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Table 1 Loci for grain yield and related traits in the diverse panel identified by both SNP-GWAS and Haplotype-GWAS and comparisons with previous studies

From: Genetic architecture of grain yield in bread wheat based on genome-wide association studies

Trait

Chr

Physical position (Mb)a

SNP-GWAS

Haplotype-GWAS

QTL/marker/genee

Markerb

Environment

R2 (%)c

Haplotyped

Environment

R2 (%)c

GY

1A

402.9–407.4

AX_110387060

E3/E4/E5/E6/B

6.9–15.5

H1290

E4/E5/E6/B

10.1–19.8

 

1A

434.0–439.9

AX_110418502

E4/E5/E6/B

6.9–17.7

H1313

E4/E5/E6/B

9.3–19.2

QYld.abrii-1A1.2 [23]

1B

539.6–542.6

AX_110508372

E4/E5/E6/B

7.1–12.8

H3650

E4/E5/E6/B

9.3–21.5

 

1B

673.6–675.7

AX_109820171

E3/E5/E6/B

7.6–14.3

H4268

E4/E5/E6/B

10.7–22.6

 

2A

30.3–31.9

AX_94546135

E4/E6/B

7.1–11.6

H5187

E4/E6/B

9.3–17.6

 

2B

106.1–108.9

AX_111210290

E2/E4/B

7.0–12.5

H7877

E1/E4/E5/E6/B

9.1–20.8

 

2D

643.1–650.8

AX_109941480

E4/E5/E6/B

7.0–12.3

H10738

E4/E5/E6/B

9.3–14.6

 

3A

721.3–724.0

AX_111492146

E5/E6/B

7.1–11.7

H11976

E3/E5/E6/B

9.1–18.2

 

3B

20.5–22.0

AX_109881378

E4/E5/E6/B

7.4–10.7

H12363

E4/E5/E6/B

9.3–17.6

 

3D

570.8–572.8

AX_95257733

E3/E4/E6/B

7.1–9.9

H15950

E1/E4/E4/E6/B

9.2–16.6

 

5A

570.2–570.3

AX_110523824

E3/E4/B

7.8–14.8

H19931

E1/E3/E4/E5/E6/B

10.0–20.1

barc151 [35]

5B

587.1–588.2

AX_110995303

E3/E6/B

7.1–10.2

H22191

E1/E2/E3/E5/E6/B

9.4–15.7

 

SN

5B

530.8–534.0

IWB56499

E1/E3/E4/B

7.1–11.9

H21909

E2/E3/E4/B

9.1–12.2

 

5B

696.3–700.9

AX_109936345

E2/E4/B

7.1–12.1

H22717

E1/E2/E3/E4/B

9.1–15.3

 

6B

605.8–607.1

IWB51629

E1/E3/B

7.5–8.1

H26344

E1/E2/E3/E4/B

9.5–16.6

 

6B

696.6–697.6

AX_95260682

E1/E3/B

7.4–9.3

H26799

E1/E2/E3/B

10.5–13.6

 

6D

468.8–471.0

AX_110652999

E2/E3/B

7.2–17.1

H27181

E1/E2/E3/E4/B

9.5–18.8

 

7D

75.9–76.9

AX_111490489

E2/E3/B

7.7–9.0

H31325

E1/E2/E3/E4/B

9.8–23.3

 

KNS

1A

36.8–42.5

AX_111579941

E1/E2/E3/E5/E6/B

7.1–11.9

H322

E1/E2/E3/E4/E5/E6/B

9.2–15.8

QGns.wa -1AS.e1 [43]

1A

497.5–498.1

AX_108737858

E1/E2/E3/E4/E5/E6/B

7.1–12.7

H1479

E1/E5/E6/B

9.3–12.5

QGnu.abrii-1A1.1 [23]

2A

117.2–117.3

IWB45503

E3/E4/E5/E6

7.2–8.6

H5556

E3/E4/E5/B

9.5–11.5

QGps.ccsu-2A.3 [34]; wmc63 [41]; gwm122 [42]

