Supplemental Table A1: Main-effect QTL detected by the multi-QTL joint analysis
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SDa / Additive±SDa / Dominant±SDa / Ratio(%)bCommon main-effect QTL identified by multi-QTL joint analysis and composite interval mapping
SL / qSL-6 / C2-1, 6 / satt640-satt422 / 14.3 / 5.54±1.36 / -0.048±0.006 / -0.009±0.012 / 90
qSL-10-1 / O-1, 10 / satt173-satt094 / 36.7 / 3.56±0.69 / 0.028±0.011 / -0.038±0.011 / 16
qSL-10-2 / O-2, 10 / satt331-satt592 / 0.7 / 12.69±6.85 / -0.081±0.016 / -0.016±0.009 / 92
qSL-10-3 / O-2,10 / satt592-sat_274 / 31.5 / 3.48±0.98 / -0.045±0.007 / 0.008±0.015 / 40
qSL-16 / J,16 / sat_224-sat_394 / 85.4 / 3.04±0.40 / -0.037±0.005 / 0.007±0.015 / 10
qSL-17-1 / D2-1, 17 / satt226-sat_354 / 76.5 / 3.82±1.40 / -0.043±0.009 / 0.000±0.009 / 20
qSL-18 / G, 18 / satt309-satt688 / 13.1 / 3.96±0.88 / -0.046±0.009 / 0.019±0.024 / 80
qSL-19 / L-2, 19 / satt166-satt527 / 4.8 / 3.56±0.92 / -0.038±0.005 / 0.014±0.011 / 48
SW / qSW-2-1 / D1b-1, 2 / satt157-sat_254 / 35.5 / 4.21±1.20 / -0.028±0.006 / 0.020±0.010 / 86
qSW-3-2 / N-2, 3 / satt255-satt237 / 9.5 / 3.50±0.56 / 0.031±0.002 / 0.003±0.009 / 24
qSW-5-2 / A1, 5 / satt449-sat_356 / 66.7 / 5.65±1.39 / -0.038±0.005 / 0.005±0.009 / 78
qSW-6-1 / C2-1, 6 / satt640-satt422 / 23.1 / 10.53±5.83 / -0.054±0.011 / -0.001±0.009 / 88
qSW-7-2 / M, 7 / satt323-satt220 / 54.0 / 5.31±1.38 / -0.039±0.005 / 0.010±0.006 / 62
qSW-10-2 / O-2, 10 / satt592-sat_274 / 21.4 / 5.14±1.19 / -0.036±0.004 / -0.006±0.007 / 16
qSW-14-2 / B2-2, 14 / satt355-satt070 / 7.5 / 3.23±0.67 / 0.022±0.009 / -0.002±0.025 / 10
qSW-18 / G, 18 / satt309-satt688 / 1.0 / 2.92±0.33 / -0.011±0.004 / -0.035±0.003 / 20
qSW-20 / I-2, 20 / sat_418-sat_419 / 35.1 / 6.21±2.70 / -0.041±0.007 / 0.001±0.008 / 84
ST / qST-3-2 / N-2, 3 / satt255-satt237 / 14.2 / 4.91±0.70 / 0.038±0.003 / -0.004±0.007 / 12
qST-3-4 / N-2, 3 / satt339-satt022 / 30.8 / 5.60±1.14 / 0.040±0.004 / -0.003±0.013 / 10
qST-5-2 / A1, 5 / satt449-sat_356 / 74.2 / 8.19±4.00 / -0.047±0.009 / 0.016±0.007 / 84
Continued
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SDa / Additive±SDa / Dominant±SDa / Ratio(%)bST / qST-6-1 / C2-1, 6 / satt640-satt422 / 4.9 / 3.66±0.82 / -0.028±0.003 / -0.010±0.005 / 76
qST-7-1* / M, 7 / Satt150-sat_258 / 8.1 / 3.18±0.43 / -0.023±0.010 / 0.015±0.020 / 10
qST-7-2 / M, 7 / sat_258-satt463 / 30.8 / 4.28±0.91 / -0.032±0.004 / 0.019±0.010 / 30
qST-18 / G, 18 / satt309-satt688 / 3.6 / 3.28±0.67 / -0.002±0.004 / -0.041±0.004 / 16
qST-20-2 / I-2, 20 / sat_418-sat_419 / 22.5 / 3.74±0.79 / -0.030±0.004 / -0.004±0.011 / 60
SLW / qSLW-1-1 / D1a-2, 1 / AW781285-satt077 / 58.3 / 5.39±1.33 / -0.040±0.008 / 0.024±0.009 / 88
qSLW-2 / D1b-2, 2 / satt266-satt282 / 18.2 / 4.85±1.88 / -0.036±0.011 / 0.026±0.015 / 44
qSLW-5-1 / A1, 5 / sat_344-satt449 / 11.5 / 3.79±1.03 / 0.036±0.005 / -0.004±0.011 / 22
qSLW-5-2 / A1, 5 / satt449-sat_356 / 71.4 / 5.53±2.09 / 0.044±0.008 / -0.001±0.010 / 88
