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Table 3 Results of the association study: significant SNP-phenotype associations along with the co-located QTL

From: Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

Chr

Gene

Marker

Position

Syn/Ns

Tissue

Trait

n.obs

p.MLM

p.adj.GLM

QTL

1

VvLAR1

int2687

intron 4

 

skin

catT

112

2.92E-04

9.99E-04

Yes

  

e5-2734

exon 5

Syn

skin

catT

112

1.22E-05

9.99E-04

Yes

  

e1-82

exon 1

Ns (Ala ↔ Thr)

skin

mDP

115

7.08E-04

0.025

Yes

  

e1-132

exon 1

Syn

skin

mDP

113

5.44E-04

9.99E-04

Yes

  

e1-138

exon 1

Syn

skin

mDP

105

0.0013

0.0021

Yes

  

e1-156

exon 1

Ns (Asn ↔ Lys)

skin

mDP

111

5.19E-04

9.99E-04

Yes

  

e3-665

exon 3

Syn

skin

mDP

117

3.41E-04

9.99E-04

Yes

  

e3-734

exon 3

Syn

skin

mDP

110

5.66E-04

9.99E-04

Yes

  

int2405

intron 3

 

skin

mDP

94

1.85E-04

9.99E-04

Yes

  

e4-2524

exon 4

Syn

skin

mDP

103

5.58E-04

9.99E-04

Yes

  

int2636

intron 4

 

skin

mDP

104

6.49E-04

9.99E-04

Yes

  

e5-2722

exon 5

Syn

skin

mDP

107

4.82E-04

9.99E-04

Yes

  

e5-2776

exon 5

Syn

skin

mDP

107

4.82E-04

9.99E-04

Yes

  

e5-2779

exon 5

Syn

skin

mDP

107

5.61E-04

9.99E-04

Yes

  

e5-2785

exon 5

Syn

skin

mDP

107

5.61E-04

9.99E-04

Yes

  

e5-2872

exon 5

Ns (Ile ↔ Met)

skin

mDP

104

6.37E-04

9.99E-04

Yes

  

e5-2896

exon 5

Syn

skin

mDP

104

6.37E-04

9.99E-04

Yes

  

e5-2902

exon 5

Syn

skin

mDP

104

6.37E-04

9.99E-04

Yes

  

e1-156

exon 1

Ns (Asn ↔ Lys)

skin

Ftranscis_all

109

0.0032

0.0509

No

  

int2687

intron 4

 

skin

Ftranscis_all

114

0.0025

0.042

No

  

e5-2734

exon 5

Syn

skin

Ftranscis_all

114

1.84E-04

9.99E-04

No

11

VvMYBPA2

intron06Y

intron

 

skin

concP

117

9.77E-04

9.99E-04

No

  

p19_GA

promoter

 

skin

concK

55

4.37E-04

9.99E-04

No

  

p18

promoter

 

skin

mDP

54

1.76E-04

9.99E-04

No

  

p19_GA

promoter

 

skin

mDP

55

3.36E-06

9.99E-04

No

  

intron05M

intron

 

seed

galT

82

0.0015

0.3377

No

  

1293 W

exon 3

Syn

seed

galT

93

0.0014

0.3067

No

  

1322 W

exon 3

Ns (Leu ↔ His)

seed

galT

92

0.0013

0.3387

No

  

1398Y

exon 3

Syn

seed

galT

92

0.0029

0.6773

No

  

1473Y

exon 3

Syn

seed

galT

93

0.0026

0.5135

No

13

VvCHI1

Y183

exon 4

Syn

skin

concP

108

0.0025

0.049

No

15

VvMYBPA1

p277R

promoter

 

skin

epiT

125

0.0018

0.03

No

  

702W

exon 2

Ns (Ser ↔ Thr)

seed

Ftranscis_T

68

0.0036

0.6783

No

  1. p.MLM, p-value from mixed model, p.adj.GLM, adjusted p-value from GLM. Bold cases indicate significant associations in both MLM and GLM results. QTL, the candidate genes were under QTLs of the same PA variables as those associated with SNP.