Trait 1 (Grain Length)

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>

------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 3.878 -0.1898 0.05648

2 A 2.844 -0.1434

3 A 1.288

------

Sum 3.812 2.677 1.245

Total 7.734

***************************************************

Here are the R2 values

Genetic: 0.2155

Residual: 0.7845

------

QTL(s) Type 1 2 3

------

1 A 0.1081 -0.0053 0.0016

2 A 0.0792 -0.0040

3 A 0.0359

------

Sum 0.1062 0.0746 0.0347

Total 0.2155

***************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------

Trait 2(grain breadth)

Here is a summary of the QTL

#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>

------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 0.442 0.2774 0.0322

2 A 0.1561 0.02258

3 A 0.08454

------

Sum 0.5969 0.3061 0.1119

Total 1.015

***************************************************

Here are the R2 values

Genetic: 0.3261

Residual: 0.6739

------

QTL(s) Type 1 2 3

------

1 A 0.1420 0.0891 0.0103

2 A 0.0502 0.0073

3 A 0.0272

------

Sum 0.1918 0.0984 0.0360

Total 0.3261

***************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------

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>

------;;;;;;;;;;;------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 3.426 2.074 -0.0866

2 A 1.102 0.02717

3 A 0.765

------

Sum 4.419 2.153 0.7353

Total 7.307

***************************************************

Here are the R2 values

Genetic: 0.3230

Residual: 0.6770

------

QTL(s) Type 1 2 3

------

1 A 0.1514 0.0917 -0.0038

2 A 0.0487 0.0012

3 A 0.0338

------

Sum 0.1954 0.0952 0.0325

Total 0.3230

*************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------

Trait 5 (Amylose content)

Here is a summary of the QTL

#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>

------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 6.466 0.1126 0.2634

2 A 0.416 -0.02571

3 A 0.5294

------

Sum 6.654 0.4594 0.6482

Total 7.762

*************************************************

Here are the R2 values

Genetic: 0.4232

Residual: 0.5768

------

QTL(s) Type 1 2 3

------

1 A 0.3526 0.0061 0.0144

2 A 0.0227 -0.0014

3 A 0.0289

------

Sum 0.3628 0.0251 0.0353

Total 0.4232

***************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------

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>

------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 6.493 -0.6909 -0.2877

2 A 6.785 0.1489

3 A 3.403

------

Sum 6.004 6.514 3.333

Total 15.85

**************************************************

Here are the R2 values

Genetic: 0.1713

Residual: 0.8287

------

QTL(s) Type 1 2 3

------

1 A 0.0702 -0.0075 -0.0031

2 A 0.0733 0.0016

3 A 0.0368

------

Sum 0.0649 0.0704 0.0360

Total 0.1713

***************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------

Trait 7 (Aroma)

Here is a summary of the QTL

#Note: c1 <c2> - Recombinant frequency between QTL and adjacent marker of left <right>

------

Position (Main effect) Epistatic effect Position

------

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

------

QTL(s) Type 1 2 3

------

1 A 21.4 -0.48 2.839

2 A 11.81 0.2373

3 A 3.668

------

Sum 22.58 11.69 5.207

Total 39.48

***************************************************

Here are the R2 values

Genetic: 0.4525

Residual: 0.5475

------

QTL(s) Type 1 2 3

------

1 A 0.2453 -0.0055 0.0325

2 A 0.1354 0.0027

3 A 0.0420

------

Sum 0.2588 0.1340 0.0597

Total 0.4525

***************************************************

Estimates of QTL positions, effects and interactions

------

QTL(pair) Type Chrom. Marker Position LOD Effect Effect (%)

------

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

------