Skip to main content

Table 3 Summary of association and linkage mapping results related to bearing habit, budbreak date and female flowering dates

From: Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

Dataset

GWAS using FarmCPU model

QTLs detection using MIM method

SNP

Chr a

Physical position

Significance b

R2 c

Alleles/Effect d

Peak SNP e

LG f

Physical position

Confidence interval g

LOD h

P.E.V. i

d j

Bearing habit

 2019

AX-171108125

6

33,909,308

4.08E-09

30.8

C/T (0.7)

       

AX-171083929

8

3,102,647

1.47E-08

32.5

A/G (−0.8)

       

AX-171191765

11

20,831,267

2.98E-14

34.3

C/G (2.6)

       

Budbreak date

 1989–2016

AX-171509395

5

21,137,700

1.38E-10

9.0

C/T (4.1)

       

AX-171490851

7

37,022,231

5.76E-11

35.0

C/G (−4.9)

       

AX-170810238

8

23,687,589

7.78E-12

25.6

C/T (−4.1)

       

 2018–2019

AX-171179714

1

6,514,832

8.95E-19

30.6

G/T (−5.9)

AX-171180038

F1

177,178

2.8–10.8

11.9

23.7

5.2

AX-171557178

2

36,586,423

2.84E-14

27.3

A/T (−4.7)

AX-170771092

U1

5,814,444

0.0–2.8

29.5

44.3

−6.9

AX-171040881

4

591,186

3.70E-09

4.8

G/T (−3.2)

AX-171486072

U6

2,467,998

0.0–46.7

6.5

6.7

−2.6

AX-171522523

8

5,949,933

5.41E-09

3.2

A/T (−2.6)

AX-170627138

U11

26,651,484

0.0–30.2

4.7

4.7

−2.0

AX-171509630

15

1,111,543

9.92E-09

6.8

A/G (2.6)

AX-170901703

U12

19,779,190

39.0–67.4

6.8

7.7

2.8

      

AX-170818106

F14

9,871,222

3.6–50.0

6.0

11.2

3.5

 2018

AX-171520811

1

6,537,230

2.54E-10

29.1

A/G (4.3)

AX-171180038

F1

177,178

0.0–14.4

6.3

31.0

5.4

AX-171557178

2

36,586,423

4.31E-09

25.1

A/T (−3.4)

AX-170771092

U1

5,814,444

0.0–2.6

15.4

50.2

−7.0

AX-170682386

15

1,162,635

1.05E-08

18.8

A/G (3.6)

AX-170760959

U6

2,438,026

0.0–61.4

3.4

7.9

−2.6

AX-170691861

16

3,791,224

1.47E-10

25.5

C/T (−4.3)

       

 2019

AX-171557178

2

36,586,423

2.70E-11

26.2

A/T (−4.6)

AX-171180038

F1

177,178

0.0–21.4

5.6

23.9

5.4

AX-171489741

4

3,486,412

8.12E-10

26.2

C/G (−4.8)

AX-170771092

U1

5,814,444

0.0–10.3

11.1

34.8

−6.7

AX-171139350

6

31,522,110

6.17E-09

<  0.1

C/T (3.6)

AX-170901703

U12

19,779,190

27.8–76.4

3.7

9.2

3.3

AX-170938460

7

22,604,203

8.50E-13

26.8

A/G (5.0)

       

AX-171047138

10

36,604,822

7.89E-09

0.1

A/G (4.5)

       

AX-170691931

16

3,762,646

2.69E-10

24.0

A/G (−4.9)

       

Beginning female flowering date

 2018–2019

AX-170990138

1

9,298,520

1.56E-09

35.0

A/G (−3.4)

AX-171521263

F1

201,441

3.4–10.2

12.9

30.6

5.2

AX-170938895

7

23,018,189

6.62E-13

31.4

A/C (4.0)

AX-170771092

U1

5,814,444

<  0.5

35.1

46.5

−7.1

      

AX-170684860

U3

2,653,247

0.0–105.6

5.0

2.6

1.9

      

AX-171583903

U6

2,237,730

0.0–82.9

5.9

4.1

−2.1

      

AX-170825127

U11

25,463,971

0.0–8.3

9.3

6.5

−2.8

      