2D

633.2–634.5

IWB57054

E1/E2/E3/E4/E5/E6/B

7.4–17.7

H10675

E1/E3/E6/B

9.3–15.4

 

3A

36.8–37.2

AX_110657474

E1/E2/E3/E5/E6/B

7.4–11.1

H11017

E1/E2/E3/E5/E6/B

9.7–14.5

 

3A

719.3–725.8

AX_108992368

E2/E3/E4/E5/E6/B

7.1–12.4

H11953

E3/E4/E5/E6/B

9.1–15.1

QGnu.abrii-3A [23]; QKNS.caas-3AL [40]

5B

416.4–418.0

AX_109538915

E1/E4/E5/E6/B

7.1–10.5

H21421

E1/E4/E6/B

9.3–14.6

gwm213 [41]

5B

489.3–492.9

AX_109537496

E1/E2/E3/E4/E6/B

7.4–10.9

H21713

E1/E2/E3/E4/E5/E6/B

9.5–14.8

 

7A

49.1–50.0

AX_89571435

E2/E3/E4/E5/E6/B

7.2–12.6

H27643

E1/E3/E4/E5/E6/B

9.3–13.9

 

TKW

1B

658.7–662.5

AX_111147652

E1/E2/E4/E6/B

7.1–10.2

H4181

E1/E2/E3/E4/E5/E6/B

9.2–15.4

QTgw.cau-1B, QGl.cau-1B.1 [51]

2A

760.6–760.7

AX_111579921

E2/E4/E5/B

7.0–8.5

H7248

E1/E2/E3/E4/E5/E6/B

9.3–18.1

 

2B

106.0–107.1

IWB50438

E1/E2/E4

6.7–9.1

H7872

E1/E2/E3/E4/E5/E6/B

9.3–27.0

 

4B

40.4–44.9

AX_110713957

E1/E2/E3/E4/E5/E6/B

7.1–12.7

H17589

E1/E2/E3/E4/E5/E6/B

9.4–22.0

QTgw-4B1 [48]

4B

159.2–163.0

AX_109427900

E1/E2/E6/B

7.1–9.2

H17841

E1/E2/E3/E4/E5/E6/B

9.4–25.1

 

4B

670.4–670.5

IWB47765

E1/E5/E6/B

6.9–9.2

H18552

E1/E2/E3/E4/E5/E6/B

10.2–17.9

 

5A

706.2–708.0

AX_110958315

E1/E3/E4/E6/B

8.2–13.0

H20367

E1/E2/E3/E4/E5/E6/B

9.2–19.8

QTKW.caas-5AL.1 [40]

5B

692.7–696.4

AX_108769612

E3/E4/E5/E6/B

7.2–9.9

H22684

E1/E2/E3/E4/E5/E6/B

9.3–15.8

Excalibur_c23801_115 [27]; wsnp_Ex_c16045_24471413 [45]; Ku_c7546_861 [46]

6B

450.6–454.1

AX_110368497

E2/E3/E5/E6/B

6.8–8.3

H25900

E1/E2/E3/E4/E6/B

12.2–14.1

 

6B

675.4–677.5

AX_109917592

E1/E3/E6/B

7.2–9.7

H26662

E1/E3/E4/E5/E6/B

15.8–20.6

QTKW.caas-6BL [17]

6D

461.4–468.0

AX_109481324

E2/E3/E6

6.8–8.3

H27181

E1/E2/E3/E4/E5/E6/B

9.3–16.5

 

7D

63.0–69.7

AX_109927697

E2/E3/E4/E5/E6/B

7.1–12.3

H31315

E1/E2/E3/E4/E5/E6/B

10.4–17.8

QKL.caas-7DS [17]

QGw.ccsu-7D.1 [44]

KL

1B

26.9–30.8

AX_110032293

E3/E4/E5/E6/B

7.1–12.7

H2345

E2/E3/E4/E5/E6/B

9.2–13.5

 

1B

642.6–642.7

AX_108849700

E1/E2/E3/E5/E6/B

7.0–9.6

H4081

E2/E5/E6/B

9.2–12.0

QKL.caas-1BL [17]; tplb0043a07_1411 [45]

