Table 2 Significant loci associated with grape berry traits as determined from GEMMA analysis and annotations of the candidate genes

From: Genome-wide association study of berry-related traits in grape [Vitis vinifera L.] based on genotyping-by-sequencing markers

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

  1. aThe genes located in the regions were within approximately 1 Mb upstream or downstream of the SNPs of interest
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