / NAU5236–JESPR220 / 3.1 / –0.12 / 6.36 / RILs
qLI-A5-1 / A5-1 / E2 / 1.01 / NAU3899–BNL3452 / 2.81 / –0.16 / 0 / 5.53 / 0.00 / A / IF2
E6 / 0.01 / NAU3899–BNL3452 / 4.16 / –0.15 / –0.02 / 7.59 / –0.13 / IF2
e3 / 4.14 / NAU3269–NAU2217 / 3.55 / –0.18 / 6.95 / RILs
e7 / 1.39 / BNL3452–NAU879 / 3.53 / –0.16 / 6.39 / RILs
e8 / 1.39 / BNL3452–NAU879 / 3.64 / –0.12 / 5.94 / RILs
qLI-A6-1 / A6 / E4 / 12.01 / NAU2684–NAU3859 / 2.8 / 0.18 / –0.19 / 9.24 / –1.05 / D / IF2
qLI-D6-1 / D6 / E6 / 10.27 / NAU5373–NAU3588 / 2.62 / –0.08 / 0.1 / 4.87 / –1.21 / OD / IF2
E2 / 13.68 / NAU3588–E18M8 / 2.7 / –0.13 / 0.13 / 6.39 / –1.02 / IF2
e2 / 0.01 / NAU5210–CIR071 / 3.03 / –0.15 / 5.96 / RILs
E4 / 19.55 / NAU2838–NAU6478 / 3.25 / –0.06 / 0.23 / 7.8 / –3.73 / IF2
qLI-A7-1 / A7 / e6 / 10.41 / NAU1043–NAU3654 / 3.35 / –0.14 / 6.62 / A / RILs
E1 / 4.01 / NAU1043–NAU3654 / 3.6 / –0.16 / 0.02 / 7.17 / 0.13 / IF2
E6 / 4.01 / NAU1043–NAU3654 / 2.61 / –0.13 / 0 / 5.77 / 0.00 / IF2
qLI-D7-1 / D7 / E3 / 0.01 / NAU6430–BNL2986 / 3.1 / –0.13 / 0.16 / 6.05 / –1.22 / OD / IF2
qLI-D8-1 / D8-2 / E3 / 16.01 / NAU3587–NAU3810 / 2.51 / –0.15 / 0.02 / 5.19 / 0.13 / A / IF2
qLI-A9-1 / A9 / E1 / 36.03 / NAU2666–NAU6668 / 2.91 / 0.13 / 0.12 / 8.9 / 0.92 / A / IF2
e8 / 23.19 / NAU2200–NAU2398 / 4.35 / 0.13 / 7.08 / RILs
e1 / 24.02 / NAU2398–NAU2666 / 3.1 / 0.15 / 5.21 / RILs
e7 / 27.03 / NAU2666–NAU6668 / 3.71 / 0.17 / 6.77 / RILs
qLI-D9-1 / D9-2 / E2 / 49.78 / NAU2658–BNL1672 / 3.61 / –0.18 / 0.1 / 7.72 / –0.55 / PD / IF2
qLI-A11-1 / A11-2 / E2 / 30.91 / NAU1233–NAU3260 / 3.78 / –0.22 / –0.02 / 10.39 / –0.09 / A / IF2
E6 / 32.91 / NAU1233–NAU3260 / 3.9 / –0.16 / –0.06 / 9.78 / –0.38 / IF2
e1 / 35.91 / NAU1233–NAU3260 / 8.07 / –0.25 / 14.87 / RILs
e6 / 35.91 / NAU1233–NAU3260 / 6.1 / –0.18 / 11.28 / RILs
e8 / 35.91 / NAU1233–NAU3260 / 4.16 / –0.13 / 7.01 / RILs
