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Table 1 Peak SNP, beneficial allele and candidate genes associated with unsaturated FA identified by GWAS

From: Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions

Trait

Year

Chr.

Peak SNP

Peak SNP position

Number of significant SNPs

-log (P-value) of Peak SNP

R2 (%) of Peak SNP

Allele 1

Allele 2

Average trait value of accessions with allele 1

Average trait value of accessions with allele 2

Average value of population

IDs of FA related genes

Known QTL

Reference

Oleic acid

2013

1

rs18996061

18,996,061

1

4.05

16.08

T

A

20.28

31.46

20.42

   

2013

3

rs6779592

6,779,592

1

4.58

17.65

A

C

20.31

29.22

20.42

   

2013

6

rs10058820

10,058,820

1

3.87

15.53

G

C

20.25

25.68

20.42

   

2013

8

rs35562739

35,562,739

1

3.96

15.81

A

T

20.26

28.49

20.42

   

2013

10

rs30082069

30,082,069

1

4.12

16.27

C

T

20.23

23.24

20.42

   

2013

14

rs39135305

39,135,305

1

3.73

15.11

C

T

20.26

26.03

20.42

   

2013

15

rs259146

259,146

2

4.77

18.25

A

T

20.23

23.61

20.42

   

2013

15

rs18512918

18,512,918

1

4.43

17.19

T

C

20.20

24.44

20.42

   

2013

15

rs47976104

47,976,104

1

3.80

15.34

G

T

20.21

23.96

20.42

   

2013

16

rs6724381

6,724,381

1

4.01

15.95

T

C

20.33

35.33

20.42

   

2013

16

rs36081420

36,081,420

1

5.80

21.44

T

G

18.79

20.77

20.42

Glyma.16G200200Glyma.16G003500

  

2013

17

rs7339569

7,339,569

1

4.12

16.27

C

A

20.26

27.85

20.42

   

2013

17

rs10758737

10,758,737

1

3.93

15.71

G

T

20.25

27.28

20.42

   

2013

20

rs47531251

47,531,251

1

4.67

17.92

G

A

20.26

28.44

20.42

Glyma.20G158300Glyma.20G245500

  

2014

3

rs35644650

35,644,650

2

5.01

23.46

G

T

21.21

25.89

21.42

   

2014

6

rs8371282

8,371,282

1

4.24

21.62

G

T

21.31

24.07

21.42

   

2014

7

rs18395919

18,395,919

1

4.13

21.38

G

T

21.27

24.73

21.42

Glyma.07G151300

  

2014

8

rs20308530

20,308,530

3

5.14

23.76

A

C

21.20

25.89

21.42

Glyma.08G233200

  

2014

9

rs34018579

34,018,579

5

3.77

20.56

C

A

21.19

24.22

21.42

   

2014

15

rs33757180

33,757,180

1

3.68

20.34

C

A

21.28

24.35

21.42

   

2014

16

rs33751855

33,751,855

1

3.63

20.24

A

G

21.36

26.92

21.42

   

2014

18

rs5683686

5,683,686

1

3.60

20.16

G

T

21.28

27.54

21.42

Glyma.18G062000

Ole 3–2

 

2014

19

rs31881460

31,881,460

1

4.45

22.11

G

T

21.16

23.78

21.42

 

Ole 2–2

 

2015

1

rs50012108

50,012,108

1

4.39

11.38

T

A

19.05

22.51

19.19

   

2015

3

rs35817332

35,817,332

2

3.76

9.71

G

A

18.95

22.22

19.19

   

2015

4

rs29355727

29,355,727

1

5.66

14.79

C

T

18.95

27.66

19.19

   

2015

6

rs50110801

50,110,801

2

4.05

10.45

T

A

18.96

21.08

19.19

   

2015

7

rs3937684

3,937,684

1

3.64

9.40

G

T

19.07

25.48

19.19

Glyma.07G046200

Ole 7–1

 

2015

11

rs24645193

24,645,193

1

4.16

10.75

G

T

19.07

21.62

19.19

   

