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Table 1 Peak SNP and benefical allele associated with resistance to the Hg Type 2.5.7 (race 1) identified by GWAS

From: Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7

SNP

Chromosome

Position

-log10(p)

MAF

Model

Resistant allele

Susceptible alleles

Average FI of accessions with resistant allele

Average FI of accessions with susceptible allele

Average FI of population

rs7631207

8

7,631,207

11.89

0.12

CMLM

C

G

22.71

111.07

104.19

rs7640250

8

7,640,250

11.89

0.12

CMLM

C

G

22.71

111.07

104.19

rs7671170

8

7,671,170

11.89

0.12

CMLM

G

C

22.71

111.07

104.19

rs7662003

8

7,662,003

10.51

0.12

CMLM

T

C

39.36

110.13

104.19

rs7664479

8

7,664,479

10.51

0.14

CMLM

C

A

39.02

109.75

104.19

rs7622492

8

7,622,492

10.2

0.11

CMLM

A

G

24.19

110.39

104.19

rs7661660

8

7,661,660

9.82

0.12

CMLM

C

A

39.36

109.97

104.19

rs46625879

18

46,625,879

7.12

0.1

CMLM

G

T

44.55

107.59

104.19

rs36423980

7

36,423,980

5.74

0.17

CMLM

A

G

49.27

112.53

104.19

rs3853672

14

3,853,672

5.53

0.1

CMLM

A

T

53.89

107.40

104.19

rs7631207

8

7,631,207

11.89

0.12

ECMLM

C

G

22.71

111.07

104.19

rs7640250

8

7,640,250

11.89

0.12

ECMLM

C

G

22.71

111.07

104.19

rs7671170

8

7,671,170

11.89

0.12

ECMLM

G

C

22.71

111.07

104.19

rs7662003

8

7,662,003

10.51

0.12

ECMLM

T

C

39.36

110.13

104.19

rs7664479

8

7,664,479

10.51

0.14

ECMLM

C

A

39.02

109.75

104.19

rs7622492

8

7,622,492

10.2

0.11

ECMLM

A

G

24.19

110.39

104.19

rs7661660

8

7,661,660

9.82

0.12

ECMLM

C

A

39.36

109.97

104.19

rs46625879

18

46,625,879

7.12

0.1

ECMLM

G

T

44.55

107.59

104.19

rs36423980

7

36,423,980

5.74

0.17

ECMLM

A

G

49.27

112.53

104.19

rs3853672

14

3,853,672

5.53

0.1

ECMLM

A

T

53.89

107.40

104.19

rs7671170

8

7,671,170

38.91

0.12

FARMCPU

G

C

22.71

111.07

104.19

rs46625879

18

46,625,879

23.93

0.1

FARMCPU

G

T

44.55

107.59

104.19

rs35898587

7

35,898,587

19.04

0.07

FARMCPU

A

C

48.30

107.38

104.19

rs16268025

8

16,268,025

11.48

0.06

FARMCPU

A

G

71.46

106.50

104.19

rs38522986

15

38,522,986

6.12

0.05

FARMCPU

A

G

52.14

107.16

104.19