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Table 3: Validation of 42 SNPs at the RDV2 locus

From: Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection

  

Sequenom MassARRAY

TASSEL

SNP ID

Position

Genotype

MF

MAF

Genotype

MF

MAF

S14_2062712

2062712

GG/GT

0.72

0.28

GG/GT

0.72

0.28

S14_2846470

2846470

CC/TC

0.72

0.28

CC/TC

0.72

0.28

S14_3066185

3066185

AA/GA

0.72

0.28

AA/GA

0.72

0.28

S14_3222720

3222720

TT/TA

0.72

0.28

TT/TA

0.72

0.28

S14_3296164

3296164

CC/TC

0.72

0.28

CC/TC

0.72

0.28

S14_3596942

3596942

CC/CT

0.72

0.28

CC/CT

0.72

0.28

S14_4065142

4065142

TT/GT

0.72

0.28

TT/GT

0.72

0.28

S14_4196799

4196799

AA/AG

0.72

0.28

AA/AG

0.72

0.28

S14_4921219

4921219

CC/CT

0.74

0.26

CC/CT

0.74

0.26

S14_5274160

5274160

TT/CT

0.74

0.26

TT/CT

0.74

0.26

S14_5737727

5737727

AA/TA

0.74

0.26

AA/TA

0.74

0.26

S14_5771919

5771919

AA/CA

0.74

0.26

AA/CA

0.74

0.26

S14_5804788

5804788

AA/GA

0.74

0.26

AA/GA

0.74

0.26

S14_6008125

6008125

GG/CG

0.74

0.26

GG/CG

0.74

0.26

S14_6071298

6071298

GG/AG

0.74

0.26

GG/AG

0.74

0.26

S14_6071669

6071669

CC/CA

0.74

0.26

CC/CA

0.74

0.26

S14_6175917

6175917

TT/CT

0.74

0.26

TT/CT

0.74

0.26

S14_6596440

6596440

TT/TA

0.74

0.26

TT/TA

0.74

0.26

S14_7684469

7684469

AA/AG

0.74

0.26

AA/AG

0.75

0.25

S14_8894287

8894287

GG/GT

0.75

0.25

GG/GT

0.76

0.24

S14_9154944

9154944

TT/GT

0.76

0.24

TT/GT

0.76

0.24

S14_9705369

9705369

TT/CT

0.76

0.24

TT/CT

0.77

0.23

S14_3076105

3076105

TT

1

0

TT/TC

0.76

0.24

S14_3084705

3084705

GG

1

0

GG/GT

0.77

0.23

S14_3216815

3216815

CC

1

0

CC/CT

0.76

0.24

S14_3256262

3256262

GG

1

0

GG/GC

0.76

0.24

S14_3256274

3256274

AA

1

0

AA/AT

0.76

0.24

S14_3321418

3321418

CC

1

0

CC/CT

0.77

0.23

S14_3596980

3596980

TT

1

0

TT/TA

0.76

0.24

S14_3891954

3891954

CC

1

0

CC/CT

0.77

0.23

S14_4228151

4228151

TT

1

0

TT/TA

0.76

0.24

S14_6003431

6003431

CC

1

0

CC/CG

0.74

0.26

S14_7623091

7623091

GG

1

0

GG/GA

0.75

0.25

S14_7744603

7744603

AA

1

0

AA/AC

0.74

0.26

S14_7776601

7776601

GG

1

0

GG/GA

0.74

0.26

S14_7829543

7829543

AA

1

0

AA/AG

0.73

0.27

S14_7831615

7831615

CC

1

0

CC/CT

0.74

0.26

S14_7939992

7939992

CC

1

0

CC/CT

0.72

0.28

S14_8196757

8196757

AA

1

0

AA/AG

0.72

0.28

S14_8660835

8660835

GG

1

0

GG/GC

0.73

0.27

S14_9036371

9036371

GG

1

0

GG/GA

0.75

0.25

S14_9154939

9154939

GG

1

0

GG/GA

0.75

0.25

  1. SNPs validated by Sequenom MassARRAY from 56 F1 individuals were compared with results from the TASSEL GBS data. Based on alignment with the PN40024 reference genome, SNPs from chromosome 14 were selected from position 2062712 to 9705369 for validation. The top section of the table contains 22 SNPs in which genotypes determined by Sequenom MassARRAY closely matched results produced by the TASSEL GBS pipeline. The bottom section lists SNPs genotyped by Sequenom MassARRAY, which did not match with results from the TASSEL GBS pipeline. MF Major Allele Frequency, MAF Minor Allele Frequency.