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Table 2 SNPs associated with each of the wild soybean seed composition traits

From: A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

Trait

SNP

Chr

bp

P

- Log10 P

 

Allelic effect

%

h2

PROTEIN

ss715617976

14

24367698

3.10E-05

4.51

A

0.551

3.41

0.22

PROTEIN

ss715631057

18

45438677

3.42E-05

4.47

A

0.574

3.09

 

OIL

ss715585518

3

34839398

9.21E-06

5.04

A

0.527

3.53

0.32

OIL

ss715637730

20

36705945

1.31E-05

4.88

A

0.479

3.31

 

OIL

ss715637732

20

36710220

3.24E-05

4.49

A

0.422

2.99

PALMITIC ACID

ss715595323

6

5303094

1.91E-05

4.72

A

−0.567

3.87

0.45

PALMITIC ACID

ss715597684

7

37911072

5.07E-06

5.29

A

−0.646

3.40

 

PALMITIC ACID

ss715617910

14

22537916

4.15E-05

4.38

C

0.801

3.13

STEARIC ACID

ss715618427

14

17499955

5.17E-05

4.29

A

0.704

2.95

0.50

STEARIC ACID

ss715618430

14

17561477

3.37E-05

4.47

A

0.753

3.15

 

STEARIC ACID

ss715625341

16

6804502

5.31E-06

5.27

C

−0.745

3.76

OLEIC ACID

ss715596070

7

11603310

1.25E-05

4.90

G

0.545

3.39

OLEIC ACID

ss715617910

14

22537916

2.06E-05

4.69

C

0.693

3.13

0.36

OLEIC ACID

ss715623399

16

1258943

2.23E-06

5.65

A

−0.472

2.93

 

OLEIC ACID

ss715623400

16

1260003

6.66E-06

5.18

A

−0.374

2.76

OLEIC ACID

ss715633271

19

12874336

5.24E-05

4.28

G

−0.588

2.49

LINOLEIC ACID

ss715582510

2

39934224

8.71E-06

5.06

A

−0.691

3.60

0.49

LINOLEIC ACID

ss715582512

2

39940256

1.57E-05

4.80

A

−0.692

3.41

 

LINOLEIC ACID

ss715596075

7

11584261

2E-05

4.70

C

0.546

2.72

LINOLEIC ACID

ss715596074

7

11585878

1.39E-05

4.86

C

−0.562

3.35

LINOLEIC ACID

ss715596072

7

11592971

9.15E-06

5.04

C

−0.577

3.52

LINOLEIC ACID

ss715596071

7

11602516

1.88E-05

4.73

A

−0.549

3.64

LINOLEIC ACID

ss715596070

7

11603310

2.10E-06

5.68

G

−0.636

3.38

LINOLEIC ACID

ss715596058

7

11756838

3.62E-06

5.44

C

0.696

4.17

LINOLEIC ACID

ss715604488

9

44197778

3.2E-05

4.50

A

−0.430

4.04

LINOLENIC ACID

ss715583655

2

573749

5.04E-05

4.30

C

0.745

3.72

0.44

LINOLENIC ACID

ss715583662

2

578327

1.46E-05

4.84

C

0.741

3.34

 

LINOLENIC ACID

ss715617909

14

22514991

3.99E-05

4.40

C

−0.842

3.01

LINOLENIC ACID

ss715617910

14

22537916

6.71E-06

5.17

C

−0.891

2.92

  1. Shown are the locations (in base pairs, bp), standardized allelic effects, and the percentage (%) of the total phenotypic variation explained for SNPs (r 2 X 100) on all chromosomes (Chr) associated with the wild soybean traits. The allelic effect is the standardized effect of the allele listed (A, C, G) compared with the alternate allele and also represents the standardized difference in the means of the two homozygous genotypes. All –log10 P scores (where P = the probability of SNP/trait associations) exceeding 5.348 are significant at the 5% experimentwise level and those exceeding 4.248 are significant at the chromosome-wide level. Heritabilities (h2) calculated using all SNPS also are given for each trait
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BMC Genomics

ISSN: 1471-2164

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