2A

740.4–745.0

IWB32119

E1/E2/E3/E4/E5/E6/B

7.2–14.2

H7042

E1/E2/E3/E4/E5/E6/B

9.2–13.8

TaFlo2-A1 [49]

3B

782.9–783.0

AX_111116403

E1/E2/E5/E6/B

7.2–9.9

H15574

E2/E5/E6/B

9.3–11.9

 

5B

52.9–55.2

IWB50649

E1/E2/E3/E4/E5/E6/B

7.2–11.7

H20632

E3/E5/E6/B

10.5–12.6

QTgw.abrii-5B1.1 [23]; QTgw.cau-5B, QGl.cau-5B.2 [47]

5D

475.8–476.3

AX_111122970

E1/E2/E3/E4/E6/B

7.2–12.4

H22993

E1/E2/E3/E4/E5/E6/B

9.4–15.4

 

KW

1A

9.6–12.0

IWB6999

E2/E3/E4/B

7.1–9.3

H46

E1/E2/E3/E4/E5/E6/B

9.1–17.5

QGw.ccsu-1A.1 [44]

1A

532.6–533.4

IWB7676

E2/E3/E4/E6/B

7.0–10.4

H1679

E1/E2/E3/E4/E5/E6/B

9.2–16.3

QTgw.cau-1A [47]

2A

27.3–29.9

AX_111037158

E1/E3/E4/E5/E6

7.2–9.6

H5176

E1/E2/E3/E4/E5/E6/B

9.4–20.2

wmc177 [42]

2A

758.6–760.7

AX_111579921

E2/E4/E5/E6

7.1–10.9

H7248

E2/E3/E4/E5/E6/B

9.2–22.4

 

2B

105.8–108.7

AX_111634754

E1/E2/E3/E4/E5/E6/B

7.0–15.0

H7877

E1/E2/E3/E4/E5/E6/B

9.1–36.7

 

2B

415.0–418.9

AX_111819405

E2/E3/E4/E5/E6/B

7.0–10.6

H8418

E1/E2/E3/E4/E5/E6/B

9.4–16.3

 

3A

714.4–716.3

AX_111047166

E2/E3/E4/E5/B

7.0–10.9

H11918

E1/E2/E3/E4/E5/E6/B

9.1–27.2

QTgw-3A1 [48]

3D

570.2–575.5

IWB17930

E2/E3/E4/E5/E6/B

6.8–10.3

H15950

E1/E2/E3/E4/E5/E6/B

9.2–21.4

 

4A

670.0–676.0

AX_110046841

E2/E3/E4/E6/B

7.0–10.3

H17106

E1/E2/E3/E4/E6/B

12.1–19.1

QTKW.caas-4AL [40]; QTgw.cau-4A.2, QGl.cau-4A.2 [47]

4B

670.4–672.9

IWB47765

E1/E3/E6/B

7.0–12.4

H18552

E2/E3/E4/E5/E6/B

11.5–18.8

 

5A

569.2–573.0

AX_110523824

E3/E4/E6/B

7.0–11.7

H19921

E2/E3/E4/E6/B

9.2–20.9

QGl.cau-5A.1 [47]

5A

702.1–708.1

AX_110958315

E3/E4/E5/E6/B

7.4–13.3

H20333

E2/E3/E4/E5/E6/B

9.4–22.2

QTKW.caas-5AL.1 [40]

5B

520.8–520.9

IWB20926

E1/E2/E3/E6/B

7.2–10.1

H21840

E1/E2/E3/E4/E5/E6/B

9.2–19.4

QTgw.abrii-5B1.2 [23]

6B

706.9–709.2

AX_109820966

E3/E4/E5/E6/B

6.9–10.3

H26817

E1/E2/E3/E4/E5/E6/B

9.4–17.9

 

7D

58.5–66.5

AX_109396082

E1/E2/E3/E4/E5/E6/B

7.0–12.5

H31312

E3/E4/E6/B

9.5–20.0

QKL.caas-7DS [17]