qSLW-6 / C2-1, 6 / satt640-satt422 / 22.3 / 4.19±1.15 / 0.036±0.005 / -0.013±0.008 / 90
qSLW-10-1 / O-2, 10 / satt331-satt592 / 1.2 / 5.90±1.80 / -0.052±0.007 / -0.008±0.012 / 82
qSLW-10-2 / O-2, 10 / satt592-sat_274 / 48.7 / 5.52±1.86 / -0.046±0.008 / 0.016±0.012 / 82
qSLW-13-1 / F, 13 / satt649-satt269 / 0.4 / 6.97±1.27 / 0.050±0.005 / 0.007±0.008 / 96
qSLW-16-2 / J, 16 / sat_224-sat_394 / 107.2 / 4.09±0.91 / 0.005±0.007 / -0.052±0.006 / 50
qSLW-17-2 / D2-1, 17 / sat_292-satt615 / 25.9 / 3.92±0.79 / -0.038±0.004 / 0.004±0.005 / 10
qSLW-17-3 / D2-1, 17 / satt226-sat_354 / 73.4 / 4.66±1.36 / -0.040±0.007 / -0.003±0.013 / 46
qSLW-17-4 / D2-2, 17 / satt672-satt413 / 5.6 / 8.21±3.59 / -0.054±0.009 / 0.015±0.011 / 44
qSLW-17-5 / D2-2, 17 / satt413-satt256 / 19.4 / 7.73±2.69 / -0.047±0.013 / 0.017±0.019 / 66
qSLW-18 / G, 18 / satt309-satt688 / 12.8 / 4.62±1.09 / -0.038±0.005 / 0.011±0.011 / 98
qSLW-19-1 / L-1, 19 / satt652-satt284 / 5.5 / 3.25±0.71 / -0.032±0.003 / -0.003±0.012 / 20
qSLW-X3 / X3 / satt260-satt382 / 0.9 / 5.39±2.13 / -0.035±0.011 / 0.029±0.012 / 60
Continued
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SDa / Additive±SDa / Dominant±SDa / Ratio(%)bSLT / qSLT-10-1 / O-2, 10 / satt331-satt592 / 3.3 / 5.04±2.12 / -0.088±0.014 / -0.006±0.027 / 46
qSLT-10-2 / O-2, 10 / satt592-sat_274 / 17.7 / 6.17±3.61 / -0.086±0.026 / 0.051±0.030 / 42
qSLT-13 / F, 13 / satt649-satt269 / 0.0 / 9.85±1.40 / 0.121±0.009 / 0.003±0.013 / 96
qSLT-20 / I-1, 20 / satt419-satt354 / 1.1 / 9.79±3.24 / 0.119±0.018 / 0.014±0.021 / 86
qSLT-X3 / X3 / satt260-satt382 / 3.1 / 4.45±1.07 / -0.054±0.017 / 0.074±0.028 / 62
SWT / qSWT-3-1 / N-1, 3 / satt631-satt683 / 8.1 / 9.02±4.95 / -0.065±0.016 / 0.020±0.013 / 42
qSWT-3-2 / N-1, 3 / satt683-sat_280 / 19.6 / 8.78±3.95 / -0.065±0.013 / -0.002±0.013 / 48
qSWT-6 / C2-1, 6 / satt640-satt422 / 25.2 / 8.20±1.32 / -0.061±0.005 / 0.023±0.007 / 98
qSWT-13-1 / F, 13 / satt649-satt269 / 0.7 / 5.90±1.44 / 0.055±0.007 / 0.003±0.006 / 100
qSWT-15 / E, 15 / satt045-satt263 / 7.1 / 3.15±0.47 / 0.035±0.004 / -0.021±0.011 / 20
qSWT-20-1 / I-1, 20 / satt419-satt354 / 1.3 / 7.27±2.49 / 0.063±0.009 / 0.007±0.010 / 92
Main-effect QTL identified only by multi-QTL joint analysis
SL / qSL-1 / D1a-2, 1 / AW781285-satt077 / 58.1 / 5.54±1.03 / -0.047±0.007 / 0.025±0.011 / 92
qSL-2-1 / D1b-1,2 / satt157-sat_254 / 27.8 / 4.11±0.99 / -0.038±0.007 / 0.020±0.013 / 80
qSL-3-1 / N-2, 3 / satt255-satt237 / 12.1 / 4.54±1.35 / 0.048±0.007 / -0.004±0.010 / 32
qSL-3-2 / N-2, 3 / satt237-satt339 / 19.3 / 3.95±0.96 / 0.045±0.006 / -0.001±0.009 / 28
qSL-7-1 / M, 7 / satt463-satt245 / 40.1 / 4.66±1.51 / -0.049±0.007 / 0.010±0.007 / 12
qSL-7-2 / M, 7 / satt245-satt323 / 52.0 / 6.36±1.63 / -0.055±0.008 / 0.020±0.009 / 52
qSL-7-3 / M, 7 / satt626 / 69.2 / 5.08±2.24 / -0.050±0.011 / 0.008±0.009 / 10
qSL-13 / F, 13 / satt649-satt269 / 0.3 / 5.43±1.13 / 0.050±0.005 / 0.012±0.008 / 98
