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Table 3 Summary genome-wide association study (GWAS) of loci significantly associated with different leaf major wax components and their constituents in a spring Camelina sativa diversity panel (Please see the independent excel table)

From: Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport

SNP

Chr.

Position

Alleles

P.value

Bonferroni Corrected

MAF

FDR Adjusted P-values

Nearest Gene

Gene Annotation

Protein Function

Associated Traits

S1_10,108,457

1

10,108,457

A/G

5.64E-10

3.49E-06

0.5281690141

0.00000

LOC104786434

clavaminate synthase-like protein At3g21360

metal ion binding; oxidoreductase activity

WE48

    

3.17E-10

1.96E-06

 

0.00000

   

WE46

    

1.12E-06

6.93E-03

 

0.00346

   

WE44

    

2.74E-11

1.69E-07

 

0.00000

   

WE42

    

8.99E-10

5.57E-06

 

0.00000

   

WE_total

S1_14,592,616

1

14,592,616

G/A

2.24E-06

1.39E-02

0.1150234742

0.00106

LOC104707605

uncharacterized

NA

WE_total

    

6.92E-07

4.28E-03

 

0.00043

   

AG19

S3_25,592,310

3

25,592,310

T/C

1.07E-07

6.61E-04

0.0915492958

0.00008

LOC104778100

uncharacterized

NA

WE_total

    

3.89E-09

2.41E-05

 

0.00001

   

AG19

S5_17,084,259

5

17,084,259

A/C

3.46E-06

2.14E-02

0.9319248826

0.00513

LOC104789323

uncharacterized

NA

WE44

    

3.49E-09

2.16E-05

 

0.00001

   

WE42

    

5.48E-08

3.40E-04

 

0.00005

   

WE_total

    

3.75E-07

2.32E-03

 

0.00029

   

AG19

S5_23,163,110

5

23,163,110

A/G

1.08E-06

6.70E-03

0.9084507042

0.00112

LOC104789501

40S ribosomal protein S11–1-like

RNA binding

WE42

    

6.48E-07

4.01E-03

 

0.00036

   

WE_total

S5_23,163,133

5

23,163,133

A/C

1.08E-06

6.70E-03

0.9084507042

0.00112

LOC104789501

40S ribosomal protein S11–1-like

RNA binding

WE42

    

6.48E-07

4.01E-03

 

0.00036

   

WE_total

S5_29,786,454

5

29,786,454

T/C

3.25E-09

2.01E-05

0.0704225352

0.00000

LOC104789700

uncharacterized

NA

WE48

    

2.31E-08

1.43E-04

 

0.00003

   

WE46

    

1.32E-06

8.19E-03

 

0.00068

   

WE_total

S6_7,999,118

6

7,999,118

A/G

3.82E-08

2.37E-04

0.0046948357

0.00024

LOC104780231

brefeldin A-inhibited guanine nucleotide-exchange protein 5

vesicle trafficking, PAMP-triggered immunity (PTI), effector-triggered immunity (ETI), and salicylic acid (SA)-regulated immunity

ALK33

    

9.75E-07

6.04E-03

 

0.00604

   

ALK_total

S7_24,153,024

7

24,153,024

C/T

1.20E-09

7.43E-06

0.929577465

0.00000

LOC104704901

probable purine permease 14

NA

AG19

S7_4,441,246

7

4,441,246

T/C

4.65E-06

2.88E-02

0.1384976526

0.00221

LOC109125528

uncharacterized

NA

WE48

S7_4,787,171

7

4,787,171

A/G

7.15E-11

4.43E-07

0.9201877934

0.00000

LOC104700327

B-box zinc finger protein 25-like

negative regulator of seedling photomorphogenesis

WE48

    

2.58E-09

1.60E-05

 

0.00000

   

WE46

    

1.60E-10

9.91E-07

 

0.00000

   

WE_total

S7_9,579,071

7

9,579,071

G/T

4.26E-07

2.64E-03

0.117370892

0.00029

LOC104700816

uncharacterized

NA

AG19

S8_12,332,278

8

12,332,278

C/T

5.84E-07

3.62E-03

0.765258216

0.00090

LOC109126081

RNA-directed DNA polymerase homolog

RNA-directed 5′-3′ RNA polymerase activity; RNA-directed DNA polymerase activity

Mar25

S8_21,155,371

8

21,155,371

C/T

4.36E-09

2.70E-05

0.8004694836

0.00000

LOC104709776

glutathione S-transferase T3-like

conjunction of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles and detoxification against certain herbicides

