Figure S2. Genetic maps and QTL locations for ‘Beihong’ (BH, maternal parent) × and ‘E.S.7-11-49’ (ES, paternal parent). Markers are listed to the right

Figure S2. Genetic maps and QTL locations for ‘Beihong’ (BH, maternal

parent) × and ‘E.S.7-11-49’ (ES, paternal parent). Markers are listed to the

right of each LG and genetic distances on the left. The SNP markers in blue are

common to both parents. QTLs controlling sugar- and acid-related traits are

shown in bar and represented by blue arrows extended by lines. Confidence

intervals of QTLs are according to their scale on genetic map. Distances are in

Kosambi cM. The year of observation is denoted by 11, 12 and 13 for 2011, 2012

and 2013, respectively. SSC represents soluble solid content, G/F is the

glucose-to-fructose ratio and β ratio is the tartaric acid-to-malic acid ratio.

1978370.02971630.72051861.42280704.22209087.31330838.411761810.28374713.822951614.927139117.319059124.1

13438327.9

14133734.7

23248741.76117043.318870744.3

18856152.710571357.220700658.014680359.4

17785367.48270268.9

7393873.88763276.0

22544181.7

BH LG01 ES LG01

3071820.02152350.91846261.31626344.21574437.51509079.218823911.46968312.43240217.26404223.94491825.913532427.417357928.518054830.022204536.613023639.416875840.116777042.67140543.510420245.73084547.29829448.317772048.64920552.020148953.110248253.410115054.26117054.621927055.914817757.024617459.313074660.23736461.08546361.430669163.616966567.53007671.07393871.57081772.016635072.819685674.213899774.421091078.2

SSC13

1228180.02296051.71284182.5767073.61177704.61696365.51958246.92691817.825035311.222897112.121747313.9632915.720855916.518543918.716015719.418378320.023423221.430796523.56229825.03423626.59153132.43592233.424128934.523690940.0

6814463.320581864.328419864.711340965.27748065.817437767.7

1228180.0909881.81945054.51696365.71692336.53070067.412081510.56462210.929823211.419543112.012422013.016178714.221450016.124466920.619561521.018378326.818293229.211974630.918634535.420829339.028684739.812522943.36394150.613144752.123690952.713435653.41732854.121601857.616483959.330084059.717841360.728371062.327630862.93085863.613846363.924015664.26037764.423631565.028530365.721864865.929099966.027267966.110385566.927530598.9125072103.919325104.3297068104.9115503106.8153319106.9

G/F11

BH LG02 ES LG02

15655569.2

1720150.01492846.11402516.83072328.92342489.45934013.53378315.1229361 21807915.622350716.211152521.325344623.318436424.824680425.225165925.912458926.810504633.330749534.06385738.628439438.9

26214446.228355248.15700452.329499753.612410756.222385356.616521759.1

668166.620588368.9

2342480.01167962.9298253 1507396.3

23445511.5

16045328.014594231.6

10917342.4

17237647.5

18578356.527433956.817014557.73052360.825361962.029009268.0

11989096.4

G/F11α ratio11

BH LG03 ES LG03

1372950.026747212.225484818.018290218.623229420.217696921.213409622.323747724.227953228.227513528.429533029.924913536.124022137.023309838.88676240.57444747.216423248.819105751.115545554.415224154.93538855.619373957.522938160.121187261.325514961.62946962.812841666.223177266.316240968.019167368.98836570.721689272.514463775.625088478.523903783.220001785.38106186.727846889.1286057101.0165465102.7209768104.3