qLI-A11-2 / A11-2 / E6 / 1.01 / NAU5192–E17M8 / 3.8 / –0.14 / 0.02 / 7.52 / 0.14 / A / IF2
e4 / 0.01 / NAU5192–E17M8 / 2.98 / –0.23 / 6.49 / RILs
e7 / 0.01 / NAU5192–E17M8 / 4.81 / –0.19 / 9.02 / RILs
qLI-A12-1 / A12-2 / E6 / 7.01 / NAU4020–NAU6643 / 3.04 / –0.14 / 0.01 / 7.14 / 0.07 / A / IF2
qLI-D12-1 / D12-1 / E1 / 0.01 / BNL3994–JESPR234 / 3.69 / –0.14 / 0.08 / 6.64 / –0.55 / PD / IF2
E2 / 7.01 / BNL3994–JESPR234 / 5.41 / –0.17 / 0.19 / 11.82 / –1.1 / IF2
E3 / 9.01 / BNL3994–JESPR234 / 3.38 / –0.16 / 0.1 / 7.41 / –0.63 / IF2
E6 / 4.01 / BNL3994–JESPR234 / 4.43 / –0.13 / 0.1 / 9.04 / –0.78 / IF2
qLI-A13-1 / A13 / E1 / 56.6 / NAU3398–NAU3393 / 2.55 / –0.09 / 0.2 / 7.46 / –2.31 / OD / IF2
FBN / qFBN-D2-1 / D2-2 / e8 / 0.01 / BNL3259–NAU2190 / 4.25 / 0.25 / 9 / A / RILs
qFBN-A3-1 / A3-2 / E4 / 19.12 / NAU4789–NAU4324 / 3.7 / 0.28 / –0.05 / 8.82 / –0.18 / A / IF2
qFBN-A5-1 / A5-1 / E2 / 3.83 / NAU879–NAU3269 / 3.17 / 0.63 / –0.28 / 7.77 / –0.44 / PD / IF2
e6 / 6.61 / NAU3828–NAU3823 / 3.02 / 0.37 / 6.76 / RILs
qFBN-D5-1 / D5-2 / E1 / 10.01 / BNL3442–NAU4605 / 4.89 / 0.42 / 0.23 / 14.53 / 0.55 / PD / IF2
qFBN-D7-1 / D7 / e8 / 30.92 / BNL2986–NAU2820 / 5.32 / –0.34 / 16.92 / A / RILs
e6 / 51.02 / NAU6468–NAU5152 / 4.95 / –0.32 / 15.86 / RILs
qFBN-D8-1† / D8-3 / E6 / 2.01 / E21M8–NAU5263 / 3.6 / –0.11 / 0.52 / 12.4 / –4.66 / OD / IF2
E2 / 5.01 / E21M8–NAU5263 / 3.31 / –0.53 / 0.71 / 10.35 / –1.33 / IF2
E4 / 9.01 / E21M8–NAU5263 / 2.63 / –0.19 / 0.25 / 8.33 / –1.31 / IF2
qFBN-A9-1 / A9 / E4 / 31.03 / NAU2666–NAU6668 / 3.06 / –0.32 / 0.19 / 10.23 / –0.6 / PD / IF2
qFBN-D9-1 / D9-2 / E3 / 36.45 / NAU923–BNL3140 / 3.99 / 0.58 / –0.49 / 10.49 / –0.83 / D / IF2
E5 / 40.21 / NAU923–BNL3140 / 3.29 / 0.35 / –0.3 / 9.71 / –0.84 / IF2
qFBN-A11-1 / A11-1 / E6 / 0.01 / E22M1–NAU2809 / 3.28 / 0.01 / 0.6 / 14.63 / 43.27 / OD / IF2