qSL-14-2 / B2-2, 14 / sat_355-satt534 / 54.9 / 3.45±0.78 / 0.037±0.004 / 0.006±0.012 / 46
qSL-15 / E, 15 / satt685-sat_381 / 44.9 / 3.80±0.89 / -0.039±0.005 / 0.014±0.008 / 42
qSL-17-2 / D2-2, 17 / satt413-satt256 / 25.7 / 4.24±1.07 / -0.040±0.005 / 0.007±0.012 / 68
Continued
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SD / Additive±SD / Dominant±SD / Ratio(%)SL / qSL-20 / I-2, 20 / sat_418-sat_419 / 27.9 / 4.09±0.78 / -0.042±0.004 / -0.005±0.012 / 76
qSL-X3 / X3 / satt260-satt382 / 2.6 / 3.84±1.07 / -0.019±0.006 / 0.051±0.014 / 26
SW / qSW-2-3 / D1b-3, 2 / satt274-satt459 / 1.3 / 3.34±0.63 / 0.027±0.003 / -0.008±0.008 / 30
qSW-3-1 / N-1, 3 / satt631-satt683 / 1.3 / 6.09±1.42 / -0.039±0.004 / -0.003±0.008 / 92
qSW-3-3 / N-2, 3 / satt237-satt339 / 19.7 / 3.91±1.15 / 0.033±0.005 / 0.007±0.009 / 38
qSW-3-4 / N-2, 3 / satt339-satt022 / 30.4 / 3.82±0.63 / 0.032±0.004 / -0.002±0.014 / 10
qSW-5-1 / A1, 5 / sat_344-satt449 / 37.1 / 5.21±2.15 / -0.035±0.007 / 0.005±0.010 / 10
qSW-7-1 / M, 7 / satt245-satt323 / 48.9 / 5.70±1.84 / -0.040±0.007 / 0.008±0.006 / 14
qSW-10-1 / O-2, 10 / satt331-satt592 / 2.0 / 4.92±1.31 / -0.036±0.005 / -0.004±0.005 / 72
qSW-14-1 / B2-1, 14 / satt577-sat_342 / 14.0 / 2.89±0.34 / 0.027±0.001 / 0.009±0.006 / 12
qSW-15 / E, 15 / satt685-sat_381 / 38.7 / 3.15±0.43 / -0.026±0.001 / 0.008±0.013 / 10
qSW-16 / J, 16 / satt431-sat_224 / 72.1 / 3.21±0.86 / -0.029±0.004 / 0.013±0.008 / 14
qSW-19-2 / L-2, 19 / satt166-satt527 / 5.6 / 4.01±0.87 / -0.032±0.003 / 0.005±0.007 / 88
qSW-X4 / X4 / satt632-sat_228 / 20.9 / 3.23±0.46 / -0.026±0.003 / 0.005±0.014 / 22
ST / qST-2-1 / D1b-1, 2 / satt157-sat_254 / 36.1 / 3.26±0.61 / -0.011±0.017 / 0.031±0.017 / 10
qST-2-2 / D1b-3, 2 / satt274-satt459 / 0.4 / 3.77±0.96 / 0.028±0.004 / -0.014±0.006 / 38
qST-3-3 / N-2, 3 / satt237-satt339 / 19.6 / 6.13±1.27 / 0.043±0.005 / -0.006±0.007 / 68
qST-4 / C1, 4 / AW277661-satt294 / 6.9 / 2.93±0.67 / 0.025±0.004 / 0.008±0.009 / 12
qST-5-1 / A1, 5 / sat_344-satt449 / 37.4 / 3.83±1.14 / -0.031±0.007 / -0.014±0.008 / 10
qST-7-4 / M, 7 / satt323-satt220 / 54.1 / 4.51±0.95 / -0.036±0.004 / 0.010±0.007 / 44
qST-10-2 / O-2, 10 / satt592-sat_274 / 36.4 / 3.16±0.43 / -0.027±0.004 / -0.007±0.012 / 16
qST-14-1 / B2-2, 14 / satt355-satt070 / 30.1 / 3.43±0.62 / 0.028±0.003 / 0.007±0.007 / 28
qST-14-2 / B2-2, 14 / sat_355-satt534 / 43.0 / 3.57±0.99 / 0.029±0.005 / 0.005±0.010 / 14
Continued
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SD / Additive±SD / Dominant±SD / Ratio(%)ST / qST-15 / E, 15 / satt263-satt685 / 30.4 / 3.24±0.77 / -0.025±0.004 / 0.016±0.008 / 30
qST-16-1 / J, 16 / satt431-sat_224 / 73.0 / 3.20±0.70 / -0.019±0.008 / 0.030±0.009 / 12
qST-16-2 / J, 16 / sat_224-sat_394 / 83.3 / 2.78±0.34 / -0.014±0.007 / 0.032±0.008 / 10
qST-19 / L-2, 19 / satt166-satt527 / 5.2 / 3.02±0.44 / -0.027±0.002 / -0.001±0.008 / 54
qST-20-1 / I-1, 20 / satt419-satt354 / 1.7 / 5.74±1.55 / -0.039±0.005 / 0.002±0.008 / 88