Fructose12

206568241410149167107712170827104419243954232294112315176444184865

207613130104172607249135

227903

230080112982

155455217705

181319211162270825

244311279654176045113591155473227788226338237649279450217678282965

297044165465

0.01.54.06.38.59.19.7

10.211.412.813.9

1505614.415.317.018.619.6

7723022.624.0

7893527.929.432.0

5335538.139.240.2

5006341.26298441.4

42.242.444.0

1468344.950.551.552.161.563.464.264.564.865.070.170.3

2523170.56302072.0

76.981.0

53216106.6

BH LG04 ES LG04

2745370.0

1783021.6

1600783.9228484.3878035.01587545.5

2303717.3251247.4

1374969.5

20625811.8

22410614.7

6464919.0

2820300.01758874.72326067.13047797.71844298.11493998.31834188.4124723 2702031872898.5

2220349.228763512.12599513.47806816.5

1471026.6

23365332.72233136.021042436.320269137.9

24832250.927189252.024359955.322558756.324612957.1758857.310252858.54475260.2

267260.0

2129975.6

10242711.8

25474315.1

23973516.1

3385420.2

4403122.8

BH LG05-1 ES LG05BH LG05-2

342560.02390800.21186721.1433262.02543915.22902165.91432568.026683010.0394627.113673329.822262130.922905332.024592833.326228235.316005336.519168537.84673140.86073543.16552346.67614447.115629348.919811049.721248549.922988750.121222350.713188350.914527951.018700351.513251853.018349655.025994555.38942755.523888755.86662056.31101156.610077356.78760057.823894259.325578059.410672159.54416659.721290960.020788961.230313461.410718164.028949564.423246371.6

1056140.01308860.62484877.62810279.121363610.224001513.41254813.723059114.39018414.8

6049624.124592825.216005326.426938226.818809228.715317734.429467337.714113641.518843642.323288442.821863449.323215050.2

11744959.99192762.49503667.924799271.53574474.218960477.721486078.52129779.08204179.6

Malic11Total acid11

BH LG06 ES LG06

1749

560.

012

1344

0.3

2081

251.

6

2534

886.

923

1951

7.6

1294

708.

4

1480

2211

.520

3443

12.8

1110

1413

.266

525

14.3

2454

217

.6

8734

020

.8

2243

3125

.0G

/F13

3039

00.

098

859

1.4

5577

52.

925

8350

3.5

1919

904.

026

0224

5.9

2391

508.

7

2703

1911

.225

2205

12.2

1903

3113

.924

9604

15.5

1346

4216

.326

5690

17.9

2100

8918

.7

2484

8322

.948

829

23.6

1005

6524

.215

8232

25.5

2534

8827

.522

2711

27.9

1294

7028

.510

8164

30.2

4353

331

.676

162

32.2

2411

1432

.817

1510

33.6

1480

2233

.914

4587

34.5

1497

9134

.913

6289

35.4

1639

8236

.790

193

37.3

1415

7841

.449

495

41.9

2525

0144

.629

6046

45.4

3038

0654

.983

439

55.4

1434

5257

.411

4244

57.9

4358

860

.3

5659

264

.5

8086

070

.613

2496

72.6

1014

8375

.5

2715

3477

.779

235

78.8

3014

581

.380

448

81.5

1973

1686

.427

8900

87.4

1413

2088

.719

8326

89.4

2071

9891

.021

5359

91.3

2573

9091

.819

6091

92.0

2715

7892

.910

3514

93.8

2371

3295

.278

391

95.8

8762

897

.421

5946

98.1

BH

LG

07

ES

LG

07

367670.075170.72203180.92879631.11692233.11290903.72448524.11386536.01795317.81919928.11737479.4125221 29427410.34863611.121474713.08780614.6937915.32609622.026723.66459724.415677224.96046327.31409430.65918332.723813533.724840335.328465935.79327337.08773438.021650339.830559840.7762543.424700845.310852747.429165049.613797556.321132056.820204956.924812764.028774365.917394270.93938873.9

2404900.0137080.92769641.22295301.31694981.51054422.4

285134.8

2061996.5

23904013.0

20782117.8

13787220.7

367670.02820870.9765291.51952601.62261912.3293362.62448522.9296897 1772823.7374664.01263764.115059110.713824011.24035115.810815720.12851321.225725323.53267030.27086633.120961138.216755140.14707042.725271343.18773445.19362145.525681648.628620248.926742452.823904054.29465056.015532157.815361258.028324759.39477660.53691460.716106162.826372563.017394270.11613271.16986773.03527873.7