QGw.ccsu-7D.1 [44]

SL

2B

44.6–47.3

AX_109985540

E1/E2/E3/E4/E5/B

7.0–14.3

H7643

E1/E3/E4/E5/B

9.2–14.0

BS00022060_51 [27]

5A

510.1–510.3

AX_109367907

E1/E3/E4/E5/E6/B

7.4–12.8

H19589

E4/E5/B

9.0–11.8

QSL.caas-5AL.2 [17]

5A

534.9–540.1

AX_110919697

E1/E2/E3/E4/E5/E6/B

6.7–11.8

H19737

E1/E2/E3/E4/B

9.3–14.9

 

5A

568.3–574.3

AX_110523824

E1/E2/E3/E4/E5/E6/B

7.3–13.0

H19954

E2/E5/E6/B

9.8–10.3

QSl-5A1 [48]

5B

398.2–398.3

AX_94562344

E3/E4/E5/E6/B

8.0–11.0

H21291

E2/E3/E5/E6/B

9.2–15.1

 

5B

590.5–591.1

AX_110971192

E1/E3/E4/E6/B

7.4–10.3

H22208

E1/E3/E4/E6/B

9.1–12.6

 

7B

723.9–727.6

IWB71567

E1/E2/E3/E4/E5/E6/B

7.1–13.8

H30972

E1/E2/E3/E4/E6/B

9.1–19.3

 

7D

621.9–630.4

AX_110645784

E1/E2/E3/E4/E5/E6/B

7.6–15.0

H31712

E1/E2/B

10.7–20.0

 

SDW

1A

568.5–573.5

AX_95255804

E3/E4/E5/E6/B

7.2–9.7

H2018

E3/E4/E6/B

9.1–12.6

 

3A

721.3–725.8

IWA94

E3/E4/E5/E6/B

7.1–19.0

H11992

E3/E4/E5/E6/B

9.5–15.2

 

4B

89.5–95.1

IWB35533

E3/E4/E6/B

7.1–10.7

H17675

E4/E5/B

9.3–11.4

 

5B

473.9–477.8

AX_111183518

E3/E5/E6/B

7.0–16.3

H21628

E3/E4/E5/E6/B

9.7–18.5

 

5B

698.0–698.5

AX_111051286

E3/E4/E6/B

7.1–10.6

H22718

E3/E4/B

9.9–11.2

 

HD

2A

27.3–27.4

AX_111037158

E1/E2/E3/E4/E5/B

7.5–12.2

H5170

E1/E2/E3/E4/E5/E6/B

11.3–15.7

 

2A

704.8–710.1

AX_89674107

E1/E2/E3/E4/E6/B

6.8–8.6

H6769

E1/E2/E6

9.3–13.9

 

2A

755.8–757.0

AX_109964711

E1/E2/E3/E4/E6/B

6.8–9.4

H7248

E1/E2/E4/E6

9.2–13.8

wPt-1499 [51]

2B

106.0–108.7

AX_110624209

E1/E2/E3/E4/E5/E6/B

6.6–10.7

H7877

E1/E2/E4/E6/B

9.4–22.0

 

5B

520.1–524.4

IWB20926

E1/E2/E4/E6/B

6.6–10.7

H21844

E1/E2/E4/E6

9.1–15.9

wPt-1409 [51]

7A

511.5–517.4

AX_109921812

E1/E2/E3/E4/E5/B

6.9–9.4

H28667

E1/E3/E5/B

9.2–14.2

 

7A

556.2–561.0

AX_111660137

E1/E2/E3/E4/E5/B

6.7–12.3

H28779

E1/E2/E4/E5/E6

9.4–12.9

wPt-4796 [51]

7B

701.0–703.7

IWB75191

E1/E2/E3/E4/E5/E6/B

6.6–13.1

H30856

E1/E2/E3/E4/E5/E6/B

9.3–16.3

 

PH

1A

434.1–440.2

AX_109449226

E1/E2/E3/E4/E5/E6/B

6.9–13.1

H1306

E1/E2/E3/E4/E5/E6/B

9.3–16.1

 

