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Table 5 Transcriptomic candidates underlying ver meta-QTLs or ver/ph meta-QTLs selected by GO annotation for gene expression regulation, signalling or development

From: Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

Gene IDa

Chr

Start

End

Annotation

mQTLb

Transcriptomic candidatec

VIT_01s0011g02950

1

2,618,690

2,632,669

Zinc finger (C3HC4-type ring finger)

ver_1.1

[48]

VIT_01s0011g03070

1

2,751,566

2,753,036

ERF/AP2 Gene Family (VvRAV1)

ver_1.1

[44, 46]

VIT_01s0011g03520

1

3,190,826

3,192,777

Constans-like 16

ver_1.1

[44, 46]

VIT_02s0025g04730

2

4,100,066

4,103,095

Glyoxylate reductase

ver_2.1

[44, 46]

VIT_02s0154g00070

2

4,804,832

4,807,460

Abnormal floral organs

ver_2.1

[44, 46]

VIT_02s0154g00080

2

4,813,347

4,818,031

Multi-copper oxidase (SKU5)

ver_2.1

[44, 46]

VIT_02s0012g00310

2

6,204,735

6,223,899

Lon protease

ver_2.2

[48]

VIT_02s0012g00570

2

6,554,241

6,560,259

Pseudo-response regulator 2 (APRR2) (TOC2)

ver_2.2

[44, 46]

VIT_02s0012g00590

2

6,600,611

6,610,281

Unknown protein

ver_2.2

[48]

VIT_02s0012g00990

2

7,043,508

7,046,965

LOL1 (LSD ONE like 1)

ver_2.2

[44, 46]

VIT_02s0012g01010

2

7,087,110

7,089,452

Leucine-rich repeat

ver_2.2

[48]

VIT_02s0012g01040

2

7,120,118

7,122,681

NAC domain-containing protein (VvNAC13)

ver_2.2

[44, 46, 48]

VIT_02s0033g00300

2

14,144,838

14,148,929

myb family

ver_2.3

[44, 46]

VIT_02s0033g00390

2

14,291,727

14,292,732

VvMybA2

ver_2.3

[44, 46]

VIT_02s0033g00410

2

14,351,791

14,352,807

VvMybA1

ver_2.3

[44, 46]

VIT_02s0033g00450

2

14,420,525

14,421,283

VvMybA3

ver_2.3

[44, 46, 48]

VIT_03s0038g00860

3

689,247

693,308

Basic Leucine Zipper Transcription Factor (VvbZIP05)

ver/ph_3.1

[48]

VIT_03s0038g01090

3

862,995

863,398

Auxin responsive SAUR protein

ver/ph_3.1

[44, 46]

VIT_03s0038g01110

3

866,357

866,897

Auxin-responsive SAUR31

ver/ph_3.1

[44, 46]

VIT_03s0038g01310

3

921,733

927,965

Auxin responsive SAUR protein

ver/ph_3.1

[48]

VIT_03s0038g02130

3

1,468,239

1,469,371

Cold shock protein-1

ver/ph_3.1

[48]

VIT_03s0180g00040

3

5,973,785

5,975,813

Cyclin D3_2

ver/ph_3.2

[48]

VIT_03s0091g00210

3

6,507,392

6,509,263

Ethylene-responsive protein

ver/ph_3.2

[44, 46]

VIT_03s0091g00260

3

6,548,677

6,549,577

Zinc finger protein 4

ver/ph_3.2

[44, 46, 48]

VIT_03s0091g00870

3

7,342,165

7,357,074

Adenylylsulfate kinase 1 (AKN1)

ver/ph_3.2

[48]

VIT_03s0091g01060

3

7,673,917

7,675,754

Cyclin delta-2

ver/ph_3.2

[48]

VIT_03s0088g00290

3

8,315,170

8,315,924

Phytosulfokines PSK2

ver/ph_3.2

[44, 46]

VIT_03s0088g01180

3

9,438,885

9,442,060

Proline iminopeptidase

ver/ph_3.2

[48]