2648160.01013555.21334066.628735815.625500418.928685520.818505521.825814033.313370434.523749838.120523244.65467848.027772850.025410150.611903352.513519053.112649754.627135854.721287456.830069958.17320558.618429560.73677061.025316561.325678061.623703062.621782163.130296864.310352266.017462867.612174368.125132870.013016271.3

1258950.02280526.21850559.61061615.211303215.516684521.127169231.124272831.815312933.117868634.019651537.428439138.412009039.111568639.812188640.327390044.611766646.523703051.313252355.619685258.212174358.85361360.26041162.0

3711886.9

G/F12

BH LG09 ES LG09

559930.0969360.72909891.51976093.31398614.81734425.6693727.118577210.24233615.519021917.3

19609326.027297129.4

14566939.1

1679842.6

29893253.5

18783365.3

5970071.45538074.027787575.1

15916579.9

615060.02454240.52299730.91961451.62428052.11065312.61398613.1704313.71976093.81857727.61023878.42875110.811114411.28160012.227857714.122805815.614618916.427731817.5395319.510368023.1697123.98486625.014764426.32545426.927297127.320882628.614943632.816168833.520855134.112637835.416655242.322798547.519462548.028760550.915859755.229036056.52841358.213695363.316790664.027787564.928341066.611150267.510614169.223282178.422524181.6

BH LG10 ES LG10

74.5

2121100.0703121.8333942.5464632.82390864.42755065.12318475.41862426.01621127.61312419.823726211.027601011.111381412.415527412.818762615.114971115.823454919.24801422.420018423.323426924.415579626.412906537.729942039.327099643.513533947.323878150.26742652.520207754.12677057.72305059.624463661.63107962.712240864.718567665.74992867.24005967.828341671.720182572.74269573.3175277

Fructose13

2406410.02788023.01751963.51862424.7158875.61466138.623934810.014327112.213124113.219332219.66051323.020018424.36748625.323426926.0

19689836.2

22826645.510424846.214107150.55029551.02958856.42843557.718299858.811519861.8

23367479.7

BH LG11 ES LG11

2179

050.

029

8221

6.6

5558

87.

783

168.

417

2489

16.5

1569

5818

.910

0728

25.2

2160

8928

.011

7444

28.7

2375

3730

.744

6234

.617

8343

35.2

2272

7336

.428

6011

37.5

2732

1038

.020

6314

39.2

6212

941

.320

3507

41.9

6756

042

.771

239

43.4

6398

748

.021

2091

49.0

2208

9749

.510

7248

52.0

9919

554

.381

907

56.0

2731

0956

.624

924_

58.1

1760

3760

.110

8348

60.7

1376

3261

.129

9072

63.8

1105

9366

.187

116

66.6

8316

0.0

5558

82.

217

9851

6.3

3642

36.

811

7292

8.1

2761

998.

315

6958

8.8

3491

79.

188

656

11.7

1514

9713

.711

7012

14.0

2234

3414

.717

8343

15.1

2474

9615

.444

6215

.730

1797

16.4

2578

017

.196

905

17.3

1510

5018

.071

239

20.7

6756

021

.024

8340

21.3

4432

321

.462

129

21.9

1505

7322

.616

3090

22.8

2811

3123

.513

8252

24.8

6398

725

.730

5645

26.8

1680

8527

.823

8047

30.2

1097

5230

.528

9823

31.0

1667

3531

.452

612

33.4

1258

4835

.512

0783

36.5

4142

036

.724

2069

38.9

2735

140

.817

6037

41.1

4820

741

.860

027

42.0

1055

7742

.210

8348

43.0

2990

7244

.116

1991

45.2

5949

745

.754

307

48.2

9757

750

.124

9497

50.4

1500

77

52.3

BH

LG

12

ES

LG

12

2422

190.