SLW / qSLW-3-1 / N-1, 3 / satt631-satt683 / 1.2 / 4.14±1.02 / 0.037±0.005 / -0.001±0.009 / 76
qSLW-7 / M, 7 / satt220-satt626 / 68.4 / 4.03±1.64 / -0.035±0.007 / 0.021±0.007 / 26
qSLW-8 / A2, 8 / satt233-satt329 / 44.2 / 3.38±0.49 / 0.032±0.003 / -0.006±0.007 / 18
qSLW-15 / E, 15 / satt685-sat_381 / 50.4 / 4.54±1.94 / -0.032±0.015 / 0.029±0.013 / 30
qSLW-16-1 / J, 16 / satt215-satt244 / 46.5 / 4.06±1.21 / 0.036±0.005 / -0.004±0.010 / 44
qSLW-17-1 / D2-1, 17 / satt669-sat_292 / 16.1 / 3.94±0.99 / -0.026±0.025 / 0.013±0.028 / 10
qSLW-20-1 / I-1, 20 / satt419-satt354 / 2.9 / 3.28±0.61 / 0.032±0.004 / 0.010±0.011 / 32
qSLW-20-2 / I-2, 20 / sat_418-sat_419 / 29.2 / 3.99±1.02 / 0.035±0.004 / -0.003±0.011 / 82
SLT / qSLT-1-1 / D1a-1, 1 / satt580-sat_110 / 5.5 / 3.63±1.09 / -0.005±0.028 / 0.088±0.035 / 28
qSLT-1-2 / D1a-2, 1 / AW781285-satt077 / 55.9 / 3.29±0.63 / -0.062±0.006 / 0.034±0.025 / 22
qSLT-3-1 / N-1, 3 / satt631-satt683 / 13.5 / 3.55±1.45 / -0.070±0.012 / 0.012±0.024 / 12
qSLT-3-2 / N-1, 3 / satt683-sat_280 / 25.8 / 3.55±0.78 / -0.068±0.008 / 0.024±0.008 / 16
qSLT-5-1 / A1, 5 / sat_344-satt449 / 21.4 / 3.34±0.66 / 0.064±0.017 / 0.023±0.035 / 22
qSLT-5-2 / A1, 5 / satt449-sat_356 / 74.4 / 7.15±2.09 / 0.102±0.013 / -0.017±0.018 / 82
qSLT-8 / A2, 8 / satt233-satt329 / 47.2 / 3.56±0.91 / 0.064±0.014 / -0.018±0.030 / 34
qSLT-16-2 / J, 16 / sat_224-sat_394 / 106.6 / 3.46±0.90 / 0.021±0.010 / -0.094±0.014 / 24
qSLT-17-1 / D2-1, 17 / satt226-sat_354 / 73.8 / 3.83±0.68 / -0.069±0.013 / 0.028±0.029 / 12
qSLT-17-2 / D2-2, 17 / satt672-satt413 / 6.3 / 3.56±0.72 / -0.072±0.008 / 0.008±0.012 / 12
Continued
Trait / QTL / Chr / Marker interval / Position (cM) / LOD±SD / Additive±SD / Dominant±SD / Ratio(%)SLT / qSLT-17-3 / D2-2, 17 / satt413-satt256 / 22.0 / 3.93±1.13 / -0.072±0.011 / 0.014±0.012 / 30
qSLT-18 / G, 18 / satt309-satt688 / 9.8 / 3.85±0.62 / -0.065±0.009 / 0.047±0.022 / 12
qSLT-19 / L-1, 19 / satt652-satt284 / 20.7 / 3.82±0.79 / -0.056±0.026 / 0.056±0.030 / 10
SWT / qSWT-1 / D1a-1, 1 / satt580-sat_110 / 5.2 / 3.18±0.65 / -0.003±0.012 / 0.051±0.008 / 22
qSWT-5 / A1, 5 / satt449-sat_356 / 72.6 / 4.46±1.08 / 0.045±0.006 / -0.013±0.011 / 92
qSWT-8 / A2, 8 / satt233-satt329 / 45.2 / 2.98±0.28 / 0.036±0.002 / 0.013±0.012 / 10
qSWT-13-2 / F, 13 / BE806387-satt659 / 54.4 / 3.64±0.50 / -0.044±0.003 / 0.003±0.009 / 10
qSWT-14 / B2-1, 14 / satt577-sat_342 / 3.4 / 2.86±0.35 / 0.035±0.001 / 0.007±0.016 / 14
qSWT-17 / D2-1, 17 / sat_267 / 61.6 / 3.49±0.45 / 0.041±0.009 / 0.019±0.021 / 24
qSWT-18 / G, 18 / satt309-satt688 / 13.7 / 3.53±0.95 / -0.006±0.008 / 0.055±0.006 / 16
qSWT-20-2 / I-1, 20 / satt354-satt270 / 47.9 / 4.05±0.90 / 0.041±0.006 / 0.028±0.008 / 76
qSWT-20-3 / I-2, 20 / sat_418-sat_419 / 35.7 / 5.00±1.27 / -0.047±0.006 / 0.012±0.008 / 98
a SD: standard deviation. Ratiod: the frequency of such samples which had the LOD statistic greater than 2.5 to the total number of imputed samples (50). LOD: log of odd.
