Table 2.
Significant loci associated with grape berry traits as determined from GEMMA analysis and annotations of the candidate genes
| Trait | Marker | P | P.adjust | Gene | Annotation | Region annotationa |
|---|---|---|---|---|---|---|
| Berry color | chr2:14316046 | 2.56E-09 | 1.19E-06 | VIT_202s0033g00460 | transcription factor mybA3 |
VIT_202s0033g00410 transcription factor myba3; VIT_202s0033g00450 transcription factor myba3 |
| chr2:15641010 | 4.18E-07 | 3.89E-05 | VIT_202s0033g00880 | 60S ribosomal protein L8-3 | ||
| chr2:15842558 | 3.25E-07 | 5.05E-05 | VIT_202s0033g00960 | nuclear-interacting partner of alk | ||
| chr2:15983296 | 4.07E-07 | 4.74E-05 | VIT_202s0033g01000 | benzyl alcohol o-benzoyltransferase | ||
| chr2:17439426 | 2.17E-07 | 5.06E-05 | VIT_202s0087g00230 | aspartic proteinase nepenthesin-1 | ||
| Berry development period | chr16:20841803 | 6.62E-06 | 2.15E-03 | VIT_216s0098g00420 | probable receptor-like protein kinase at1g67000-like |
VIT_216s0098g00390 probable receptor-like protein kinase at1g67000-like; VIT_216s0098g00400 probable receptor-like protein kinase at1g67000-like; VIT_216s0098g00460 gdsl esterase lipase at4g10955; VIT_216s0098g00480 gdsl esterase lipase at4g10955 |
| chr16:3676395 | 7.97E-06 | 1.30E-03 | VIT_216s0115g00110 | myosin-like protein |
VIT_216s0115g00170 seed maturation protein VIT_216s0115g00190 DNA-directed RNA polymerases and iii subunit rpabc4-like |
|
| Cluster size | chr5:1096673 | 7.86E-07 | 2.45E-02 | VIT_205s0077g01350 | AMSH-like ubiquitin thioesterase 3-like | |
| chr5:1096614 | 8.33E-05 | 6.45 E-01 | VIT_205s0077g01350 | AMSH-like ubiquitin thiolesterase 3-like | ||
| Berry weight | chr18:1954157 | 2.39E-07 | 9.94E-05 | VIT_218s0001g01370 | wall-associated receptor kinase 2-like |
VIT_218s0001g01360 toprim domain-containing protein VIT_218s0001g01390 gibberellin 20-oxidase |
| chr19:8859958 | 2.56E-06 | 5.30E-04 | VIT_219s0015g00730 | cellulose synthase-like protein e6-like |
VIT_219s0015g00710 cellulose synthase-like protein e1 VIT_219s0015g00740 protein plastid movement impaired 2-like VIT_219s0015g00750 sucrase-like protein VIT_219s0015g00750 sec14 cytosolic factor-like |
|
| chr19:8859967 | 6.02E-06 | 8.33E-04 | VIT_219s0015g00730 | cellulose synthase-like protein e6-like | ||
| chr17:14485590 | 7.81E-06 | 8.11E-04 | VIT_217s0119g00330 | uncharacterized protein | uncharacterized protein | |
| Berry flesh texture | chr16:21539912 | 3.32E-08 | 1.24E-05 | VIT_216s0098g01280 | senescence-associated protein din1 |
VIT_216s0098g01140 calcium-dependent protein; VIT_216s0098g01180 aldo-keto reductase oxidoreductase; VIT_216s0098g01230 cytochrome b5; VIT_216s0098g01560 glucan endo-beta-glucosidase; VIT_216s0098g01590 calcium-binding EF-hand family protein |
| Berry flavor | chr5:5515972 | 6.95E-06 | 2.32E-03 | VIT_205s0020g03860 | homocysteine S-methyltransferase 2 |
VIT_205s0020g03640 c-8 sterol isomerase; VIT_205s0020g03710 gcn5-related n-acetyltransferase-like protein; VIT_205s0020g03930 sulfate bicarbonate oxalate exchanger and transporter sat-1 |
aThe genes located in the regions were within approximately 1 Mb upstream or downstream of the SNPs of interest