022

344

1.5

1489

525.

563

384

7.6

2044

739.

150

026

15.6

1693

18.7

2491

5623

.115

1393

29.1

2132

4530

.817

7111

33.2

1159

3141

.492

088

41.6

1144

4942

.021

2711

43.9

1506

1445

.117

2431

46.5

1423

9047

.429

2123

47.7

8944

647

.823

1007

2348

948

.011

1318

49.9

1692

6854

.612

6558

62.4

1158

2463

.056

513

66.4

2106

369

.111

1464

70.2

2325

2471

.415

6184

72.6

2493

476

.519

4546

79.2

9849

40.

091

906

1.2

6140

72.

071

486

2.6

3617

94.

867

963

7.9

3022

909.

460

082

12.8

1908

8213

.916

9864

14.8

4294

216

.673

771

17.3

2873

7419

.321

4998

20.7

4319

621

.516

9322

.714

4825

24.5

5576

826

.410

8146

28.3

7545

130

.016

3222

31.8

1771

1132

.915

6116

38.6

8258

538

.729

1565

40.2

3079

6940

.615

0614

41.1

5852

842

.719

5486

43.0

1990

7443

.411

1318

44.9

8768

345

.514

2065

46.6

2356

1047

.724

1791

48.1

3045

6648

.743

743

49.8

5276

654

.820

296

56.5

2375

1556

.824

7249

58.5

3072

0360

.613

1274

65.7

2744

3666

.628

3610

69.5

2151

5274

.516

1499

74.9

1137

8775

.219

6855

75.3

1479

6676

.923

6259

78.5

1945

4680

.094

756

80.9

3067

9582

.3

BH

LG

13

ES

LG

13

Tota

l aci

d12

1083770.0

17098411.79510014.010258515.216093019.320549524.221071424.710349227.65373029.018601829.517002029.913464731.219822531.92324932.421599332.69853333.119555033.719928034.222009534.45660836.119462137.211947138.57330450.614012759.417566569.7

16890978.016934682.022144183.6

1580720.0715571.82214782.73049953.32307113.71495894.52459204.61738308.02574939.023437914.5615.41772716.518608418.016361718.96696823.18680324.35732925.129502427.216705829.821075734.47383436.029868440.614927546.210170551.525601552.312948655.121702356.626354957.32794858.624000660.528790661.54532062.225608664.024085267.417255575.525108975.919963278.416934690.1

Fructose11

BH LG14 ES LG14

Glucose11, Total sugar11

Glucose11Total sugar11

SSC11Fructose11Glucose11Total sugar11

SSC11

188310.0

1128064.2

5419311.917712813.0

16333523.830511226.214765728.7

20885937.4

5537841.5

2055844.622459047.522656149.313757551.7

27491058.9

27113066.7

1818810.0578951.81836192.6

2733556.81772117.9

7148811.330120912.227477014.5

16519820.411385720.915037823.68975326.821871530.125260132.610955033.317242433.513888634.013398035.111823235.76555336.8

4688043.1

9817458.5

1221910.0

689981.3

1503783.2

2187156.3268357.1

1925258.4

20504510.6

13148911.73900712.1

27385014.65269215.120346815.8

10477318.9

12255620.3


1744720.0

1182143.0

1002098.1

18620530.713579732.4

27025834.9

20489938.216505639.528885739.9

5159547.5

16124550.5

544350.0825001.11357972.2693715.01796947.83006148.620489911.423164314.23090714.713084417.0

5968622.6

5159530.010745331.019942633.2

3455038.3

4725241.9

11507047.712084248.5

19426956.0

BH LG16 ES LG16

2261820.0

2717136.1956428.411240210.220807410.6

1567318.412476920.717122923.329233025.028017725.721461929.930627931.524023734.124294336.827234337.19993937.211027037.729611240.412150842.412631143.617190044.530392248.128137048.9

17038256.68647659.021828660.5

9344463.7

2968010.0664130.3827631.42532152.32660684.52427566.5976677.02952068.82146489.34334210.39400512.317007413.229851414.18400115.428072418.47014021.414314224.47940725.525068629.927539330.730596831.728448532.56145435.630392239.97688041.416741143.318179645.621089246.520514147.630784952.219835452.822901153.821411455.72637259.0

Fructose11

BH LG17 ES LG17

G/F13

G/F13

1100

710.

