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Table 2 16 QTL hotspots associated with leaf chlorophyll-content traits detected in the ZH RIL population

From: QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map

QTL hotspota

QTL nameb

Chrc

Bin name

CIv1.1 (bp)d

Bin length (bp)

Position (cM)

LODe

ADDf

R2 (%)g

CIv2.0 (bp)h

qCT1Z-1

qBSP1e

1

Bin23

3,014,519-3,035,286

20,768

22.9

2.51

−1.08

5.81

3,037,245-3,038,559

qASP1f

1

Bin24

3,035,287-3,300,327

265,041

24.8

4.02

−1.06

9.76

3,060,271-3,302,133

qCT1Z-2

qASP1b-1

1

Bin46

11,517,849-26,055,466

14,537,618

50.6

6.84

1.47

16.55

11,591,808-24,499,599

qTSP1b

1

Bin46

11,517,849-26,055,466

14,537,618

50.6

5.13

1.66

11.97

11,591,808-24,499,599

qCT2Z-1

qASP2e

2

Bin28

6,826,912-6,946,505

119,594

33.6

2.60

−0.84

5.84

6,909,163-7,031,971

qBSP2d

2

Bin30

7,060,106-7,152,841

92,736

34.8

3.66

−1.07

8.79

7,145,546-7,228,940

qTSP2e

2

Bin30

7,060,106-7,152,841

92,736

34.8

4.23

−1.25

10.08

7,145,546-7,228,940

qBSP2f

2

Bin33

7,454,452-9,601,062

2,146,611

38.6

2.77

−1.00

6.93

7,539,451-9,689,680

qCT2Z-2

qChl_A/B2f

2

Bin54

15,046,557-15,213,830

167,274

59.1

3.10

0.13

7.54

15,251,037-15,422,632

qChl_B2f

2

Bin62

16,848,795-27,416,648

10,567,854

67.2

2.50

−0.16

5.10

17,128,244-26,385,905

qCT3Z

qMSP3e

3

Bin73

36,603,803-36,725,014

121,212

59.4

3.94

1.41

10.06

34,589,840-347,02,370

qASP3e

3

Bin75

37,109,279-37,138,700

29,422

61.7

3.07

0.92

6.85

35,106,012-35,113,620

qCT6Z-1

qASP6f

6

Bin34

5,908,302-5,959,466

51,165

37.1

2.54

−0.80

6.07

5,914,573-5,964,561

qASP6d

6

Bin42

6,959,298-7,246,025

286,728

44.2

3.92

−0.75

9.14

6,972,002-7,247,613

qCT6Z-2

qTSP6b

6

Bin89

15,950,387-16,194,517

244,131

109.8

3.10

0.93

7.45

16,011,413-16,229,680

qMSP6e-1

6

Bin92

16,664,681-16,817,080

152,400

112.4

3.66

1.82

8.86

16,709,212-16,859,338

qCT7Z

qMSP7a-1

7

Bin73

15,667,842-15,734,307

66,466

54.3

3.23

−1.18

7.21

15,769,608-15,813,498

qASP7a

7

Bin80

16,504,261-16,803,624

299,364

60.4

2.74

−0.84

6.07

16,597,814-16,889,324

qChl_B7e-1

7

Bin80

16,504,261-16,803,624

299,364

60.4

5.05

−0.39

12.75

16,597,814-16,889,324

qChl_A/B7d

7

Bin80

16,504,261-16,803,624

299,364

60.4

2.83

−0.18

8.69

16,597,814-16,889,324

qMSP7a-2

7

Bin80

16,504,261-16,803,624

299,364

60.4

2.58

−1.06

5.81

16,597,814-16,889,324

qCT8Z

qTSP8f-1

8

Bin7

2,225,026-2,271,343

46,318

12.6

3.10

1.30

7.64

2,238,240-2,275,653

qMSP8b

8

Bin10

2,712,995-2,737,327

24,333

15.4

2.80

0.98

7.05

2,719,028-2,741,745

qCT11Z

qChl_A/B11e-2

11

Bin77

16,152,967-16,449,587

296,621

61.4

2.91

0.14

7.16

26,145,820-26,431,037

qBSP11e

11

Bin78

