Skip to main content

Table 2 Association of SNPs with different salt related traits at 10 days of treatment with HKT genes (with R2 > 5 % and p < 0.01)

From: Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm

Gene

Trait

SNP

Site

p

R2 (%)

SNP type

MAF

Gene

Trait

SNP

Site

p

R2 (%)

SNP type

MAF

HKT 1;1

N_R

S0231

30724332

0.003

34.43

Int

37

HKT 1;5

N_S

S0077

11459042

0.002

31.57

Int

36

K_S

S1955

30726056

0.003

30.75

Syn

5

N_S

S3893

11462858

0.005

33.00

P/A140

20

SPAD

S2094

30726195

0.003

31.90

S/N258

32

K_S

S0077

11459042

0.003

30.92

Int

36

SPAD

S2331

30726432

0.003

31.90

S/F179

30

N_R

S0887

11459852

0.003

34.12

Int

13

SPAD

S2546

30726647

0.003

31.90

Syn

30

N_R

S0919

11459884

0.009

34.42

Int

35

HKT 1;2

K_S

S0221

30545988

0.003

31.83

5’ NC

36

N_R

S0958

11459923

0.009

34.65

Int

35

K_S

S1430

30547197

0.009

25.16

Int

21

N_R

S0959

11459924

0.003

34.12

Int

13

K_S

S2282

30548049

0.003

31.54

Int

31

N_R

S0974

11459939

0.008

35.09

Int

6

HKT 1;3

N_R

S0337

4103487

0.005

33.93

C/R16

30

N_R

S1036

11460001

0.002

37.37

Int

5

SPAD

S0091

4103241

0.009

27.83

5’ NC

12

K_R

S1036

11460001

0.008

26.80

Int

5

N_R

S0744

4103894

0.008

38.19

Syn

22

N_R

S1379

11460344

0.003

34.44

K/Q429

49

SPAD

S0744

4103894

0.008

35.21

Syn

22

N_R

S1913

11460878

0.003

34.62

Int

43

SPAD

S1682

4104832

0.009

27.83

Int

10

N_R

S2043

11461008

0.004

33.62

Int

29

SPAD

S1762

4104912

0.005

31.75

Int

45

K_S

S2146

11461111

0.002

34.93

Int

45

SPAD

S2347

4105497

0.003

34.78

A/V488

23

K_S

S2347

11461312

0.006

27.43

Int

28

SPAD

S2374

4105524

0.004

32.49

R/Q497

46

K_S

S2865

11461830

0.001

36.63

Int

14

SPAD

S2392

4105542

0.009

27.68

T/M503

13

K_S

S3893

11462858

0.009

31.17

Int

20

HKT 1;4

SPAD

S0886

30734275

0.003

34.72

3’NC

32

HKT 2;1

K_S

S3062

29541671

0.008

32.35

5’ NC

7

SPAD

S1267

30734656

0.003

34.72

3’NC

32

N_R

S3062

29541671

0.004

39.70

5’ NC

7

SPAD

S2284

30735673

0.002

37.42

Int

32

SPAD

S4153

29542762

0.009

25.80

5’ NC

38

SPAD

S2804

30736193

0.003

34.72

Int

32

SPAD

S4377

29542986

0.002

33.96

5’ NC

36

SPAD

S2974

30736363

0.002

37.03

Int

33

K_S

S5815

29544424

0.002

40.52

5’ NC

21

SPAD

S3185

30736574

0.002

37.03

Int

32

K_S

S5817

29544426

0.007

32.66

5’ NC

7

SPAD

S3228

30736617

0.007

36.36

Int

33

HKT 2;3

K_S

S0356

19241884

0.002

34.84

Int

10

SPAD

S3307

30736696

0.003

34.87

Int

28

SPAD

S0761

19242289

0.003

31.88

I/T77

34

SPAD

S3544

30736933

0.003

34.72

Int

32

K_S

S1001

19242529

0.009

25.08

I/T157

5

SPAD

S4678

30738067

0.003

35.09

Int

35

SPAD

S2053

19243581

0.003

31.79

Syn

34

        

HKT 2;4

K_S

S0334

29534433

0.004

37.20

Int

37

  1. (N_S sodium concentration in shoot, K_S potassium concentration in shoot, N_R sodium concentration in root, K_S potassium concentration in root, Int intron, Syn synonymous, NC non-coding, MAF minor allele frequency in %)