Supplemental Table A2: QTL-by-Cytoplasm interactions detected by the multi-QTL joint analysis
Trait / Cytoplasmic effect / QTL / Chr / Marker innterval / Position (cM) / Additive×
Cytoplasm / Dominance
×
Cytoplasm / LOD / Ratio(%)
Common QTL-by-Cytoplasm interactions identified by multi-QTL joint analysis and composite interval mapping
SL / -0.075±0.013 / qSL-2c-2 / D1b-2, 2 / satt266-satt282 / 19.8 / 0.023±0.015 / -0.044±0.016 / 3.66±1.12 / 52
qSL-10c / O-2, 10 / satt592-sat_274 / 44.5 / -0.043±0.005 / -0.010±0.013 / 4.08±0.99 / 24
qSL-14c / B2-1, 14 / satt577-sat_342 / 2.3 / -0.009±0.013 / -0.052±0.003 / 3.40±0.70 / 10
qSL-18c / G, 18 / satt309-satt688 / 5.9 / 0.036±0.005 / -0.026±0.013 / 3.76±0.84 / 42
SW / -0.063±0.015 / qSW-2c-1 / D1b-1, 2 / satt157-sat_254 / 33.9 / 0.002±0.006 / 0.043±0.004 / 3.51±0.83 / 52
qSW-2c-2 / D1b-2, 2 / satt266-satt282 / 3.5 / 0.026±0.011 / -0.023±0.013 / 3.77±0.96 / 34
qSW-3c-2 / N-2, 3 / satt255-satt237 / 6.2 / -0.029±0.003 / -0.006±0.009 / 3.31±0.61 / 14
qSW-6c / C2-2, 6 / satt643-staga001 / 59.4 / -0.014±0.004 / -0.036±0.004 / 3.31±0.45 / 28
ST / -0.068±0.018 / qST-3c-2 / N-2, 3 / satt339-satt022 / 41.0 / -0.012±0.011 / 0.037±0.009 / 3.49±1.01 / 12
qST-10c-2 / O-2, 10 / satt331-satt592 / 3.3 / 0.003±0.001 / 0.044±0.006 / 3.62±1.16 / 12
qST-7c / M, 7 / sat_258-satt463 / 27.4 / -0.029±0.003 / 0.002±0.013 / 3.17±0.68 / 16
qST-20c / I-2, 20 / sat_418-sat_419 / 3.9 / 0.010±0.008 / 0.039±0.008 / 3.54±0.74 / 54
SLW / qSLW-1c-1 / D1a-2, 1 / AW781285-satt077 / 57.5 / -0.035±0.006 / -0.001±0.009 / 3.47±1.17 / 46
qSLW-2c / D1b-2, 2 / satt266-satt282 / 33.2 / 0.009±0.005 / -0.047±0.004 / 3.31±0.65 / 34
qSLW-5c / A1, 5 / sat_344-satt449 / 6.1 / 0.034±0.006 / -0.008±0.007 / 3.48±1.32 / 18
qSLW-6c-1 / C2-1, 6 / satt640-satt422 / 21.0 / -0.036±0.006 / -0.016±0.011 / 4.45±1.15 / 84
qSLW-10c / O-2, 10 / satt592-sat_274 / 50.3 / -0.039±0.008 / 0.010±0.010 / 4.89±1.44 / 62
qSLW-13c / F, 13 / satt649-satt269 / 2.3 / 0.011±0.004 / -0.046±0.003 / 3.47±0.38 / 14
qSLW-16c-2 / J, 16 / sat_224-sat_394 / 107.1 / 0.013±0.007 / -0.051±0.010 / 4.15±1.35 / 34
qSLW-17c / D2-2, 17 / satt672-satt413 / 1.3 / -0.032±0.003 / 0.014±0.007 / 3.52±0.80 / 18
qSLW-18c / G, 18 / satt309-satt688 / 12.9 / 0.045±0.005 / 0.016±0.007 / 6.52±1.26 / 98
Continued
Trait / Cytoplasmic effect / QTL / Chr / Marker innterval / Position (cM) / Additive×
Cytoplasm / Dominance
×
Cytoplasm / LOD / Ratio(%)
SLW / qSLW-19c-1 / L-1, 19 / satt652-satt284 / 31.6 / -0.032±0.009 / -0.015±0.014 / 3.81±1.22 / 76
qSLW-19c-2 / L-2, 19 / satt166-satt527 / 0.6 / 0.014±0.009 / 0.041±0.008 / 3.56±0.95 / 42
qSLW-X3c / X3 / satt260-satt382 / 5.3 / 0.029±0.007 / 0.015±0.009 / 3.43±0.97 / 26
SLT / -0.151±0.044 / qSLT-2c / D1b-2, 2 / satt266-satt282 / 34.8 / 0.033±0.009 / -0.096±0.009 / 3.82±0.70 / 36
qSLT-6c / C2-2, 6 / satt277-satt643 / 38.3 / -0.014±0.008 / 0.100±0.013 / 3.80±1.04 / 78
