Table 2 Genome wide association studies to predict candidate genes associated with flowering, maturity and plant height.

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

Pathway

Predicted gene

Associated traits

N-level

Chr

SNP position

NSNPs

Dis. (kb)

R2 (%)

Gene function

Light perception

CDF1-AT5G62430

GDD, PTU

N75, N100

A02

36,472,064–36,472,185

6

14.33

14.31

Regulates light perception and signalling

PH

N75

36,486,270–36,487,130

5

0.03

19.18

FD-AT4G35900

DFL

N100

A08

18,952,302–18,955,620

10

38.68

10.69

Regulates light perception and signalling and flowering transition

CO-AT5G15840

PH

N125

B08

9,748,710–9,748,737

2

43.93

13.95

Regulates light perception, signalling and flowering time

CRY1-AT4G08920

DFI, DFL

N75, N100, N125

B03

338,948–346,586

15

2.01

20.23

Regulates light perception and signalling

Circadian pathway

CKB4-AT2G44680

DFL

N75

A05

2,937,409–2,945,567

5

16.89

9.79

Regulation of circadian clock

GI-AT1G22770

DFL

N75

A09

39,780,608–39,780,959

3

56.1

11.79

Regulation of circadian rhythm and photoperiodic flowering

Floral meristem identity genes

AGL24-AT4G24540

GDD

N100

A02

34,934,199–34,934,540

6

26.26

12.76

Regulates Flower development and meristem identity and mediates floral transition in response to vernalization

GDD, HTU, PTU

N125

A03

33,169,034–33,177,336

4

12.43

3.65

DCF, MRT

N125

B02

59,088,464

1

24.51

10.57

PH

N75

64,496,077–64,496,528

3

3.5

19.27

DFI, DFL

N100

64,497,529–64,499,514

3

0.21

13.19

AP1-AT1G69120

PTU

N75

A02

34,755,893–34,758,537

5

0.04

11.48

Regulates flower development and meristem identity

HTU

N100

B02

59,351,856–59,353,415

8

25.11

12.22

AP2-AT4G36920

DFL

N75

66,542,016–66,546,535

6

28.89

9.8

Promotes early floral meristem identity

JMJ14-AT4G20400

DFL

N100

B03

10,133,662–10,134,104

2

6.84

12.33

Inhibit the floral transition

Flowering regulation

KHZ1-KHZ2-AT5G06770

GDD, HTU, PTU

N125

A02

1,202,251–1,217,865

78

2.56

3.27

Regulates floral transition redundantly

FLOR1-AT3G12145

GDD, HTU, PTU

N125

1,202,251–1,217,865

78

2.96

3.27

FLC-AT5G10140

PH

N100

1,762,477

1

20.82

10.61

Represses floral transition

FLM-AT1G77080

DFL

N125

37,090,239–37,093,082

23

38.02

15.59

Prevents premature flowering

GDD, HTU, PTU

N100

37,133,361–37,136,964

5

0.82

14.10

FLD-AT3G10390

GDD,HTU

N75

A03

19,913,046–19,923,910

8

0.94

3.12

Up-regulation of FLC expression

AGL6-AT2G45650

DCF, MRT

N75

A05

3,354,215

1

13.69

20.63

Regulates flowering time

SOC1-AT2G45660

DCF, MRT

N75

3,354,890–3,357,582

3

17.80

18.57

COP1-AT2G32950

DCF, MRT

N75

7,544,327–7,546,996

24

1.91

18.94

Repressor of photomorphogenesis

FKF1-AT1G68050

DFI

N100

A07

1,786,248

1

15.08

13.82

Regulates transition to flowering

FT-AT1G65480

MRT

33,488,659

1

21.21

12.46

Promotes the transition from vegetative growth to flowering

DFL

B06

6,716,803–6,718,200

5

33.81

12.23

ARP6-AT3G33520

DCF

N75, N100

A08

52,619–52,842

10

25.97

17.18

Regulates flowering and FLC gene

FVE-AT2G19520

PH

N125

A09

10,079,474

1

3.43

15.75

Regulates flowering

N100

B04

16,336,556–16,341,785

7

0.66

10.19

FRI-AT4G00650

MRT

N125

A10

6,054,217–6,054,243

2

39.16

15.52

DCF, PH

N75

B08

16,066,635

1

30.42

16.04

MAF5-AT5G65080

DCF

N125

B06

8,515,215–8,524,113

6

46.85

12.47

Prevents premature flowering

HAM1-AT5G64610

DCF, MRT

N75

B07

11,563,802–11,564,171

5

0.61

16.43

Essential for gametophyte development

Gibberellin pathway

GID1A-AT3G05120

DFI

N75

A05

30,987,755–30,990,279

3

0.42

16.51

Functions as soluble gibberellin receptor

DFL, DCF

N75, N125

B02

62,297,219–62,297,220

2

35.29

10.61

GA1-AT4G02780

DCF, MRT

N100

B02

46,682,290

1

43.96

13.04

Gibberellin biosynthesis

 

DFI

N100

B08

14,118,234

1

5.71

11.71

 

FAF2-AT1G03170

DFI

N125

B03

115,277

1

0.06

17.53

Regulates shoot meristem size

ATJ3-AT3G44110

DFL

N100

B05

49,722,910

1

45.77

11.8

Plant development

  1. Chr chromosome, NSNPs number of associated significant SNPs, Dis. (kb) distance of annotated gene from nearest significant associated SNPs with the trait, R2 phenotypic variation explained in percentage.
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