011

7817

11.2

1449

0511

.426

002

13.4

1122

7415

.722

4060

16.0

2322

9913

2897

16.1

2209

4716

.230

5189

16.3

2441

7619

.825

6759

20.3

2598

6221

.955

773

24.7

6690

126

.441

160

28.1

7401

529

.630

5862

30.6

2917

831

.120

3347

32.0

6512

132

.625

1393

37.0

1055

5537

.228

7065

40.6

1472

4742

.631

698

43.7

1695

1946

.250

182

48.3

2144

3252

.614

3572

55.3

3051

0257

.226

4763

59.0

1270

0961

.128

0521

61.9

7072

764

.122

2353

64.9

1459

9765

.525

4573

66.4

2132

5367

.325

2335

68.6

2022

2071

.424

9000

71.7

2798

2372

.914

2500

74.5

9958

286

.413

6385

90.4

2180

8990

.825

1446

93.7

2531

1595

.444

704

96.5

3281

298

.193

925

101.

3

Tota

l aci

d12

Mal

ic11

β r

atio

12

SS

C12

Mal

ic12

β r

atio

11,

12 Mal

ic11

, 12

β r

atio

11,

12To

tal a

cid1

219

4210

48.5

2207

0349

.220

7059

50.5

2330

8855

.224

6601

55.4

2989

4464

.221

5808

68.1

2018

9968

.516

6745

68.8

2805

2169

.317

3855

69.8

6436

570

.416

5308

70.6

2340

6671

.016

5256

71.3

2915

7071

.610

4930

74.1

1853

5476

.610

9294

77.6

2151

7479

.212

4767

79.5

3042

8479

.717

8287

81.4

1127

6683

.113

5426

84.4

2154

1085

.620

9262

86.2

1365

4390

.0

3305

592

.4

1267

080.

010

0608

0.5

1468

01.

213

9438

1.5

2339

702.

422

8018

3.4

8778

14.

788

874

6.0

2137

366.

622

2207

6.8

1167

977.

267

196

8.2

1811

199.

071

796

9.6

9534

410

.015

2337

12.5

2864

3713

.911

9919

14.3

2464

1515

.521

199

17.3

4292

18.9

1194

2321

.8

2187

3427

.517

5965

28.5

1187

8529

.7

1466

4833

.043

392

33.1

1798

833

.912

6531

35.1

2419

0037

.015

694

38.9

1721

5841

.696

891

41.9

2530

542

.111

410

43.0

3053

2943

.412

0619

45.0

BH

LG

18

ES

LG

18

Mal

ic12

Tota

l aci

d12

β r

atio

11

1848190.01423961.32829233.91114896.6902149.01605616.910462921.512314824.09481326.11708528.824245035.216615836.14037940.421269743.211384846.323487449.56727250.89746354.516336857.21875163.19046566.31755168.2

24495494.322650496.0

189013109.6245305110.0132225110.894756111.6190174112.1

262980.01079890.3861292.6163355.61000316.81758519.219579810.412005612.5

11799920.6

9749625.8

10462930.4

9168535.49481337.024766237.923780839.25810341.1

27839850.115931752.316254153.35265053.99273156.78998957.71394558.223487459.72715161.523880463.529286866.93722569.87737770.1

BH LG19 ES LG19

Documents

Figure S2. Genetic maps and QTL locations for ‘Beihong’ (BH, maternal parent) × and ‘E.S.7-11-49’ (ES, paternal parent). Markers are listed to the right