16,449,588-16,610,503

160,916

62.6

3.07

−1.18

7.10

26,412,450-26,574,724

qCT13Z

qASP13b-1

13

Bin133

39,361,093-39,386,817

25,725

134.5

2.74

−0.67

6.30

40,532,836-40,567,479

qASP13b-2

13

Bin143

40,173,283-40,428,061

254,779

143.3

2.71

−0.66

6.25

41,618,514-41,874,899

qCT15Z-1

qASP15a

15

Bin94

16,683,420-17,383,420

700,001

100.2

5.27

−1.19

11.94

16,695,707-17,350,040

qChl_B15f-1

15

Bin94

16,683,420-17,383,420

700,001

100.2

2.55

−0.17

5.71

16,695,707-17,350,040

qMSP15a-1

15

Bin94

16,683,420-17,383,420

700,001

100.2

5.94

−1.63

13.86

16,695,707-17,350,040

qCT15Z-2

qChl_A15f

15

Bin128

48,582,583-48,741,529

158,947

124.4

3.68

0.23

8.99

49,382,502-49,534,743

qChl_B15f-2

15

Bin128

48,582,583-48,741,529

158,947

124.4

3.97

0.20

8.94

49,382,502-49,534,743

qCT16Z

qTSP16e

16

Bin17

5,525,628-5,588,607

62,980

34.4

3.29

1.08

7.69

5,551,673-5,607,211

qASP16e

16

Bin18

5,588,608-5,809,086

220,479

34.9

3.30

0.96

7.61

5,618,869-5,828,808

qCT18Z

qMSP18f-1

18

Bin32

3,157,973-3,350,322

192,350

20.4

3.41

1.24

7.68

3,182,661-3,349,093

qMSP18f-2

18

Bin40

4,116,314-4,142,492

26,179

25.6

3.30

1.21

7.44

4,139,387-4,161,508

qCT19Z

qTSP19f

19

Bin77

40,662,371-40,701,058

38,688

70.1

3.28

1.33

8.17

40,859,609-40,891,331

qMSP19d

19

Bin78

40,701,059-40,809,377

108,319

71.4

2.66

−0.85

6.57

40,896,924-41,007,822

  1. aThe name of the QTL hotspot is a composite of multiple chlorophyll-content traits (CT); Zhonghuang 24 × Huaxia 3 RIL population (Z)
  2. bThe name of the QTL is a composite of the chlorophyll-content traits: TSP: Top leaves SPAD value, MSP: Mid leaves SPAD value, BSP: Bottom leaves SPAD value, ASP: Average SPAD value, Chl_A: Chlorophyll a content, Chl_B: Chlorophyll b content, Chl_A/B: Chlorophyll a/b ratio; a: the R1 growth stage in the spring of 2017 at Zengcheng; b: the R4 growth stage in the spring of 2017 at Zengcheng; c: the R6 growth stage in the spring of 2017 at Zengcheng; d: the R1 growth stage in the summer of 2017 at Zengcheng; e: the R4 growth stage in the summer of 2017 at Zengcheng; f: the R6 growth stage in the summer of 2017 at Zengcheng
  3. cChr refers to the chromosome
  4. dThe physical position corresponding to the 95% confidence interval for the detected QTL based on Glyma.Wm82. a1. v1. 1 gene model
  5. eLOD indicates the logarithm of the odds score
  6. fPositive and negative values indicated additive effect by the alleles of ‘Zhonghuang 24’ and ‘Huaxia 3’, respectively
  7. gR2 indicates the phenotypic variance explained by individual QTL
  8. hThe most proximal Glyma.Wm82. a2. v1 gene model physical intervals of the detected QTLs were transformed by focusing on the positions of the interval nearest 3′ and 5′ ending genes