†Indicates the QTL was simultaneously identified in the F2/F2:3 population of the same cross in Qin et al. (2009).

a Disconnected linkage groups belonging to identical chromosome were numbered from the top as shown in Figure 1, and were denoted by the name of the chromosome, followed by a hyphen and the serial number.

b Environments for RILs and IF2s were indicated as ‘e’ and ‘E’ respectively: e1, Jiangpu 2002; e2, Guanyun 2002; e3, Jiangpu 2003; e4, Guanyun2003; e5, Jiangpu2007; e6, combining e1 and e2 for the year 2002; e7, combining e3 and e4 for the year 2003; e8, combined analysis using means of e5, e6 and e7. E1, Jiangpu 2004; E2, Jiangpu2005; E3, Jianpu 2008; E4, Linqing 2008; E5, combining E3 and E4 for the year 2008; E6, combined analysis using means of E1, E2 and E5.

a D/A: Dominance/Additive.

d GA, gene action modes classified as A, additive (|d/a| = 0–0.2); PD, partial dominance (|d/a| = 0.21–0.80); D, dominance (|d/a| = 0.81–1.20) and OD, overdominance (|d/a| > 1.2) according to Stuber et al. (1987).

Table S2 Epistatic QTL by environment detected by multi-marker joint analysis in the IF2s

Traits / Adjacent markers / Chromosome / Power / LOD / AE1a / DE1b / AE2a / DE2b / AE3a / DE3b / AE4a / DE4b / R2%c
SY / NAU997 / A3–1 / 0.62 / 3.59 / 1.60 / 0.57 / 3.66 / –0.13 / –2.98 / 0.82 / –2.27 / –1.25 / 3.1
BNL3442 / D5–2* / 1.00 / 4.77 / 4.23 / 0.66 / –0.55 / 0.48 / 0.54 / –0.82 / –4.23 / –0.32 / 3.7
NAU5210 / D6* / 0.43 / 4.55 / 1.66 / –2.73 / 1.33 / –0.22 / –4.65 / 2.14 / 1.66 / 0.81 / 3.5
BNL686 / D9–1* / 0.55 / 3.89 / –4.65 / –1.54 / 1.69 / –0.76 / 0.29 / –0.46 / 2.67 / 2.75 / 3.7
BNL3646 / D10–1* / 1.00 / 7.35 / –5.86 / 4.87 / 3.60 / –0.92 / –2.14 / –1.87 / 4.39 / –2.09 / 8.6
NAU5466 / A12–1 / 0.71 / 3.31 / 1.76 / –0.29 / 0.26 / –1.97 / –4.79 / 1.54 / 2.77 / 0.71 / 3.7
LY / NAU997 / A3–1 / 0.70 / 3.46 / 0.80 / –0.94 / 1.33 / –0.65 / –1.39 / 0.26 / –0.74 / 1.33 / 2.7
BNL3442 / D5–2* / 1.00 / 5.82 / 1.66 / –0.96 / –0.30 / 0.85 / 0.43 / –0.57 / –1.79 / 0.68 / 3.1
NAU3588–TMG10 / D6* / 0.49 / 7.64 / 0.26 / 0.23 / 1.27 / –1.12 / –2.52 / 0.71 / 1.00 / 0.18 / 4.2
BNL3646 / D10–1* / 0.95 / 8.93 / –2.28 / 2.69 / 0.77 / –0.55 / –0.57 / –1.33 / 2.09 / –0.80 / 6.5
NAU4047–NAU5466 / A12–1 / 0.83 / 4.78 / 0.46 / –0.35 / 0.59 / –0.71 / –1.94 / 0.36 / 0.90 / 0.71 / 2.4
NAU985a–NAU6354 / D13* / 0.38 / 5.47 / 0.29 / –1.92 / 0.61 / –1.72 / 0.12 / –0.62 / –1.03 / 4.25 / 5.9
BP / BNL3442 / D5–2* / 1.00 / 8.18 / 0.95 / –0.94 / –0.36 / 0.27 / 0.26 / –0.36 / –0.86 / 1.04 / 3.6
NAU5210 / D6* / 0.92 / 5.24 / 0.28 / –0.42 / 0.98 / 0.23 / –0.79 / 0.29 / –0.47 / –0.10 / 2.5
BNL686 / D9–1* / 0.75 / 5.50 / –0.97 / –0.42 / 0.38 / –0.87 / 0.28 / 0.19 / 0.32 / 1.10 / 2.9
BNL3646–E14M4b / D10–1* / 1.00 / 8.28 / –1.24 / 0.77 / 0.49 / –0.40 / –0.39 / –0.18 / 1.13 / –0.19 / 5.4
LP / BNL3259 / D2–2 / 0.31 / 3.16 / –0.14 / –0.13 / –0.24 / –0.15 / –0.69 / –0.88 / 1.07 / 1.16 / 7.5
NAU6478–E22M8 / D6* / 0.54 / 4.26 / –0.16 / –0.43 / –0.86 / –0.16 / –0.27 / –0.35 / 1.29 / 0.93 / 8.4
LI / NAU2190–E14M4a / D2–2 / 0.30 / 3.41 / –0.55 / –0.32 / –0.68 / 0.14 / –0.55 / 0.23 / 1.78 / –0.05 / 12.9
NAU2838–NAU6478 / D6* / 0.42 / 3.93 / –0.12 / 0.55 / 0.83 / 0.39 / 0.45 / –0.12 / –1.16 / –0.82 / 8.4
FBN / BNL3442 / D5–2* / 0.74 / 3.25 / –0.11 / –0.67 / 0.92 / –0.33 / –0.49 / 0.17 / –0.32 / 0.83 / 9.7
NAU1043 / A7 / 0.45 / 4.77 / 0.86 / –0.14 / 0.46 / 0.49 / –0.42 / –0.23 / –0.91 / –0.13 / 13.4
BNL3140 / D9–2* / 0.53 / 3.45 / –0.13 / 0.49 / –0.16 / –0.54 / 0.46 / –0.87 / –0.17 / 0.92 / 6.0

*Simultaneously detected as main-effect QTL by CIM analysis.

a interaction between additive and environment.

b interaction between dominance and environment.

c phenotypic variation collectively explained by AE and DE.