AX-170901663

U12

19,737,912

44.5–60.8

8.1

6.9

2.7

      

AX-170818106

F14

9,871,222

0.0–60.5

4.3

3.8

2.5

      

AX-170786852

U16

20,462,383

21.7–77.2

5.1

3.9

2.0

 2018

AX-170990138

1

9,298,520

1.79E-11

35.4

A/G (−4.2)

AX-171180038

F1

177,178

0.0–14.2

6.6

32.2

5.7

AX-171029453

4

4,123,643

7.38E-13

23.6

C/T (−4.9)

AX-170771092

U1

5,814,444

0.0–3.1

14.6

47.6

−7.2

 2019

AX-170990138

1

9,298,520

3.33E-13

34.8

A/G (−4.5)

AX-171180038

F1

177,178

0.0–16.4

5.6

21.6

4.7

AX-171029453

4

4,123,643

1.55E-10

25.6

C/T (−4.2)

AX-170771092

U1

5,814,444

0.0–2.3

23.0

44.4

−7.6

AX-170938895

7

23,018,189

2.99E-13

35.1

A/C (5.1)

AX-170684860

U3

2,653,247

0.0–23.8

5.3

5.8

2.7

AX-170586625

16

626,899

2.92E-12

2.6

C/T (−4.2)

AX-171569583

U6

12,329,274

26.3–62.5

7.5

8.5

−3.3

      

AX-170825127

U11

25,463,971

39.9–68.1

7.5

8.5

−3.2

      

AX-170901663

U12

19,737,912

0.0–3.6

7.5

8.7

3.3

Peak female flowering date

 1989–2016

AX-170990138

1

9,298,520

8.15E-13

39.6

A/G (−3.7)

       

AX-171596225

6

14,925,533

1.39E-09

26.7

A/G (3.0)

       

AX-171029018

7

48,197,343

3.80E-09

0.1

A/C (2.2)

       

AX-171161427

7

37,022,706

9.52E-09

35.9

C/T (3.0)

       

AX-171093716

10

23,540,554

5.39E-09

8.3

A/G (−4.6)

       

AX-171553780

10

6,443,284

1.65E-08

0.4

A/T (2.2)

       

AX-171161986

13

3,292,458

2.11E-08

30.9

A/G (2.8)

       

 2018–2019

AX-170990138

1

9,298,520

4.75E-11

36.2

A/G (−4.5)

AX-171180038

F1

177,178

2.6–11.2

9.7

22.3

5.0

AX-171204022

7

25,355,784

6.12E-09

31.2

A/G (−3.6)

AX-170771092

U1

5,814,444

0.0–1.9

42.5

49.0

−8.3

      

AX-170869355

F2

35,198,358

18.9–67.9

5.2

7.4

−3.2

      

AX-171121327

U3

1,942,419

0.0–33.7

6.4

4.3

2.3

      

AX-171204628

U9

21,282,336

32.9–57.3

5.9

3.7

2.3

      

AX-170627138

U11

26,651,484

0.0–7.3

13.1

7.7

−3.5

      

AX-170901663

U12

19,737,912

37.3–65.2

10.0

6.9

3.0

 2018

AX-170990138

1

9,298,520

1.41E-08

35.4

A/G (−3.6)

AX-171521263

F1

201,441

0.0–22.0

4.5

23.4

5.4

AX-170975750

6

22,755,843

1.39E-08

<  0.1

A/G (−3.8)

AX-170771092

U1

5,814,444

0.0–4.9

13.7

45.5

−7.8

AX-170676955

9

8,265,700

3.56E-09

6.7

A/G (−3.3)

AX-170697456

U4

5,261,727

0.0–49.2

3.3

8.5

3.0

      

AX-170787652

U15

151,849

0.0–33.6

3.8

10.0

−3.5

 2019

AX-170990138

1

9,298,520

2.70E-11

35.6

A/G (−4.4)

AX-171180038

F1

177,178

0.0–25.2

4.5

18.2

4.5

AX-170938895

7

23,018,189

6.82E-15

36.7

A/C (5.1)

AX-170771092

U1

5,814,444

0.0–2.0

24.0

46.4

−7.7

      