WE48

    

5.08E-08

3.15E-04

 

0.00004

   

WE46

    

9.12E-07

5.64E-03

 

0.00112

   

WE42

    

3.98E-06

2.47E-02

 

0.00164

   

WE_total

S8_23,054,597

8

23,054,597

T/C

2.07E-06

1.28E-02

0.061032864

0.00107

LOC104709847

cytochrome P450 81D1-like (pseudo)

metal binding

AG19

S8_5,912,798

8

5,912,798

A/C

6.67E-06

4.13E-02

0.9084507042

0.00283

LOC104706385

uro-adherence factor A-like

cell wall anchored protein--erythrocyte binding activity

WE48

    

5.83E-06

3.61E-02

 

0.00226

   

WE_total

S9_7,943,388

9

7,943,388

A/G

3.68E-06

2.28E-02

0.9014084507

0.00190

LOC104710709

protein arginine methyltransferase NDUFAF7 homolog, mitochondrial

assembly or stability of mitochondrial NADH:ubiquinone oxidoreductase complex

WE48

S11_13,254,172

11

13,254,172

T/G

6.98E-06

4.32E-02

0.0633802817

0.00393

LOC109124846

vacuolar protein sorting-associated protein 25-like

delivery of transmembrane proteins into the lumen of the lysosome for degradation

WE46

S11_47,072,592

11

47,072,592

A/G

1.17E-06

7.27E-03

0.9014084507

0.00073

LOC104726883

peroxisomal membrane protein PEX14

peroxisome movement

WE48

    

3.33E-06

2.06E-02

 

0.01032

   

ALC32

    

3.68E-08

2.28E-04

 

0.00011

   

ALC34

    

2.61E-07

1.62E-03

 

0.00081

   

ALD30

S11_47,072,593

11

47,072,593

A/T

1.17E-06

7.27E-03

 

0.00073

   

WE48

S11_49,518,817

11

49,518,817

C/T

4.14E-06

2.57E-02

0.6267605634

0.00513

LOC104727408

GATA transcription factor 5-like

regulation of some light-responsive genes

WE44

S12_10,333,667

12

10,333,667

C/G

3.76E-10

2.33E-06

0.9460093897

0.00000

LOC104731181

glutamate--cysteine ligase, chloroplastic-like

resistance to fungal and bacterial pathogens-regulation of salicylic acid (SA) and phytoalexin (camalexin) production.

WE48

    

1.97E-10

1.22E-06

 

0.00000

   

WE46

    

1.68E-06

1.04E-02

 

0.00347

   

WE44

    

4.13E-11

2.56E-07

 

0.00000

   

WE_total

    

1.26E-06

7.80E-03

 

0.00071

   

AG19

S12_20,455,684

12

20,455,684

G/A

2.72E-07

1.68E-03

0.1408450704

0.00056

LOC104732333

uncharacterized

NA

Mar25

S12_9,157,483

12

9,157,483

G/T

2.39E-06

1.48E-02

0.8920187793

0.00106

LOC104731044

kinesin-like protein KIN-7I

somatic cell cytokinesis, cell-plate formation and its expansion

WE_total

S13_1,532,622

13

1,532,622

G/A

6.46E-06

4.00E-02

0.7699530516

0.00400

LOC104734437

probable lysine-specific demethylase ELF6

transcriptional gene regulation; repressor of the photoperiodic flowering pathway and of FT.

Mar25

S13_21,456,713

13

21,456,713

A/G

1.70E-06

1.05E-02

0.7769953052

0.00211

LOC104738457

uncharacterized

NA

Mar25

S13_5,037,723

13

5,037,723

C/A

6.43E-07

3.98E-03

0.0751173709

0.00112

LOC104735215

U-box domain-containing protein 52-like

protein ubiquitination

WE42

S15_11,699,414

15

11,699,414

C/T

2.51E-09

1.55E-05

0.896713615

0.00002

LOC104746477

uncharacterized

NA

Mar25

S15_25,879,428

15

25,879,428

C/T

2.44E-06

1.51E-02

0.9107981221

0.00137

LOC104748799

uncharacterized

NA

WE48

    

