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Table 2 Major QTL in the MAGIC population identified in both MLM-based GWAS and QTL analysis optimized for complex populations. QTL are listed that were significant in both analyses and show clear peaks in GWAS. A complete list of significant marker trait associations is available for GWAS (Additional file 10) and QTL mapping (Additional file 11)

From: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

QTL name

Trial

GWAS

QTL Mapping

Most significant markera

p value

MAF

Effectb

Pos. (cM)

Nearest marker

LOD

PVE (%)c

DF1.1

2013

Pv2.1_01_4147947_C/G

5.46E-07

0.37 (G)

−0.46

32

Pv2.1_01_5474208_C/T

9.30

4.30

DPM1.1

2013

Pv2.1_01_763904_G/A

1.60E-06

0.27 (A)

0.43

36.5

Pv2.1_01_6773375_T/A

21.70

15.90

DF1.2

2013

Pv2.1_01_14672594_C/T

1.05E-35

0.34 (C)

1.63

38

Pv2.1_01_11238077_T/A

58.85

35.76

2014

Pv2.1_01_17627372_A/G

2.36E-12

0.35 (G)

−0.28

40

Pv2.1_01_14582969_G/C

34.42

16.50

DPM1.2

2013

Pv2.1_01_14672594_C/T

2.77E-09

0.34 (C)

0.82

38.5

Pv2.1_01_13085941_C/A

8.19

5.47

2014

Pv2.1_01_11567887_T/TA

2.13E-07

0.18 (T)

0.61

    

Yd1.1

2013

Pv2.1_01_11250640_A/G

3.11E-08

0.16 (A)

−52.81

38

Pv2.1_01_11238077_T/A

8.76

2.03

2014

Pv2.1_01_11221702_T/A

3.57E-07

0.21 (T)

−28.79

    

PHI2.1

2013

Pv2.1_02_47566148_G/A

2.61E-08

0.37 (G)

−1.08

71

Pv2.1_02_47643879_G/T

10.73

7.62

DF3.1

2013

Pv2.1_03_39652029_G/A

5.23E-07

0.14 (A)

0.62

50

Pv2.1_03_39061112_G/C

7.50

3.43

2014

    

50

Pv2.1_03_39061112_G/C

8.11

3.54

DPM3.1

2013

Pv2.1_03_39534987_C/A

2.08E-08

0.16 (C)

−0.75

48

Pv2.1_03_37341462_T/C

11.41

8.36

2014

    

51.5

Pv2.1_03_39819948_G/A

10.24

5.11

100SdW4.1

2014

Pv2.1_04_1328790_G/A

4.08E-08

0.27 (A)

0.51

3

Pv2.1_04_522512_A/T

8.36

4.74

SdFe6.1

2014

Pv2.1_06_5311627_C/T

2.77E-07

0.17 (C)

2.09

2

Pv2.1_06_8725963_G/A

7.33

4.06

SdFe6.2

2016

Pv2.1_06_22844368_T/G

3.36E-07

0.08 (G)

−2.67

35

Pv2.1_06_23945432_T/C

6.46

8.68

DPM8.1

2013

Pv2.1_08_1070342_C/T

2.54E-09

0.11 (T)

−1.45

5

Pv2.1_08_1091562_T/G

7.92

5.56

2014

Pv2.1_08_706882_A/G

3.58E-11

0.13 (G)

−1.77

4

Pv2.1_08_946243_C/T

18.15

9.09

SdZn8.1

2014

Pv2.1_08_60922896_C/G

4.39E-07

0.06 (C)

0.85

83

Pv2.1_08_60982396_C/G

6.81

2.65

  1. aMarker ID contains the physical position of the polymorphism in the reference version 2.1 and the genotype of the reference / alternative allele
  2. bEffect of alternative allele
  3. cPVE = Phenotypic variation explained
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