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Table 4 List of candidate genes identified through integration of GWAS, WGCNA and differential expression analysis

From: Integrating genome-wide association study with transcriptomic data to predict candidate genes influencing Brassica napus root and biomass-related traits under low phosphorus conditions

Darmor_ID

HP1-T1

HP1-T2

HP1CK-T1

HP1CK-T2

LP1-T1

LP1-T2

LP1CK-T1

LP1CK-T2

HP2-T1

HP2-T2

HP2CK-T1

HP2CK-T2

LP2-T1

LP2-T2

LP2CK-T1

LP2CK-T2

QTL cluster

Distance from lead SNP (Kb)

Description

Hub genes in the MEbrown (GWAS + WGCNA)

 BnaA04g23490D

29.04

16.93

36.05

70.89

17.85

13.13

25.81

72.68

27.42

15.17

23.84

80.26

33.70

10.92

28.13

76.21

RT-A04-1

− 249.41

Rhodanese-like domain-containing protein 7

 BnaA09g08440D

3.00

2.21

2.95

5.04

3.31

1.81

2.27

4.24

2.67

1.57

2.26

4.52

2.30

2.11

2.70

5.41

RT-A09-2

249.992

BTB/POZ domain-containing protein NPY2

 BnaC03g41900D

4.84

4.19

5.35

6.46

4.70

4.43

4.82

7.96

5.45

3.42

5.41

7.94

4.47

3.82

4.34

6.86

RT-C03-2

− 276.77

F-box/kelch-repeat protein At1g51550

 BnaC07g30970D

14.99

17.71

17.37

11.43

16.22

20.68

19.31

11.02

18.75

19.21

19.33

10.65

16.34

20.22

18.62

11.28

RT-C07-1

− 118.79

Exocyst complex component EXO70E2

 BnaC09g18800D

10.58

9.65

11.60

15.68

10.66

8.90

11.02

16.66

9.81

8.23

10.80

18.13

9.27

7.66

11.29

15.37

RT-C09-1

127.89

F-box protein SKIP31

Significant DEGs from GWAS + RNA-sequecing data

 BnaA04g23610D

21.06

19.97

6.63

2.69

14.23

14.47

5.15

1.78

15.37

17.43

8.03

2.09

8.24

15.31

6.31

1.64

RT-A04-1

− 292.05

Nodulin MtN21 /EamA-like transporter family protein

 BnaA09g04320D

0.32

0.11

1.80

4.13

0.64

0.29

1.94

4.61

0.62

0.24

1.50

6.33

0.73

0.11

1.40

5.81

RT-A09-1

248.43

ChaC-like family protein

 BnaA09g04350D

2.34

0.57

9.49

16.89

0.90

1.27

5.38

20.24

1.51

0.97

6.22

17.87

1.90

0.56

3.07

15.99

RT-A09-1

238.58

Mitochondrial substrate carrier family protein

 BnaA09g04930D

5.41

7.14

2.86

0.52

9.88

12.89

4.98

1.44

9.02

8.95

4.22

0.56

10.34

11.30

4.61

1.22

RT-A09-1

− 54.61

SALT OVERLY SENSITIVE 3 (SOS3)

 BnaA09g08940D

0.80

0.52

2.72

2.50

0.72

0.56

2.92

1.40

0.83

1.00

2.45

1.65

0.66

0.24

2.04

2.15

RT-A09-2

− 41.72

NAC domain containing protein 36 (NAC036)

 BnaA09g09290D

0.84

0.56

1.93

2.10

0.78

0.38

2.66

3.45

0.52

0.63

0.97

3.12

1.00

0.51

3.38

4.18

RT-A09-2

− 231.26

Winged-helix DNA-binding transcription factor family protein

 BnaC02g23620D

34.34

17.21

151.15

91.50

8.26

8.04

88.39

82.32

20.59

10.28

110.35

99.37

16.67

11.49

59.72

93.75

RT-C02-1

− 257.99

Plant defensin 1.2 (PDF1.2)

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Biotechnology for Biofuels and Bioproducts

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