TABLE 2.
Markers and results of association tests for 32 associated polymorphisms, three haplotypes, and eight SSRs framing the candidate genes
| Gene | Marker | Type | Promoter/exon/intron/3′-UTR | Sy/NS | Frequency or no. of alleles | F-test | P-value | Marker R2 |
|---|---|---|---|---|---|---|---|---|
| VMC6B11 | SSR | 9 | 2.08 | 4.40E-03 | 0.36 | |||
| VVNTM1 | SSR | 6 | 9.63 | 1.41E-09 | 0.45 | |||
| VVNTM2 | SSR | 4 | 25.35 | 7.03E-12 | 0.45 | |||
| VvMybA2 | S84 | SNP | Promoter | 0.07 | 13.36 | 3.83E-04 | 0.10 | |
| R153 | SNP | Promoter | 0.23 | 33.69 | 2.45E-12 | 0.35 | ||
| W393 | SNP | Promoter | 0.23 | 65.25 | 6.63E-20 | 0.50 | ||
| W417 | SNP | Promoter | 0.24 | 65.31 | 5.80E-20 | 0.50 | ||
| R440 | SNP | Promoter | 0.21 | 53.29 | 2.53E-17 | 0.45 | ||
| S465 | SNP | Promoter | 0.24 | 58.18 | 1.98E-18 | 0.47 | ||
| Y754 | SNP | Promoter | 0.12 | 16.69 | 4.54E-07 | 0.22 | ||
| R762 | SNP | Exon | NS | 0.16 | 38.80 | 2.00E-13 | 0.40 | |
| K980 | SNP | Exon | NS | 0.27 | 87.08 | 3.19E-24 | 0.57 | |
| R984 | SNP | Exon | Sy | 0.23 | 42.98 | 7.43E-15 | 0.40 | |
| R1020 | SNP | Exon | Sy | 0.23 | 39.31 | 7.00E-14 | 0.38 | |
| Indel 1748 | Indel | Exon | NS | 0.21 | 65.01 | 2.31E-19 | 0.53 | |
| Haplotype | 24 | 10.69 | 2.66E-15 | 0.71 | ||||
| VVNTM3 | SSR | 10 | 7.45 | 8.59E-12 | 0.43 | |||
| VvMybA1 | Gret1 | Retro | Promoter | 0.39 | 67.30 | 3.03E-18 | 0.56 | |
| K244 | SNP | Exon | NS | 0.25 | 51.00 | 1.79E-16 | 0.46 | |
| K259 | SNP | Exon | NS | 0.3 | 47.96 | 7.12E-16 | 0.44 | |
| M318 | SNP | Exon | NS | 0.19 | 45.31 | 2.87E-15 | 0.43 | |
| Y566 | SNP | 3′-UTR | 0.18 | 46.07 | 2.17E-15 | 0.44 | ||
| R567 | SNP | 3′-UTR | 0.13 | 9.66 | 1.32E-04 | 0.14 | ||
| Y620 | SNP | 3′-UTR | 0.04 | 13.69 | 3.31E-04 | 0.10 | ||
| D660 | SNP | 3′-UTR | 0.04 | 6.74 | 7.42E-05 | 0.21 | ||
| W811 | SNP | 3′-UTR | 0.13 | 9.90 | 1.10E-04 | 0.15 | ||
| Y847 | SNP | 3′-UTR | 0.4 | 52.10 | 4.77E-16 | 0.52 | ||
| Haplotype | 26 | 13.30 | 1.90E-19 | 0.81 | ||||
| VVNTM4 | SSR | 4 | 0.82 | 4.43E-01 | 0.02 | |||
| VvMybA3 | Y166 | SNP | Promoter | 0.39 | 33.29 | 2.47E-12 | 0.33 | |
| M209 | SNP | Promoter | 0.1 | 50.34 | 1.24E-16 | 0.44 | ||
| M357 | SNP | Promoter | 0.05 | 14.61 | 5.19E-11 | 0.38 | ||
| W362 | SNP | Promoter | 0.06 | 25.93 | 4.26E-10 | 0.29 | ||
| R379 | SNP | Promoter | 0.42 | 14.20 | 3.36E-06 | 0.20 | ||
| K392 | SNP | Promoter | 0.11 | 36.42 | 3.79E-13 | 0.36 | ||
| K403 | SNP | Promoter | 0.39 | 92.54 | 5.72E-25 | 0.58 | ||
| R440 | SNP | Promoter | 0.48 | 12.92 | 8.45E-06 | 0.17 | ||
| R869 | SNP | Promoter | 0.03 | 34.52 | 1.50E-12 | 0.35 | ||
| R929 | SNP | Exon | Sy | 0.47 | 20.30 | 1.61E-05 | 0.15 | |
| Haplotype | 42 | 68.74 | 2.88E-10 | 0.7365 | ||||
| VVNTM5 | SSR | 4 | 5.79 | 2.74E-04 | 0.34 | |||
| VVNTM6 | SSR | 5 | 2.86 | 4.40E-03 | 0.18 | |||
|
VVIU20 |
SSR |
2 |
6.86 |
1.80E-03 |
0.15 |
P-values <6.25E-4 were considered to be significant. R2 mk is the percentage of anthocyanin variation explained by the polymorphism alone when integrating the structure. 3′-UTR, 3′ untranslated region; Sy, synonymous change; NS, nonsynonymous change. Frequencies are given for the SNP minority allele and the number of alleles are given for SSRs and haplotypes.