VIT_05s0062g00760

5

19,469,712

19,473,848

Receptor kinase RHG4

ver/ph_5.1

[48]

VIT_11s0016g03640

11

2,972,017

2,974,625

Rac-like GTP-binding protein ARAC7 (GTPase protein ROP9)

ver/ph_11.1

[44, 46]

VIT_11s0016g03650

11

2,976,690

2,979,682

CDKF;1 (CDK-activating kinase 1A

ver/ph_11.1

[48]

VIT_11s0016g03880

11

3,163,900

3,169,609

Receptor protein kinase PERK1

ver/ph_11.1

[48]

VIT_11s0016g03900

11

3,182,349

3,186,809

AAA-type ATPase

ver/ph_11.1

[48]

VIT_11s0016g03940

11

3,224,068

3,225,265

Heat shock transcription factor C1

ver/ph_11.1

[44, 46]

VIT_12s0035g02090

12

23,983,677

23,999,372

Leucine-rich repeat family protein

ver/ph_12.1

[48]

VIT_12s0035g02120

12

24,046,092

24,050,103

Unknown

ver/ph_12.1

[48]

VIT_14s0083g00620

14

22,672,469

22,675,655

NIK1 (NSP- interacting kinase 1)

ver/ph_14.3

[44, 46]

VIT_14s0083g00640

14

22,696,160

22,698,346

Constans 2 (COL2)

ver/ph_14.3

[44, 46]

VIT_14s0083g01030

14

23,320,331

23,341,036

putative MADS-box Fruitfull 2 (VviFUL2)

ver/ph_14.3

[44, 46, 48]

VIT_14s0083g01110

14

23,435,436

23,438,457

Brassinosteroid-6-oxidase

ver/ph_14.3

[44, 46]

VIT_14s0083g01160

14

23,527,926

23,532,692

COBRA protein

ver/ph_14.3

[48]

VIT_14s0083g01210

14

23,631,468

23,634,185

feronia receptor-like kinase

ver/ph_14.3

[44, 46]

VIT_14s0083g01220

14

23,647,671

23,648,618

feronia receptor-like kinase

ver/ph_14.3

[44, 46]

VIT_14s0068g00010

14

23,691,896

23,694,505

feronia receptor-like kinase

ver/ph_14.3

[44, 46]

VIT_14s0068g00030

14

23,710,282

23,713,253

feronia receptor-like kinase

ver/ph_14.3

[44, 46]

VIT_14s0068g00040

14

23,730,955

23,731,566

No hit

ver/ph_14.3

[44, 46]

VIT_14s0068g00050

14

23,741,203

23,741,804

No hit

ver/ph_14.3

[44, 46]

VIT_14s0068g00300

14

23,997,514

24,000,870

ABRC5

ver/ph_14.3

[48]

VIT_14s0068g00330

14

24,046,880

24,048,369

PTF1 (plastid transcription factor 1) TCP13

ver/ph_14.3

[44, 46]

VIT_14s0068g00640

14

24,438,706

24,450,994

Acetyl-CoA synthetase

ver/ph_14.3

[48]

VIT_16s0022g01650

16

15,243,820

15,246,842

Receptor serine/threonine kinase PR5K

ver/ph_16.2

[48]

VIT_16s0022g02230

16

16,240,572

16,248,680

Leucine-rich repeat receptor protein kinase EXS

ver/ph_16.2

[48]

VIT_16s0022g02340

16

16,470,141

16,475,595

fructokinase-2

ver/ph_16.2

[48]

VIT_16s0100g00350

16

17,248,816

17,261,155

ABC Transporter (VvTAP3 - VvABCB23)

ver/ph_16.3

[48]

VIT_17s0000g05020

17

5,637,669

5,644,801

Squamosa promoter-binding protein 6 (SPL6)

ver/ph_17.1

[44, 46]

VIT_17s0000g05050

17

5,659,282

5,660,704

COBRA-like protein 4

ver/ph_17.1

[48]

