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Table 2 Several SNPs significantly associated with salt tolerance evaluated in GWAS using the SoySNP50K dataset for 305 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

Salt-20

3

38,610,964

23.9*

22.3*

7.2*

25.7*

99.7

C

0.40

C/G

Glyma03g32900 b

Salt14056

3

38,619,995

28.9*

24.7*

10.3*

29.1*

100

G

0.44

C/G

Glyma03g32900 b

Salt11655

3

38,622,492

24.4*

22.5*

7.8*

27.9*

99.7

T

0.41

G/T

Glyma03g32900 b

ss715592375

5

7,534,622

2.5 ns

3.1 ns

2.4 ns

4.7*

98.0

G

0.22

A/G

No gene

ss715609949

11

27,743,052

3.8 ns

2.6 ns

5.6*

4.1 ns

99.0

A

0.06

G/A

No gene

ss715611871

12

20,568,054

2.6 ns

2.5 ns

4.8*

3.3 ns

99.3

T

0.10

G/T

No gene

ss715616720

13

16,871,244

5.8*

4.9*

1.8 ns

3.2 ns

99.7

T

0.31

C/T

No gene

ss715623199

15

9,138,970

4.4*

2.2 ns

1.0 ns

1.3 ns

100

T

0.24

C/T

Glyma.15 g116200

-log10(P) threshold c

4.4

4.3

4.8

4.2

     
  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 consist 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