5.39E-06

3.34E-02

 

0.00334

   

WE46

    

1.85E-07

1.14E-03

 

0.00013

   

WE_total

S16_10,454,057

16

10,454,057

T/C

2.37E-06

1.47E-02

0.1103286385

0.00210

LOC104750305

ERAD-associated E3 ubiquitin-protein ligase HRD1B-like

protein ubiquitination

WE42

S16_11,083,391

16

11,083,391

C/T

8.64E-10

5.35E-06

0.931924883

0.00000

LOC104750339

leucine-rich repeat receptor-like protein CLAVATA2

membrane component

AG19

S16_2,915,369

16

2,915,369

T/C

6.87E-07

4.25E-03

0.1009389671

0.00425

LOC104749495

DEAD-box ATP-dependent RNA helicase 21-like

ribosome biogenesis, mRNA degradation and translation initiation.

ALC26

S16_9,912,650

16

9,912,650

T/C

1.31E-07

8.11E-04

0.112676056

0.00012

LOC104753537

uncharacterized

NA

AG19

S16_9,912,651

16

9,912,651

G/A

7.71E-08

4.77E-04

0.08685446

0.00010

LOC104753537

uncharacterized

NA

AG19

S16_9,912,652

16

9,912,652

G/A

1.31E-07

8.11E-04

0.112676056

0.00012

LOC104753537

uncharacterized

NA

AG19

S17_32,490,691

17

32,490,691

T/A

2.56E-11

1.59E-07

0.0704225352

0.00000

LOC104758647

protein SPA1-RELATED 4-like

Repressor of photomorphogenesis in the blue light

WE48

    

7.71E-11

4.77E-07

 

0.00000

   

WE46

    

1.02E-06

6.32E-03

 

0.00346

   

WE44

    

4.17E-12

2.58E-08

 

0.00000

   

WE_total

    

3.65E-07

2.26E-03

 

0.00226

   

ALK35

    

1.46E-09

9.04E-06

 

0.00000

   

AG19

S17_33,558,126

17

33,558,126

A/T

7.83E-10

4.85E-06

0.8849765258

0.00000

LOC104758812

probable acyl-activating enzyme 18, peroxisomal

peroxisomal activation of 2,4-dichlorophenoxybutyric acid (2,4-dB)

WE48

    

2.97E-08

1.84E-04

 

0.00003

   

WE46

    

2.23E-08

1.38E-04

 

0.00002

   

WE_total

S17_3,778,452

17

3,778,452

A/G

2.77E-06

1.71E-02

0.882629108

0.00214

LOC104755111

U11NAU12 small nuclear ribonucleoprotein 65 kDa protein

branch-point site recognition for normal plant development

WE42

    

5.08E-06

3.15E-02

 

0.00242

   

AG19

S18_2,191,451

18

2,191,451

C/A

6.97E-06

4.32E-02

0.3755868545

0.04316

LOC104760305

WUSCHEL-related homeobox 8-like

basal embryo development after fertilization

ALC_total

S19_10,881,936

19

10,881,936

G/C

6.85E-06

4.24E-02

0.103286385

0.00283

LOC104765950

F-box protein At5g07610-like

NA

WE48

    

2.56E-06

1.59E-02

 

0.00176

   

WE46

    

3.63E-06

2.24E-02

 

0.00249

   

WE42

S19_19,179,520

19

19,179,520

G/T

4.70E-09

2.91E-05

0.8708920188

0.00000

LOC109131004

histone deacetylase 6-like

protein deacetylase activity; degradation of misfoleded proteins

WE48

    

1.61E-07

9.99E-04

 

0.00012

   

WE46

    

1.57E-09

9.73E-06

 

0.00000

   

WE_total

S19_4,005,938

19

4,005,938

C/G

2.19E-06

1.36E-02

0.8544600939

0.00735

LOC104764661

probable DNA helicase MCM8 (pseudo)

DNA repair during meiosis

AG23

    

2.21E-06

1.37E-02

 

0.00228

   

MAR25

S20_6,023,906

20

6,023,906

G/A

1.59E-08

9.85E-05

0.1408450704

0.00005

LOC104769581

magnesium-chelatase subunit ChlH, chloroplastic

chlorophyll synthesis,plastid-to-nucleus retrograde signaling and abscisic acid (ABA) perception

MAR25

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