2015

12

rs32443263

32,443,263

1

3.96

10.23

G

T

18.94

22.04

19.19

   

2015

13

rs16802809

16,802,809

2

4.32

11.17

T

C

18.88

21.57

19.19

Glyma.13G068600Glyma.13G069100

  

2015

15

rs1748955

1,748,955

1

4.58

11.86

C

A

19.01

26.82

19.19

 

Ole 1–4

 

2015

16

rs36081420

36,081,420

2

6.29

16.53

T

C

19.10

34.81

19.19

Glyma.16G200200Glyma.16G003500

  

2015

17

rs35024325

35,024,325

2

3.92

10.12

C

A

18.93

22.96

19.19

   

2015

18

rs12585602

12,585,602

1

4.09

10.56

T

A

19.04

28.45

19.19

   

2015

19

rs43329219

43,329,219

1

4.04

10.46

G

A

18.90

22.40

19.19

 

Ole 2–2

 

2015

20

rs47531251

47,531,251

4

4.84

12.56

G

A

18.96

27.37

19.19

Glyma.20G158300Glyma.20G245500

  

Linoleic acid

2013

4

rs29355727

29,355,727

1

4.24

20.13

T

C

46.08

55.59

55.34

  

Reinprecht et al. 2006

2013

13

rs20383965

20,383,965

1

4.40

20.61

T

G

48.18

55.57

55.34

  

Hyten et al. 2004

2013

16

rs4446239

4,446,239

1

3.88

19.13

T

G

52.43

55.64

55.34

   

2013

17

rs28191708

28,191,708

1

4.12

19.79

C

T

54.12

55.81

55.34

   

2013

17

rs28979581

28,979,581

1

3.68

18.55

G

T

54.18

55.80

55.34

   

2013

17

rs34633822

34,633,822

1

4.52

20.96

C

T

52.36

55.70

55.34

   

2013

17

rs35259287

35,259,287

1

3.85

19.02

T

C

51.76

55.53

55.34

  

Kim et al. 2010

2013

18

rs21573804

21,573,804

1

3.90

19.18

A

T

52.35

55.58

55.34

   

2013

19

rs577646

577,646

1

3.90

19.18

A

G

54.00

55.63

55.34

   

2013

20

rs1608443

1,608,443

1

3.81

18.90

G

C

54.76

57.56

55.34

   

2013

16

rs36081420

36,081,420

1

3.67

18.52

C

T

43.10

55.41

55.34

Glyma.16G200200Glyma.16G003500

 

Diers and Shoemaker 1992

2013

20

rs47531251

47,531,251

1

4.19

20.01

A

G

50.96

55.51

55.34

Glyma.20G158300Glyma.20G245500

  

2014

1

rs49504957

49,504,957

1

3.90

19.01

G

T

54.09

55.35

54.26

   

2014

2

rs4953186

4,953,186

1

4.23

18.40

G

T

54.11

55.78

54.26

   

2014

3

rs6481810

6,481,810

1

4.11

18.10

C

T

53.16

54.43

54.26

  

Hyten et al. 2004

2014

8

rs39589269

39,589,269

3

3.82

17.42

G

T

54.15

55.47

54.26

   

2014

9

rs20595231

20,595,231

1

3.70

17.14

T

C

51.27

54.31

54.26

   

2014

10

rs10278177

10,278,177

1

3.70

17.14

A

T

51.93

54.41

54.26

   

2014

13

rs31318746

31,318,746

1

3.70

17.13

T

C

50.54

54.40

54.26

 

Linole 2–1

 

2014

15

rs1064298

1,064,298

1

3.65

17.02

C

T

54.07

55.64

54.26

   

2014

16

rs18741800

18,741,800

1

3.60

16.90

A

C

52.28

54.37

54.26

   

2015

1

rs50012108

50,012,108

3

6.40

17.63

A

T

53.42

56.38

56.26

   

2015

2

rs7975863

7,975,863

1

5.16

14.25

T

C

53.36

56.44

56.26

  