VIT_17s0000g05070

17

5,676,169

5,679,862

Phytochelatin synthetase

ver/ph_17.1

[44, 46, 48]

VIT_17s0000g05240

17

5,869,290

5,885,095

Nuclear transport factor 2 (NTF2)

ver/ph_17.1

[48]

VIT_17s0000g05580

17

6,213,229

6,221,132

Isopiperitenol dehydrogenase

ver/ph_17.1

[44, 46, 48]

VIT_18s0001g02000

18

2,438,485

2,442,668

Zinc finger (C2H2 type) family

ver/ph_18.1

[44, 46, 48]

VIT_18s0001g02540

18

2,802,829

2,805,078

ARR9 typeA

ver/ph_18.1

[44, 46]

VIT_18s0001g03580

18

3,389,546

3,393,993

Ubiquitin-fold modifier 1 precursor

ver/ph_18.1

[48]

VIT_18s0001g03670

18

3,422,279

3,424,214

Zinc finger (C2H2 type) family

ver/ph_18.1

[44, 46]

VIT_18s0001g04340

18

3,822,948

3,829,597

Glycine hydroxymethyltransferase

ver/ph_18.1

[48]

VIT_18s0001g04680

18

3,938,582

3,956,444

RPG related protein 1 RR1

ver/ph_18.1

[44, 46]

VIT_18s0001g06430

18

4,806,981

4,808,947

Homeobox-leucine zipper protein ATHB-6

ver/ph_18.1

[44, 46, 48]

VIT_18s0001g07090

18

5,290,562

5,293,561

Unknown protein

ver/ph_18.1

[48]

VIT_18s0001g12840

18

10,940,330

10,945,165

ADP-glucose pyrophosphorylase large subunit CagpL2

ver/ph_18.2

[48]

VIT_18s0001g13010

18

11,126,023

11,129,236

Mitogen-activated Protein Kinase (VvMPK11)

ver/ph_18.2

[48]

VIT_18s0001g13200

18

11,256,653

11,261,569

Cytokinin dehydrogenase 5 precursor

ver/ph_18.2

[44, 46]

VIT_18s0001g14130

18

12,179,540

12,181,647

Zinc finger (C2H2 type) family

ver/ph_18.2

[44, 46]

VIT_18s0001g14360

18

12,337,145

12,340,985

Tubulin beta-1 chain

ver/ph_18.2

[44, 46]

VIT_18s0001g14440

18

12,432,955

12,439,459

Molecular chaperone DnaJ

ver/ph_18.2

[44, 46]

VIT_18s0001g14450

18

12,453,766

12,456,583

Ferredoxin:nadp+ Oxidoreductase PETH

ver/ph_18.2

[44, 46]

VIT_18s0001g15720

18

13,856,940

13,861,020

Leucine Rich Repeat receptor-like kinase

ver/ph_18.2

[44, 46, 48]

VIT_18s0001g15730

18

13,865,318

13,866,466

Dof zinc finger protein DOF3.5

ver/ph_18.2

[48]

VIT_18s0076g00330

18

14,494,814

14,503,181

Basic Leucine Zipper Transcription Factor (VvbZIP50)

ver/ph_18.2

[48]

VIT_18s0076g00310

18

14,550,818

14,563,944

Translation initiation factor eIF-5B

ver/ph_18.2

[48]

  1. aFor each candidate physical position on the grape genome assembly as well as annotation is provided. Genes shown in the tables are selected by following slimGOs: GO:0000166, GO:0003676, GO:0003677, GO:0003682, GO:0003700, GO:0005102, GO:0005634, GO:0007154, GO:0007165, GO:0007275, GO:0009653, GO:0009719, GO:0009791, GO:0009908, GO:0016301, GO:0030154, GO:0038023, GO:0040007
  2. bMeta-QTL under which the candidate was found
  3. cReference of the transcriptomic study in which the candidate was found to be differentially expressed during veraison
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BMC Genomics

ISSN: 1471-2164

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