qSLT-16c-2 / J, 16 / satt132-satt414 / 12.5 / -0.069±0.009 / 0.000±0.016 / 3.42±0.91 / 42
SWT / -0.107±0.020 / qSWT-16c / J, 16 / sat_165-satt132 / 11.4 / -0.053±0.006 / -0.010±0.012 / 5.72±1.39 / 90
QTL-by-Cytoplasm interactions identified only by multi-QTL joint analysis
SL / -0.075±0.013 / qSL-1c / D1a-2, 1 / satt077 / 59.8 / -0.043±0.006 / 0.008±0.007 / 3.13±0.61 / 10
qSL-2c-1 / D1b-1, 2 / satt157-sat_254 / 34.1 / 0.001±0.009 / 0.052±0.004 / 3.09±0.45 / 38
qSL-3c / N-1, 3 / satt631-satt683 / 10.4 / -0.015±0.007 / 0.051±0.007 / 3.32±0.70 / 24
qSL-7c / M, 7 / satt626 / 69.2 / -0.039±0.005 / -0.017±0.009 / 3.49±0.78 / 10
qSL-16c-1 / J, 16 / satt244-satt431 / 53.2 / -0.013±0.002 / 0.062±0.011 / 4.50±1.54 / 14
qSL-16c-2 / J, 16 / satt431-sat_224 / 72.6 / -0.013±0.008 / 0.063±0.007 / 4.67±1.19 / 58
SW / -0.063±0.015 / qSW-3c-1 / N-1, 3 / satt631-satt683 / 6.9 / -0.002±0.005 / 0.040±0.002 / 3.18±0.35 / 16
qSW-5c / A1, 5 / sat_344-satt449 / 29.8 / -0.029±0.003 / -0.013±0.010 / 3.92±0.73 / 12
qSW-13c / F, 13 / satt649-satt269 / 2.2 / 0.005±0.005 / 0.039±0.005 / 3.09±0.83 / 40
qSW-16c-1 / J, 16 / satt431-sat_224 / 68.8 / 0.014±0.027 / 0.035±0.023 / 4.43±1.30 / 50
qSW-16c-2 / J, 16 / sat_224-sat_394 / 79.0 / -0.014±0.018 / 0.048±0.009 / 4.19±1.49 / 26
qSW-17c-1 / D2-1, 17 / satt669-sat_292 / 6.1 / 0.009±0.006 / 0.038±0.002 / 3.17±0.41 / 20
qSW-17c-2 / D2-2, 17 / satt672-satt413 / 1.9 / -0.006±0.002 / -0.041±0.002 / 3.19±0.35 / 10
ST / -0.068±0.018 / qST-2c / D1b-2, 2 / satt266-satt282 / 3.5 / 0.028±0.005 / -0.018±0.009 / 3.72±1.05 / 32
Continued
Trait / Cytoplasmic effect / QTL / Chr / Marker innterval / Position (cM) / Additive×
Cytoplasm / Dominance
×
Cytoplasm / LOD / Ratio(%)
ST / qST-3c-1 / N-1, 3 / satt631-satt683 / 4.2 / -0.001±0.007 / 0.041±0.004 / 3.33±0.61 / 28
qST-10c-1 / O-1, 10 / satt094 / 42.8 / 0.018±0.005 / -0.036±0.005 / 3.83±0.75 / 58
qST-13c / F, 13 / satt649-satt269 / 4.5 / -0.004±0.005 / 0.045±0.005 / 3.98±0.91 / 56
qST-16c / J, 16 / sat_165-satt132 / 1.4 / 0.024±0.005 / 0.026±0.008 / 4.24±1.02 / 58
qST-17c-1 / D2-1, 17 / satt669-sat_292 / 17.9 / -0.002±0.004 / 0.041±0.004 / 3.32±0.63 / 46
qST-17c-2 / D2-2, 17 / satt413-satt256 / 21.3 / -0.005±0.006 / -0.041±0.005 / 3.49±0.80 / 26
SLW / qSLW-1c-2 / D1a-3, 1 / sat_160-satt147 / 22.5 / 0.007±0.008 / -0.042±0.002 / 3.15±0.44 / 10
qSLW-3c-1 / N-1, 3 / satt683-sat_280 / 21.3 / -0.035±0.008 / 0.014±0.009 / 3.83±1.32 / 44
qSLW-3c-2 / N-2, 3 / satt255-satt237 / 1.3 / 0.037±0.005 / 0.015±0.009 / 4.28±1.09 / 66
qSLW-6c-2 / C2-2, 6 / satt277-satt643 / 34.8 / 0.005±0.003 / 0.057±0.022 / 4.31±2.08 / 10
qSLW-6c-3 / C2-2, 6 / satt643-sataga001 / 40.1 / 0.007±0.004 / 0.050±0.007 / 3.93±1.18 / 56
qSLW-7c / M, 7 / satt626 / 69.2 / -0.034±0.004 / 0.006±0.009 / 3.14±0.67 / 30
qSLW-8c-1 / A2, 8 / satt089-satt233 / 11.5 / 0.036±0.005 / -0.007±0.010 / 4.29±1.06 / 52