1B

539.6–542.6

AX_94564150

E1/E2/E4/E5/E6/B

7.0–21.1

H3651

E1/E2/E3/E4/E5/E6/B

10.4–22.8

 

1B

673.9–675.7

AX_109820171

E1/E2/E4/E5/E6/B

6.8–30.8

H4268

E1/E2/E3/E4/E5/E6/B

9.5–38.0

 

2A

30.9–32.0

AX_110988136

E1/E2/E4/E5/B

7.0–11.3

H5187

E1/E2/E3/E4/E5/B

11.4–19.8

QUIL.caas-2AS.1 [17]

2A

715.3–721.6

AX_94494373

E1/E2/E4/E6/B

6.7–10.5

H6911

E1/E2/E3/E4/E5/E6/B

10.9–16.5

QPH.caas-2AL, QUIL.caas-2AL [17]

3A

716.5–721.3

AX_111577195

E1/E2/E4/E5/E6/B

6.9–14.8

H11943

E1/E2/E3/E4/E5/E6/B

9.2–18.4

barc1113 [19]

3B

116.1–120.4

AX_109413472

E1/E2/E3/E4/E5/E6/B

6.8–12.8

H12783

E1/E2/E3/E4/E5/E6/B

9.0–17.4

gwm566 [19]

4D

16.6–19.7

AX_108916749

E1/E2/E4/E5/E6/B

6.7–14.5

H18598

E1/E2/E3/E4/E5/E6/B

10.2–16.1

QPH.caas-4DS, QUIL.caas-4DS [17]; Rht-D1b [52]

5A

669.2–671.2

AX_110446653

E1/E2/E3/E4/E5/E6/B

6.9–14.7

H20207

E1/E2/E3/E4/E5/E6/B

10.8–17.5

 

5A

708.4–708.8

IWA2646

E2/E3/E5/B

6.7–8.0

H20356

E1/E2/E3/E4/E5/E6/B

9.4–18.0

QPh.hwwgr5AL [53]

5B

576.3–580.9

AX_108921249

E1/E2/E4/E5/B

7.0–13.3

H22142

E1/E2/E3/E4/E5/E6/B

12.2–20.4

 

6B

1.4–4.9

AX_110482029

E1/E2/E4/E5/B

7.0–18.1

H24673

E1/E2/E3/E4/E5/E6/B

9.4–25.9

 

6B

42.7–42.8

AX_110671479

E1/E2/E4/B

7.2–10.8

H24862

E1/E2/E3/E4/E5/E6/B

9.4–19.0

 

7A

556.2–560.9

AX_109384874

E1/E2/E3/E5/E6/B

6.9–15.1

H28784

E1/E2/E3/E4/E5/E6/B

10.5–18.6

 

UIL

1A

142.6–148.6

AX_109901254

E1/E5/E6/B

7.5–11.1

H608

E1/E2/E5/E6/B

9.2–17.4

 

1A

434.4–440.2

AX_109449226

E1/E2/E5/E6/B

6.9–12.9

H1306

E1/E2/E5/E6/B

9.1–16.3

 

1B

539.6–542.6

AX_94564150

E1/E2/E5/B

6.8–16.1

H3650

E1/E2/E5/B

9.6–17.9

 

1B

674.8–675.7

AX_109820171

E1/E2/E5/B

8.4–16.4

H4239

E1/E2/E5/E6/B

9.2–24.0

 

3A

721.3–723.7

AX_111610555

E1/E2/E5/B

7.3–9.7

H11922

E1/E2/E5/E6/B

9.1–17.3

barc1113 [19]

5A

665.6–671.2

IWA5929

E1/E2/E5/E6/B

7.1–11.3

H20205

E1/E2/E5/E6/B

9.6–18.5

 

6B

1.4–4.9

AX_109526332

E1/E2/E5/B

7.0–11.4

H24673

E1/E2/E5/E6/B

9.3–24.8

 

