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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.