Table S3. Result of multiple interval mapping (MIM) analysis for seven rice quality traits showing significant QTLs using Model 1 of QTL cartographer
Trait 1 (grain length)
Here is a summary of the QTL
Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A 1.9812 1 16 0.001 00100 0.08127200
2 A 1.6911 7 8 0.001 00100 0.09580000
3 A 1.1399 2 1 0.001 00100 0.19762100
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 35.89
Genetic Variance: 7.734
Residual Variance: 28.16
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QTL(s) Type 1 2 3
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1 A 3.878 -0.1898 0.05648
2 A 2.844 -0.1434
3 A 1.288
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Sum 3.812 2.677 1.245
Total 7.734
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Here are the R2 values
Genetic: 0.2155
Residual: 0.7845
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QTL(s) Type 1 2 3
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1 A 0.1081 -0.0053 0.0016
2 A 0.0792 -0.0040
3 A 0.0359
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Sum 0.1062 0.0746 0.0347
Total 0.2155
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 1 16 210.2001 2.83 1.9812 10.6
2 A 7 8 57.0001 2.00 1.6911 7.5
3 A 2 1 0.1001 0.97 1.1399 3.5
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Trait 2(grain breadth)
Here is a summary of the QTL
#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A -0.6660 7 8 0.00100100 0.09580000
2 A -0.4028 7 10 0.00100100 0.31517500
3 A -0.2919 10 6 0.13645300 0.01199700
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 3.113
Genetic Variance: 1.015
Residual Variance: 2.098
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QTL(s) Type 1 2 3
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1 A 0.442 0.2774 0.0322
2 A 0.1561 0.02258
3 A 0.08454
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Sum 0.5969 0.3061 0.1119
Total 1.015
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Here are the R2 values
Genetic: 0.3261
Residual: 0.6739
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QTL(s) Type 1 2 3
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1 A 0.1420 0.0891 0.0103
2 A 0.0502 0.0073
3 A 0.0272
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Sum 0.1918 0.0984 0.0360
Total 0.3261
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 7 8 57.0001 3.00 -0.6660 19.2
2 A 7 10 78.1001 1.13 -0.4028 9.8
3 A 10 6 255.2000 0.73 -0.2919 3.6
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Trait 3 (length/breadth ratio)
Here is a summary of the QTL
#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A 1.8549 7 8 0.00100100 0.09580000
2 A 1.0706 7 10 0.00100100 0.31517500
3 A 0.8801 1 16 0.00100100 0.08127200
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 22.62
Genetic Variance: 7.307
Residual Variance: 15.31
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QTL(s) Type 1 2 3
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1 A 3.426 2.074 -0.0866
2 A 1.102 0.02717
3 A 0.765
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Sum 4.419 2.153 0.7353
Total 7.307
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Here are the R2 values
Genetic: 0.3230
Residual: 0.6770
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QTL(s) Type 1 2 3
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1 A 0.1514 0.0917 -0.0038
2 A 0.0487 0.0012
3 A 0.0338
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Sum 0.1954 0.0952 0.0325
Total 0.3230
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 7 8 57.0001 3.06 1.8549 19.5
2 A 7 10 78.1001 1.07 1.0706 9.5
3 A 1 16 210.2001 1.05 0.8801 3.3
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Trait 5 (Amylose content)
Here is a summary of the QTL
#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A -2.5681 6 1 0.00100100 0.09964700
2 A -0.6458 9 3 0.00100100 0.17786900
3 A 0.7404 10 5 0.05971500 0.02098600
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 18.34
Genetic Variance: 7.762
Residual Variance: 10.58
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QTL(s) Type 1 2 3
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1 A 6.466 0.1126 0.2634
2 A 0.416 -0.02571
3 A 0.5294
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Sum 6.654 0.4594 0.6482
Total 7.762
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Here are the R2 values
Genetic: 0.4232
Residual: 0.5768
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QTL(s) Type 1 2 3
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1 A 0.3526 0.0061 0.0144
2 A 0.0227 -0.0014
3 A 0.0289
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Sum 0.3628 0.0251 0.0353
Total 0.4232
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 6 1 0.1001 10.38 -2.5681 36.3
2 A 9 3 55.6001 0.85 -0.6458 2.5
3 A 10 5 239.1001 0.81 0.7404 3.5
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Trait 6 (Alkali spreading value)
Here is a summary of the QTL
#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A 2.5645 6 1 0.01000000 0.09097400
2 A -2.6184 7 10 0.13645400 0.21666800
3 A -1.8635 8 6 0.02996500 0.10443900
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 92.53
Genetic Variance: 15.85
Residual Variance: 76.67
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QTL(s) Type 1 2 3
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1 A 6.493 -0.6909 -0.2877
2 A 6.785 0.1489
3 A 3.403
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Sum 6.004 6.514 3.333
Total 15.85
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Here are the R2 values
Genetic: 0.1713
Residual: 0.8287
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QTL(s) Type 1 2 3
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1 A 0.0702 -0.0075 -0.0031
2 A 0.0733 0.0016
3 A 0.0368
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Sum 0.0649 0.0704 0.0360
Total 0.1713
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 6 1 1.0001 1.41 2.5645 6.5
2 A 7 10 92.0002 0.95 -2.6184 7.0
3 A 8 6 65.9001 0.58 -1.8635 3.6
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Trait 7 (Aroma)
Here is a summary of the QTL
#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>
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Position (Main effect) Epistatic effect Position
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QTL Effect Value C M c1 c2 (QTL) (C) (M) (c1) (c2)
-s
1 A 4.6388 8 8 0.01999000 0.21094900
2 A 3.4369 3 3 0.14565700 0.17260600
3 A 1.9157 4 5 0.00100100 0.10156600
-e
This is the Variance-Covariance Matrix.
Phenotypic Variance: 87.25
Genetic Variance: 39.48
Residual Variance: 47.77
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QTL(s) Type 1 2 3
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1 A 21.4 -0.48 2.839
2 A 11.81 0.2373
3 A 3.668
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Sum 22.58 11.69 5.207
Total 39.48
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Here are the R2 values
Genetic: 0.4525
Residual: 0.5475
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QTL(s) Type 1 2 3
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1 A 0.2453 -0.0055 0.0325
2 A 0.1354 0.0027
3 A 0.0420
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Sum 0.2588 0.1340 0.0597
Total 0.4525
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Estimates of QTL positions, effects and interactions
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QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)
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1 A 8 8 85.8001 5.76 4.6388 25.9
2 A 3 3 50.5001 1.62 3.4369 13.4
3 A 4 5 50.5001 1.28 1.9157 6.0
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