6B

42.7–46.9

IWB12568

E1/E2/E5/E6/B

7.1–9.5

H24865

E1/E2/E5/E6/B

9.8–20.4

 

6B

563.3–567.8

AX_86165710

E1/E2/E5/E6/B

6.7–10.5

H26273

E1/E2/E5/E6/B

9.3–15.6

 

6D

396.5–403.7

AX_109331000

E1/E2/E5/E6/B

7.0–12.6

H27113

E1/E2/E5/E6/B

15.3–19.0

barc96 [19]

6D

460.7–465.0

IWB2743

E1/E2/E5

7.2–10.5

H27272

E1/E2/E5/E6/B

9.4–14.1

 

7B

630.6–632.7

AX_109492373

E1/E2/E5/B

7.1–12.3

H30631

E1/E2/E5/E6/B

9.9–22.1

 

FLL

1A

8.3–11.0

AX_109621606

E3/E4/E5/E6/B

7.1–16.9

H99

E3/E4/E5/E6/B

9.0–20.8

 

2A

2.5–7.8

AX_109880304

E2/E3/E5/E6/B

7.4–19.6

H5121

E2/E3/E4/E5/E6/B

10.9–29.1

 

2A

87.8–87.9

AX_95085564

E4/E5/E6/B

8.6–12.7

H5461

E2/E3/E5/E6/B

9.6–17.5

 

2B

46.4–50.4

AX_111027654

E2/E6/B

7.0–19.6

H7632

E2/E3/E4/E5/E6/B

9.4–25.5

QFLL-2B [57]

3A

716.9–722.5

AX_108908243

E3/E4/E6

7.2–9.7

H11976

E3/E4/E5/E6/B

9.4–22.7

 

5A

556.6–559.7

IWB4576

E3/E4/E6/B

6.9–9.6

H19845

E2/E3/E4/E5/E6/B

9.6–16.2

QFlw.cau-5A.2, QFlan.cau-5A.3 [56]

6B

704.9–708.7

AX_109459603

E5/E6/B

8.8–9.6

H26801

E2/E3/E4/E5/E6/B

9.5–22.0

 

6D

455.5–462.2

AX_110876641

E3/E6/B

7.6–8.8

H27138

E2/E3/E4/E5/E6/B

9.8–18.0

QFll.cau-6D [56]

FLW

1A

440.4–445.5

AX_111540798

E2/E3/E4/E6/B

7.0–11.4

H1318

E2/E3/E4/B

9.1–17.3

 

3B

23.9–24.4

AX_111655083

E4/E6/B

7.3–9.7

H12389

E2/E3/E4/E5/E6/B

9.2–19.7

 

5B

531.5–533.5

IWB41225

E2/E6/B

6.9–7.9

H21876

E2/E3/E4/E5/E6/B

9.1–14.7

 

5B

557.1–559.4

AX_109519234

E2/E3/E4/E5/B

7.0–9.0

H22030

E2/E3/E4/E5/E6/B

9.3–16.7

 

6B

461.4–465.5

AX_108771909

E2/E3/E5/B

7.0–9.9

H25955

E2/E3/E4/E5/E6/B

9.6–12.2

QFlw.cau-6B [56]

  1. a The physical positions of SNP markers based on wheat (Chinese Spring) genome sequences from the International Wheat Genome Sequencing Consortium
  2. b Representative markers
  3. c Percentage of phenotypic variance explained
  4. d Representative haplotypes
  5. e The previously reported QTL, markers or genes near the loci identified in the present study
  6. GY grain yield, SN spike number per square meter, KNS kernel number per spike, TKW thousand-kernel weight, KL kernel length, KW kernel width, SL spike length, SDW spike dry weight, HD heading date, PH plant height, UIL uppermost internode length, FLL flag leaf length, FLW flag leaf width; E1: 2012–2013 Anyang; E2: 2012–2013 Suixi; E3: 2013–2014 Anyang; E4: 2013–2014 Suixi; E5: 2014–2015 Anyang; E6: 2014–2015 Shijiazhuang; B: Best linear unbiased estimation