Hyten et al. 2004

2015

3

rs35817332

35,817,332

1

4.80

13.29

A

G

53.24

56.48

56.26

   

2015

4

rs29355727

29,355,727

1

4.73

13.11

T

C

49.13

56.93

56.26

   

2015

5

rs26200085

26,200,085

2

4.67

12.70

C

T

52.23

56.33

56.26

   

2015

6

rs50110801

50,110,801

3

4.52

12.56

A

T

50.03

56.46

56.26

   

2015

7

rs22961030

22,961,030

2

4.41

12.28

T

C

53.64

56.41

56.26

   

2015

8

rs35562739

35,562,739

1

4.26

11.87

T

A

49.76

56.37

56.26

   

2015

9

rs30794068

30,794,068

1

4.26

11.86

T

G

53.05

56.36

56.26

   

2015

11

rs6577617

6,577,617

1

4.24

11.82

T

G

52.42

56.39

56.26

   

2015

13

rs16802831

16,802,831

2

4.20

11.72

T

C

54.59

56.48

56.26

 

Linole 6–9

 

2015

14

rs39135305

39,135,305

1

4.16

11.62

T

C

52.44

56.41

56.26

 

Linole 2–1

 

2015

15

rs35324780

35,324,780

2

3.97

11.12

T

C

52.96

56.43

56.26

   

2015

16

rs36081420

36,081,420

4

3.83

10.43

C

T

44.07

56.33

56.26

Glyma.16G200200Glyma.16G003500

  

2015

17

rs34339550

34,339,550

1

3.68

10.40

G

A

49.88

56.33

56.26

  

Bachlava et al. 2009

2015

18

rs39638216

39,638,216

1

3.67

10.37

T

G

52.95

56.38

56.26

  

Hyten et al. 2004

2015

19

rs14807896

14,807,896

1

3.59

10.16

T

T

53.69

56.36

56.26

   

2015

20

rs47531251

47,531,251

1

3.58

10.14

A

G

50.47

56.36

56.26

Glyma.20G158300Glyma.20G245500

  

Linolenic acid

2013

1

rs37146219

37,146,219

1

3.68

10.98

T

C

6.69

8.82

8.73

   

2013

16

rs3989930

3,989,930

1

4.33

13.01

G

T

8.59

10.37

8.73

   

2013

16

rs15449450

15,449,450

1

3.81

11.39

A

G

8.23

9.05

8.73

   

2013

20

rs3008708

3,008,708

1

3.63

10.85

G

A

5.01

8.83

8.73

   

2014

2

rs35057707

35,057,707

23

3.66

30.58

G

A

8.09

10.52

8.13

   

2014

4

rs48837377

48,837,377

1

3.77

30.79

T

C

7.26

8.21

8.13

   

2014

7

rs43158730

43,158,730

1

3.60

30.44

C

T

8.10

10.40

8.13

Glyma.07G254500

  

2014

10

rs41662636

41,662,636

1

4.16

31.58

G

T

8.00

10.04

8.13

   

2014

12

rs16701034

16,701,034

1

3.81

30.88

G

A

8.05

9.13

8.13

   

2014

16

rs5443771

5,443,771

3

4.01

31.27

G

T

8.02

8.27

8.13

   

2014

18

rs52833743

52,833,743

4

3.85

30.94

A

C

8.02

8.79

8.13

 

Linolen 4–2

Panthee et al. 2006

2014

19

rs21750320

21,750,320

1

3.83

30.90

G

C

8.05

9.66

8.13

   

2015

13

rs14900419

14,900,419

1

3.98

10.27

A

T

9.10

10.93

9.19

   

2015

14

rs45949815

45,949,815

4

3.81

9.83

T

A

9.11

11.59

9.19

Glyma.14G194300

  

2015

17

rs35024325

35,024,325

1

4.06

10.48

C

T

9.12

10.62

9.19

   

2015

19

rs13718585

13,718,585

1

3.94

10.17

A

C

7.97

9.27

9.19

   
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