qSLW-8c-2 / A2, 8 / satt233-satt329 / 29.6 / 0.035±0.006 / -0.012±0.018 / 3.49±0.68 / 14
qSLW-9c / K, 9 / satt441 / 24.4 / 0.018±0.005 / -0.039±0.012 / 3.54±0.85 / 14
qSLW-16c-1 / J, 16 / satt414-satt215 / 22.4 / -0.035±0.006 / 0.015±0.012 / 3.67±0.77 / 72
qSLW-20c / I-1, 20 / satt419-satt354 / 21.3 / -0.016±0.013 / 0.040±0.012 / 3.66±0.52 / 10
SLT / -0.151±0.044 / qSLT-1c-1 / D1a-1, 1 / satt580-sat_110 / 1.9 / 0.000±0.020 / 0.094±0.010 / 3.38±0.68 / 30
qSLT-1c-2 / D1a-2, 1 / sat_343-AW781285 / 22.4 / 0.070±0.006 / 0.003±0.021 / 3.02±0.55 / 10
qSLT-1c-3 / D1a-2, 1 / satt077 / 59.8 / -0.081±0.015 / -0.009±0.014 / 4.22±1.19 / 66
qSLT-3c-1 / N-1, 3 / satt683-sat_280 / 19.8 / -0.070±0.009 / 0.003±0.012 / 3.65±0.95 / 10
qSLT-3c-2 / N-2, 3 / satt255-satt237 / 4.2 / 0.068±0.006 / 0.006±0.022 / 3.16±0.40 / 12
Continued
Trait / Cytoplasmic effect / QTL / Chr / Marker innterval / Position (cM) / Additive×
Cytoplasm / Dominance
×
Cytoplasm / LOD / Ratio(%)
SLT / qSLT-7c / M, 7 / satt150-sat_258 / 3.0 / 0.062±0.009 / 0.012±0.035 / 3.20±0.43 / 16
qSLT-9c-1 / K, 9 / satt417-satt441 / 17.6 / 0.069±0.010 / -0.005±0.022 / 3.62±0.85 / 14
qSLT-9c-2 / K, 9 / satt441-satt138 / 25.1 / 0.063±0.006 / -0.028±0.015 / 3.33±0.47 / 26
qSLT-15c / E, 15 / satt263 / 11.1 / -0.064±0.009 / 0.033±0.007 / 3.04±0.31 / 12
qSLT-16c-1 / J, 16 / sat_165-satt132 / 8.0 / -0.071±0.011 / -0.004±0.012 / 3.85±1.14 / 14
qSLT-16c-2 / J, 16 / satt431-sat_224 / 66.8 / -0.053±0.014 / 0.067±0.011 / 3.33±0.80 / 12
qSLT-17c / D2-2, 17 / satt672 / 0 / -0.063±0.011 / 0.046±0.015 / 3.63±1.07 / 18
qSLT-18c / G, 18 / satt309-satt688 / 5.6 / 0.062±0.004 / -0.023±0.014 / 2.85±0.20 / 16
qSLT-19c / L-2, 19 / satt166-satt527 / 1.7 / 0.016±0.015 / 0.095±0.011 / 3.72±0.76 / 28
qSLT-20c / I-2, 20 / sat_418-sat_419 / 4.0 / -0.042±0.014 / -0.075±0.023 / 3.66±0.87 / 20
SWT / -0.107±0.020 / qSWT-1c-1 / D1a-1, 1 / satt580-sat_110 / 3.9 / 0.000±0.007 / 0.060±0.008 / 3.90±1.08 / 24
qSWT-1c-2 / D1a-2, 1 / sat_343-AW781285 / 27.3 / 0.034±0.012 / -0.029±0.016 / 3.40±0.64 / 22
qSWT-2c-1 / D1b-1, 2 / satt157-sat_254 / 14.4 / -0.012±0.001 / 0.055±0.003 / 3.56±0.45 / 10
qSWT-2c-2 / D1b-3, 2 / satt274-satt459 / 0.9 / -0.001±0.005 / 0.054±0.003 / 2.98±0.36 / 34
qSWT-3c / N-2, 3 / satt339-satt022 / 43.6 / 0.009±0.005 / -0.053±0.005 / 3.14±0.41 / 14
qSWT-6c-1 / C2-2, 6 / sat_402-satt277 / 6.5 / -0.009±0.015 / 0.059±0.008 / 4.20±1.19 / 10
qSWT-6c-2 / C2-2, 6 / satt277-satt643 / 34.8 / -0.013±0.009 / 0.063±0.013 / 4.35±1.11 / 28
qSWT-6c-3 / C2-2, 6 / satt643-sataga001 / 60.4 / -0.009±0.006 / -0.059±0.008 / 3.84±0.90 / 48
qSWT-7c / M, 7 / satt150-sat_258 / 2.7 / 0.039±0.003 / 0.007±0.013 / 3.47±0.65 / 42
qSWT-9c-1 / K, 9 / satt417-satt441 / 19.4 / 0.043±0.005 / 0.014±0.013 / 4.06±0.84 / 64
qSWT-9c-2 / K, 9 / satt441-satt138 / 30.1 / 0.045±0.005 / 0.017±0.008 / 4.58±1.02 / 18
qSWT-10c / O-1, 10 / satt094 / 42.8 / -0.009±0.011 / 0.055±0.006 / 3.43±0.86 / 40
Continued
