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Table 3 The most significant SNPs on each chromosome associated with salt tolerance traits detected in an association analysis using the WGRS-derived SNP dataset in the subset of 234 soybean accessions

From: Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

Marker

Chr.

Position

-log10(P)

Call Rate (%)

MA

MAF

Allele Refer

Cloned/Candidate genes a

LSS

CCR

LSC

LCC

1:4591993-SNV

1

4,591,993

1.1 ns

2.3 ns

5.5*

4.9*

100

T

0.50

T/C

No gene

2:38974662-SNV

2

38,974,662

4.5*

3.0 ns

0.7 ns

3.4 ns

100

T

0.41

T/A

No gene

2:43513959-SNV

2

43,513,959

4.0 ns

2.3 ns

1.1 ns

4.4*

100

C

0.49

T/C

Glyma.02 g247400

Salt-20

3

38,610,964

29.0*

25.6*

7.2*

27.4*

99.6

C

0.45

C/G

Glyma03g32900 b

Salt14056

3

38,619,995

32.4*

28.2*

8.2*

29.6*

100

G

0.46

C/G

Glyma03g32900 b

Salt11655

3

38,622,492

27.2*

24.1*

6.2*

25.7*

99.6

T

0.45

G/T

Glyma03g32900 b

5:2725777-SNV

5

2,725,777

1.1 ns

2.3 ns

5.5*

4.9*

100

T

0.50

T/C

Glyma.05 g031300

6:3536892-SNV

6

3,536,892

1.1 ns

2.3 ns

5.5*

4.9*

100

A

0.50

A/G

No gene

6:38850839-SNV

6

38,850,839

4.8*

2.9 ns

2.2 ns

5.2*

100

A

0.25

A/G

No gene

8:11762527-SNV

8

11,762,527

4.2 ns

3.7 ns

5.2*

6.6*

100

T

0.35

T/A

No gene

8:11859355-SNV

8

11,859,355

4.3*

3.4 ns

3.6 ns

5.3*

100

T

0.32

T/A

No gene

8:11869912-SNV

8

11,869,912

4.1 ns

3.3 ns

3.5 ns

5.0*

100

T

0.3

T/C

Glyma.08 g153800

8:11897542-SNV

8

11,897,542

4.1 ns

3.3 ns

3.3 ns

4.6*

100

C

0.3

C/T

Glyma.08 g154400

8:12168563-SNV

8

12,168,563

3.3 ns

3.5 ns

6.7*

4.4*

100

G

0.38

G/A

Glyma.08 g157400

8:12177874-SNV

8

12,177,874

2.9 ns

3.7 ns

6.9*

3.4 ns

100

A

0.48

A/T

Glyma.08 g157400

8:12198547-SNV

8

12,198,547

3.8 ns

4.1 ns

7.6*

4.6*

100

C

0.4

C/T

No gene

8:12221598-SNV

8

12,221,598

3.0 ns

2.8 ns

6.7*

4.3 ns

100

G

0.4

G/A

Glyma.08 g157700

8:18197526-SNV

8

18,197,526

3.5 ns

3.2 ns

3.1 ns

5.0*

100

T

0.07

T/C

Glyma.08 g224400

8:18363900-SNV

8

18,363,900

4.5*

3.6 ns

2.2 ns

4.6*

100

A

0.47

A/G

No gene

8:18378659-SNV

8

18,378,659

4.8*

4.5*

3.3 ns

3.7 ns

100

G

0.48

T/G

No gene

14:8102511-SNV

14

8,102,511

4.6*

3.7 ns

1.2 ns

2.2 ns

100

T

0.49

T/C

No gene

14:47627721-SNV

14

47,627,721

1.2 ns

0.9 ns

5.6*

0.9 ns

100

A

0.06

A/G

Glyma.14 g211300

15:11833367-SNV

15

11,833,367

3.0 ns

2.4 ns

3.4 ns

5.0*

100

C

0.49

C/T

Glyma.15 g143900

16:34944055-SNV

16

34,944,055

4.9*

4.1 ns

1.3 ns

2.4 ns

100

C

0.37

C/A

No gene

18:56065139-SNV

18

56,065,139

1.1 ns

2.3 ns

5.5*

4.9*

100

G

0.50

G/T

Glyma.18 g294400

18:57153685-SNV

18

57,153,685

3.2 ns

5.3*

0.8 ns

3.2 ns

100

T

0.23

T/C

No gene

18:57203235-SNV

18

57,203,235

4.9*

4.1 ns

2.5 ns

2.9 ns

100

A

0.17

A/T

No gene

19:43567289-SNV

19

43,567,289

7.5*

6.7*

2.1 ns

5.1*

100

T

0.20

T/G

Glyma.19 g175600

20:37261341-SNV

20

37,261,341

3.3 ns

4.6*

0.5 ns

1.6 ns

100

C

0.06

T/C

No gene

-log10(P) threshold c

4.3

4.4

5.1

4.3

     
  1. LSS leaf scorch score, CCR chlorophyll content ratio, LSC leaf sodium content, LCC leaf chloride content (LCC)
  2. *: Significant association with salt tolerant traits; ns: None significant association with trait
  3. a: The candidate gene in Soybase Wm82 Genome Browser version 2 consisting of significant SNP; b: The cloned gene for salt tolerance is named Glyma03g32900 in SoyBase Wm82 Genome Browser version 1; c: Threshold was calculated based on P-value using False Discovery Rate correction (Benjamini-Hochberg); MA: Minor allele; MAF: Minor allele frequency
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BMC Genomics

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