Table 3 LD block estimation for SNPs within 1 Mb regions of predicted genes associated with flowering and plant height traits.

From: Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss

Chr

Predicted gene

GWAS-SNPs

LD block estimation

SNP block

NASNPs

LD block

Block size (kb)

NSNPB

A02

KHZ1-KHZ2-AT5G06770

1,202,251–1,217,865

78

1,202,251–1,226,004

23.75

116

FLOR1-AT3G12145

1,202,251–1,217,865

78

1,202,251–1,226,004

23.75

116

FLC-AT5G10140

1,762,477

1

1,751,245–1,788,639

37.40

48

AP1-AT1G69120

34,755,893–34,758,537

5

34,557,898–34,783,055

225.16

366

AGL24-AT4G24540

34,934,199–34,934,540

6

34,934,048–34,942,039

7.99

44

CDF1-AT5G62430

36,472,064–36,472,185

6

36,461,389–36,486,270

24.88

23

36,486,270–36,487,130

5

36,461,389–36,486,270

24.88

23

36,486,488–36,495,138

8.65

27

FLM-AT1G77080

37,090,239–37,093,082

23

37,086,932–37,091,727

4.80

46

37,091,896–37,133,361

41.47

81

37,133,361–37,136,964

5

37,135,994–37,136,964

0.97

4

FLD-AT3G10390

19,913,046–19,923,910

8

19,887,999–19,956,139

68.14

51

AGL24-AT4G24540

33,169,034–33,177,336

4

33,168,278–33,179,337

11.06

19

A05

CKB4-AT2G44680

2,937,409–2,945,567

5

2,736,655–2,937,429

200.78

20

2,944,442–2,952,048

7.61

8

AGL6-AT2G45650

3,354,215

1

3,301,121–3,356,339

55.22

11

SOC1-AT2G45660

3,354,890–3,357,582

3

3,301,121–3,356,339

55.22

11

3,357,582–3,357,639

0.06

3

COP1-AT2G32950

7,544,327–7,546,996

24

7,437,216–7,445,302

8.09

14

7,451,045–7,480,422

29.38

19

GID1A-AT3G05120

30,987,755–30,990,279

3

30,987,755–30,990,279

2.53

3

A07

FKF1-AT1G68050

1,786,248

1

1,764,823–1,822,282

57.46

54

FT-AT1G65480

33,488,659

1

33,403,301–33,535,523

132.22

7

A08

ARP6-AT3G33520

52,619–52,842

10

12,259–146,533

134.28

156

FD-AT4G35900

18,952,302–18,955,620

10

18,952,302–18,952,343

0.04

2

18,952,388–18,952,521

0.13

2

18,954,147–18,954,150

0.01

2

18,954,994–18,966,049

11.06

17

A09

FVE-AT2G19520

10,079,474

1

10,075,137–10,091,939

16.80

51

GI-AT1G22770

39,780,608–39,780,959

3

39,761,855–39,825,243

63.39

97

A10

FRI-AT4G00650

6,054,217–6,054,243

2

6,016,556–6,054,243

37.69

63

B02

AP1-AT1G69120

59,351,856–59,353,415

8

59,351,856–59,352,264

0.41

7

59,352,392–59,353,135

0.74

6

59,353,276–59,353,285

0.01

3

GID1A-AT3G05120

62,297,219–62,297,220

2

62,280,062–62,302,328

22.27

119

AGL24-AT4G24540

64,496,077–64,496,528

3

64,487,988–64,555,102

67.12

77

64,497,529–64,499,514

3

64,487,988–64,555,102

67.12

77

AP2-AT4G36920

66,542,016–66,546,535

6

66,496,080–66,562,989

66.91

105

B03

FAF2-AT1G03170

115,277

1

115,081–254,900

139.82

80

CRY1-AT4G08920

338,948–346,586

15

289,286–343,540

54.26

72

JMJ14-AT4G20400

10,133,662–10,134,104

2

10,129,276–10,153,357

24.08

67

B04

FVE-AT2G19520

16,336,556–16,341,785

7

16,258,914–16,407,739

148.83

74

B05

ATJ3-AT3G44110

49,722,910

1

49,689,123–49,735,541

46.42

46

B06

FT-AT1G65480

6,716,803–6,718,200

5

6,716,803–6,736,028

19.23

39

MAF5-AT5G65080

8,515,215–8,524,113

6

8,481,230–8,519,496

38.27

19

8,524,113–8,650,692

126.58

135

B07

HAM1-AT5G64610

11,563,802–11,564,171

5

11,464,372–11,564,320

99.95

94

B08

CO-AT5G15840

9,748,710–9,748,737

2

9,743,391–9,767,625

24.24

43

GNC-AT5G56860

14,118,234

1

14,064,467–14,154,003

89.54

84

FRI-AT4G00650

16,066,635

1

16,065,157–16,070,876

5.72

18

  1. Chr chromosome, GWAS-SNPs significant SNPs identified in GWAS study, SNP block coordinates of identified significant SNPs in base pair, NASNPs number of associated SNPs, LD block estimated LD blocks for SNPs within 1 Mb region, block size (kb) distanced spanned by block in kb, NSNPB number of SNPs in LD block.
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