Trait / Cytoplasmic effect / QTL / Chr / Marker innterval / Position (cM) / Additive×
Cytoplasm / Dominance
×
Cytoplasm / LOD / Ratio(%)
SWT / qSWT-13c-1 / F, 13 / satt348-AW186493 / 42.9 / 0.037±0.003 / 0.004±0.004 / 3.05±0.45 / 18
qSWT-13c-2 / F, 13 / BE806387-satt659 / 56.6 / 0.030±0.014 / 0.027±0.023 / 3.22±0.59 / 10
qSWT-15c-1 / E, 15 / satt263-satt685 / 25.7 / -0.023±0.017 / 0.050±0.023 / 4.25±0.92 / 30
qSWT-15c-2 / E, 15 / satt685-sat_381 / 37.3 / -0.002±0.012 / 0.058±0.006 / 3.70±0.79 / 60
qSWT-17c / D2-2, 17 / satt413-satt256 / 21.4 / -0.004±0.008 / 0.055±0.003 / 3.36±0.53 / 22
qSWT-20c / I-2, 20 / sat_418-sat_419 / 2.6 / -0.001±0.007 / -0.059±0.007 / 3.81±1.03 / 30
Supplemental Table A3 QTL-by-environment interactions detected by the multi-QTL joint analysis
Trait / QTL / Chr / Marker interval / Position(cM) / A×E1 / D×E1 / A×E2 / D×E2 / A×E3 / D×E3 / LOD / Ratio (100%)
Common QTL-by-environment interactions identified by multi-QTL joint analysis and composite interval mapping
SW / qSW-6e / C2-2, 6 / satt643-staga001 / 52.4 / 0.040±0.004 / 0.006±0.010 / -0.014±0.006 / -0.008±0.010 / -0.026±0.004 / 0.001±0.012 / 3.54±0.67 / 48
qSW-10e / O-2, 10 / satt592-sat_274 / 46.1 / 0.014±0.006 / 0.034±0.014 / -0.003±0.003 / 0.006±0.018 / -0.011±0.004 / -0.040±0.004 / 2.51±0.24 / 10
ST / qST-6e / C2-1, 6 / satt640-satt422 / 23.3 / 0.026±0.006 / -0.006±0.004 / 0.007±0.005 / -0.027±0.006 / -0.032±0.004 / 0.033±0.008 / 3.63±1.18 / 22
SWT / qSWT-6e / C2-1, 6 / satt422 / 25.5 / -0.042±0.005 / 0.003±0.011 / 0.000±0.004 / 0.016±0.007 / 0.041±0.004 / -0.019±0.009 / 2.93±0.41 / 26
QTL-by-environment interactions identified only by multi-QTL joint analysis
SL / qSL-6e / C2-2, 6 / satt643-staga001 / 43.6 / 0.054±0.007 / 0.011±0.014 / -0.018±0.006 / -0.018±0.013 / -0.036±0.007 / 0.008±0.013 / 3.91±1.03 / 76
qSL-9e / K, 9 / satt138-sat_281 / 42.7 / 0.047±0.005 / 0.012±0.011 / -0.011±0.004 / -0.004±0.011 / -0.035±0.005 / -0.008±0.007 / 3.13±0.53 / 30
ST / qST-2e / D1b-1, 2 / satt157-sat_254 / 14.7 / 0.036±0.004 / -0.002±0.014 / -0.011±0.010 / 0.004±0.008 / -0.024±0.007 / -0.001±0.012 / 3.06±0.60 / 12
SWT / qSWT-4e / C1, 4 / AW277661-satt294 / 1.0 / 0.039±0.006 / 0.023±0.010 / 0.004±0.006 / -0.005±0.007 / -0.043±0.003 / -0.018±0.009 / 2.97±0.33 / 16
A×E1: Additive-by-environment 1. D×E1: Dominant-by-environment 1.
A×E2: Additive-by-environment 2. D×E2: Dominant-by-environment 2.
A×E3: Additive-by-environment 3. D×E3: Dominant-by-environment 3.
Supplemental Table A4Environmental effect detected by multi-QTL joint analysis
Trait / Effect(Environment 1) / Effect(Environment 2) / Effect(Environment 3)SL / 0.457±0.027 / -0.302±0.015 / -0.155±0.023
SW / 0.289±0.021 / -0.144±0.013 / -0.145±0.019
ST / 0.1534±0.016 / -0.155±0.012 / 0.002±0.019
SLW / 0.181±0.020 / -0.220±0.012 / 0.038±0.025
SLT / 0.456±0.025 / -0.174±0.029 / -0.281±0.032
SWT / 0.195±0.023 / 0.076±0.009 / -0.271±0.022