AX-170684716

U3

2,526,842

0.0–50.7

4.4

4.5

2.3

      

AX-171569583

U6

12,329,274

0.0–98.6

3.9

3.8

−2.2

      

AX-171222942

U8

5,077,987

0.0–98.8

3.8

3.8

2.1

      

AX-171204628

U9

21,282,336

37.2–57.3

4.5

5.1

2.5

      

AX-170582801

U11

26,090,506

0.0–7.3

9.4

11.0

−3.7

      

AX-171033431

U12

17,150,374

34.4–70.9

5.1

5.3

2.6

      

AX-170581901

U16

17,340,045

2.2–66.1

4.0

4.0

2.2

End female flowering date

 2018–2019

AX-170990138

1

9,298,520

8.81E-11

39.3

A/G (−4.1)

AX-171180038

F1

177,178

2.9–10.5

10.8

24.8

5.2

AX-171103669

1

3,411,327

8.46E-10

28.0

A/C (3.5)

AX-170771092

U1

5,814,444

<  0.5

32.9

49.9

−8.2

AX-171199539

15

16,085,753

2.06E-10

<  0.1

A/G (−3.4)

AX-170868251

F2

34,498,992

32.8–67.9

7.2

13.7

4.0

      

AX-171121327

U3

1,942,419

0.0–41.2

6.3

3.6

2.7

      

AX-170620438

U5

18,147,969

0.0–78.7

5.4

2.9

2.3

      

AX-171214747

U9

18,177,182

14.3–57.3

5.0

5.0

2.5

      

AX-170825127

U11

25,463,971

0.0–13.8

6.6

3.4

−2.7

      

AX-170818106

F14

9,871,222

0.0–56.8

5.8

7.7

3.5

 2018

AX-171572440

9

20,815,377

3.24E-09

1.3

A/G (−2.9)

AX-171521263

F1

201,441

2.6–9.8

6.6

25.4

6.4

      

AX-170771092

U1

5,814,444

0.0–7.1

13.0

48.0

−8.7

      

AX-170867988

F2

34,288,275

18.6–67.9

4.0

13.8

−4.4

 2019

AX-170990138

1

9,298,520

6.75E-11

38.1

A/G (−4.3)

AX-170771092

U1

5,814,444

0.0–3.6

19.8

40.1

−7.6

AX-171029453

4

4,123,643

1.12E-10

27.6

C/T (−4.9)

AX-171210974

U3

2,714,686

0.0–14.7

6.5

8.5

3.4

AX-170938854

7

22,982,368

1.14E-12

37.0

C/T (4.5)

AX-170682524

U5

18,023,534

0.0–14.0

6.7

8.7

3.5

AX-170766461

8

27,866,613

7.85E-09

<  0.1

A/C (−5.3)

AX-170626929

U11

26,817,955

2.3–12.5

7.0

9.1

−3.6

AX-170860236

14

9,448,288

1.25E-10

<  0.1

G/T (4.3)

AX-170901663

U12

19,737,912

13.8–84.9

3.9

4.7

2.5

AX-170586625

16

626,899

1.39E-08

1.8

C/T (−3.1)

       
  1. a Chr abbreviation for Chromosome
  2. b For GWAS panel, the significance value indicated is the p-value, which is significant if lower than the False Discovery Rate
  3. c For GWAS panel, R2 is the percentage explained variance corrected for genome-wide background
  4. d For GWAS panel, the allelic effect is the difference in mean of measured trait between genotypes with one or other allele
  5. The sign is with respect to the allele that is first mentioned
  6. e For F1 progeny using QTLs detection, the indicated SNP is the peak SNP inside the QTL interval
  7. f LG, abbreviation for Linkage Group with F and U for ‘Franquette’ and ‘UK 6–2’ parental maps respectively
  8. g For F1 progeny using QTLs detection, the position in cM indicated in brackets is the 99.9% confidence interval of the QTL
  9. h For F1 progeny using QTLs detection, the significance value indicated is the LOD score (LOD = logarithm of the odds ratio)
  10. i For F1 progeny using QTLs detection, P.E.V. is for percentage explained variance
  11. j For F1 progeny using QTLs detection, d is the estimated substitution effect of the QTL
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us